Query 022938
Match_columns 289
No_of_seqs 202 out of 2232
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 07:15:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 1.7E-43 3.7E-48 337.2 19.4 248 3-279 198-454 (541)
2 COG0539 RpsA Ribosomal protein 100.0 5.3E-40 1.2E-44 313.3 20.3 213 42-278 147-367 (541)
3 PRK07400 30S ribosomal protein 100.0 6.5E-39 1.4E-43 293.8 24.4 236 4-271 38-278 (318)
4 PRK07899 rpsA 30S ribosomal pr 100.0 7.8E-38 1.7E-42 299.6 24.2 245 3-278 41-297 (486)
5 PRK12269 bifunctional cytidyla 100.0 7E-38 1.5E-42 316.4 22.6 248 3-278 499-756 (863)
6 PRK13806 rpsA 30S ribosomal pr 100.0 4.5E-37 9.8E-42 297.3 23.4 241 3-270 208-466 (491)
7 PRK13806 rpsA 30S ribosomal pr 100.0 6.2E-36 1.3E-40 289.4 23.8 247 5-278 123-383 (491)
8 PRK06676 rpsA 30S ribosomal pr 100.0 8.6E-36 1.9E-40 281.7 23.6 247 3-279 23-282 (390)
9 PRK06299 rpsA 30S ribosomal pr 100.0 2.9E-35 6.2E-40 290.2 22.5 248 3-278 207-464 (565)
10 PRK06676 rpsA 30S ribosomal pr 100.0 2.6E-34 5.7E-39 271.5 24.8 240 5-271 113-360 (390)
11 PRK07899 rpsA 30S ribosomal pr 100.0 3.2E-34 6.9E-39 274.8 24.1 232 5-264 130-369 (486)
12 PRK06299 rpsA 30S ribosomal pr 100.0 5.4E-34 1.2E-38 281.2 24.7 243 4-279 37-291 (565)
13 TIGR00717 rpsA ribosomal prote 100.0 4E-34 8.7E-39 279.3 22.5 248 4-279 194-451 (516)
14 PRK12269 bifunctional cytidyla 100.0 5.1E-34 1.1E-38 288.4 23.3 243 4-273 585-840 (863)
15 PRK00087 4-hydroxy-3-methylbut 100.0 1.1E-33 2.5E-38 281.9 22.2 246 3-278 308-566 (647)
16 TIGR00717 rpsA ribosomal prote 100.0 2.8E-32 6E-37 266.4 22.3 228 4-258 279-516 (516)
17 PRK00087 4-hydroxy-3-methylbut 100.0 4.4E-31 9.6E-36 263.3 23.5 233 5-264 397-638 (647)
18 PRK07400 30S ribosomal protein 99.9 9.3E-24 2E-28 193.7 17.4 174 86-279 18-201 (318)
19 KOG1070 rRNA processing protei 99.8 1.3E-18 2.9E-23 176.9 13.6 193 41-261 467-672 (1710)
20 KOG1070 rRNA processing protei 99.8 1.7E-17 3.7E-22 168.9 15.8 230 13-260 1083-1325(1710)
21 PTZ00248 eukaryotic translatio 99.6 5.5E-16 1.2E-20 140.7 9.4 92 184-278 12-109 (319)
22 COG1098 VacB Predicted RNA bin 99.6 2E-16 4.4E-21 122.4 4.5 76 185-266 2-82 (129)
23 PTZ00248 eukaryotic translatio 99.6 3.2E-16 6.9E-21 142.2 4.6 135 98-244 16-171 (319)
24 COG2996 Predicted RNA-bindinin 99.6 1.1E-13 2.4E-18 121.1 19.2 174 40-268 42-226 (287)
25 PRK08582 hypothetical protein; 99.5 6.4E-14 1.4E-18 113.8 10.9 97 185-287 2-115 (139)
26 PF00575 S1: S1 RNA binding do 99.5 1E-13 2.2E-18 100.3 9.6 72 97-175 2-74 (74)
27 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 1.2E-13 2.6E-18 100.2 8.2 70 97-173 1-74 (74)
28 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 1.8E-13 4E-18 99.3 6.9 66 186-256 1-74 (74)
29 PRK09202 nusA transcription el 99.4 2.1E-13 4.6E-18 130.7 8.9 142 26-194 73-218 (470)
30 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 6.1E-13 1.3E-17 96.3 8.5 70 100-175 1-72 (73)
31 COG1098 VacB Predicted RNA bin 99.4 1.3E-13 2.7E-18 106.9 4.8 73 97-177 3-76 (129)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 7.5E-13 1.6E-17 98.1 8.5 72 96-174 11-83 (83)
33 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 7.9E-13 1.7E-17 94.6 8.3 69 100-175 1-70 (70)
34 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 6.8E-13 1.5E-17 98.3 7.1 74 179-257 5-83 (83)
35 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 1.5E-12 3.3E-17 93.0 8.3 68 100-174 1-69 (69)
36 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 2.4E-12 5.2E-17 93.4 9.4 68 97-177 2-71 (74)
37 PF00575 S1: S1 RNA binding do 99.4 1.2E-12 2.6E-17 94.6 7.6 69 185-258 1-74 (74)
38 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 2.4E-12 5.3E-17 93.3 9.0 68 185-262 1-73 (74)
39 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 1.4E-12 3.1E-17 94.3 7.6 65 189-258 1-72 (73)
40 PRK05807 hypothetical protein; 99.4 3.6E-12 7.8E-17 103.2 10.7 96 185-287 2-111 (136)
41 cd04465 S1_RPS1_repeat_ec2_hs2 99.4 3.8E-12 8.3E-17 90.4 9.0 67 100-175 1-67 (67)
42 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 6.3E-12 1.4E-16 90.7 10.0 71 98-175 2-73 (73)
43 PRK07252 hypothetical protein; 99.4 2.4E-12 5.1E-17 101.9 8.3 72 187-263 2-78 (120)
44 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 4E-12 8.7E-17 91.5 8.3 68 100-174 1-71 (71)
45 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 2.8E-12 6E-17 92.6 6.8 66 186-258 1-72 (72)
46 cd04452 S1_IF2_alpha S1_IF2_al 99.3 7.3E-12 1.6E-16 90.9 8.9 70 187-259 2-76 (76)
47 cd05707 S1_Rrp5_repeat_sc11 S1 99.3 4.4E-12 9.5E-17 90.3 7.5 67 100-173 1-68 (68)
48 PLN00207 polyribonucleotide nu 99.3 2.9E-12 6.3E-17 129.7 9.0 84 182-271 747-836 (891)
49 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 5.2E-12 1.1E-16 91.1 7.7 69 98-175 2-72 (72)
50 cd05706 S1_Rrp5_repeat_sc10 S1 99.3 8.8E-12 1.9E-16 89.9 8.7 68 186-258 1-73 (73)
51 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 1.1E-11 2.4E-16 89.6 9.1 69 98-174 2-72 (73)
52 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 9.5E-12 2.1E-16 89.0 8.7 69 100-175 1-70 (70)
53 cd05698 S1_Rrp5_repeat_hs6_sc5 99.3 4.8E-12 1E-16 90.5 7.1 65 189-258 1-70 (70)
54 TIGR01953 NusA transcription t 99.3 4.7E-12 1E-16 117.0 8.3 143 25-194 69-216 (341)
55 PRK08059 general stress protei 99.3 1.1E-11 2.5E-16 98.7 8.9 77 183-264 2-83 (123)
56 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.3 8.8E-12 1.9E-16 89.7 7.2 58 195-257 14-71 (71)
57 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 1.4E-11 3E-16 89.1 8.3 66 187-257 2-72 (73)
58 cd04452 S1_IF2_alpha S1_IF2_al 99.3 2.7E-11 5.8E-16 87.9 9.6 72 98-176 2-76 (76)
59 PHA02945 interferon resistance 99.3 1.8E-11 3.9E-16 89.6 8.5 72 187-263 10-87 (88)
60 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.3 1.2E-11 2.6E-16 88.3 7.5 64 189-257 1-69 (69)
61 cd05691 S1_RPS1_repeat_ec6 S1_ 99.3 2.3E-11 4.9E-16 87.5 8.9 70 100-176 1-71 (73)
62 PRK07252 hypothetical protein; 99.3 3E-11 6.6E-16 95.6 9.9 73 98-177 2-75 (120)
63 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 2E-11 4.4E-16 86.9 7.6 68 100-173 1-69 (69)
64 PRK12327 nusA transcription el 99.3 1.2E-11 2.7E-16 114.9 8.0 144 26-194 73-218 (362)
65 PRK08582 hypothetical protein; 99.3 3.7E-11 8E-16 97.6 9.9 73 97-177 3-76 (139)
66 cd05691 S1_RPS1_repeat_ec6 S1_ 99.3 2.8E-11 6.1E-16 87.0 8.1 68 189-261 1-73 (73)
67 cd05708 S1_Rrp5_repeat_sc12 S1 99.3 3.3E-11 7.2E-16 87.5 8.5 70 187-260 1-75 (77)
68 cd05708 S1_Rrp5_repeat_sc12 S1 99.2 6.1E-11 1.3E-15 86.1 9.5 72 99-177 2-75 (77)
69 cd05707 S1_Rrp5_repeat_sc11 S1 99.2 1.9E-11 4.1E-16 87.0 6.5 63 189-256 1-68 (68)
70 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 5.7E-11 1.2E-15 84.2 8.2 65 100-173 1-66 (66)
71 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 3.2E-11 6.9E-16 85.8 6.9 63 189-256 1-69 (69)
72 cd05689 S1_RPS1_repeat_ec4 S1_ 99.2 6.6E-11 1.4E-15 85.1 8.4 70 98-173 2-72 (72)
73 COG1093 SUI2 Translation initi 99.2 1.1E-11 2.3E-16 108.2 4.8 83 187-272 10-97 (269)
74 cd05684 S1_DHX8_helicase S1_DH 99.2 9.6E-11 2.1E-15 85.9 9.3 71 189-264 1-78 (79)
75 cd05692 S1_RPS1_repeat_hs4 S1_ 99.2 1.2E-10 2.6E-15 82.3 8.3 68 100-175 1-69 (69)
76 cd05688 S1_RPS1_repeat_ec3 S1_ 99.2 1.1E-10 2.5E-15 82.4 8.1 68 99-173 1-68 (68)
77 cd05687 S1_RPS1_repeat_ec1_hs1 99.2 1.1E-10 2.4E-15 83.4 7.6 65 189-258 1-70 (70)
78 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 5.2E-11 1.1E-15 91.4 6.2 74 98-177 2-97 (100)
79 PRK05807 hypothetical protein; 99.2 2.2E-10 4.7E-15 92.8 10.1 73 97-177 3-75 (136)
80 cd05685 S1_Tex S1_Tex: The C-t 99.2 1.2E-10 2.6E-15 82.1 7.4 67 100-173 1-68 (68)
81 cd05689 S1_RPS1_repeat_ec4 S1_ 99.1 1.7E-10 3.6E-15 83.0 7.5 66 186-256 1-72 (72)
82 cd05692 S1_RPS1_repeat_hs4 S1_ 99.1 2E-10 4.2E-15 81.2 7.7 64 189-258 1-69 (69)
83 smart00316 S1 Ribosomal protei 99.1 3.3E-10 7.1E-15 80.2 8.6 70 99-175 2-72 (72)
84 PRK08059 general stress protei 99.1 3.1E-10 6.8E-15 90.4 8.9 74 97-177 5-79 (123)
85 cd05684 S1_DHX8_helicase S1_DH 99.1 5.9E-10 1.3E-14 81.7 9.4 69 100-176 1-73 (79)
86 cd04472 S1_PNPase S1_PNPase: P 99.1 3.9E-10 8.4E-15 79.7 7.9 67 100-174 1-68 (68)
87 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 1.2E-10 2.6E-15 89.4 5.5 70 186-260 1-97 (100)
88 PRK03987 translation initiatio 99.1 4.4E-10 9.4E-15 100.5 9.3 84 187-273 7-95 (262)
89 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.1 3.4E-10 7.3E-15 80.2 6.7 61 189-256 1-66 (66)
90 PRK12328 nusA transcription el 99.1 3E-10 6.4E-15 105.2 8.1 145 25-194 76-224 (374)
91 cd05685 S1_Tex S1_Tex: The C-t 99.0 4.7E-10 1E-14 79.1 6.3 63 189-256 1-68 (68)
92 cd05688 S1_RPS1_repeat_ec3 S1_ 99.0 1.1E-09 2.5E-14 77.2 7.5 63 188-256 1-68 (68)
93 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.0 1.2E-09 2.7E-14 81.3 7.7 73 98-177 5-81 (86)
94 PHA02945 interferon resistance 99.0 2.3E-09 5E-14 78.5 8.6 71 97-177 9-84 (88)
95 cd04472 S1_PNPase S1_PNPase: P 99.0 1.4E-09 3.1E-14 76.8 7.4 63 189-257 1-68 (68)
96 cd04465 S1_RPS1_repeat_ec2_hs2 99.0 1.7E-09 3.6E-14 76.7 7.6 62 189-258 1-67 (67)
97 smart00316 S1 Ribosomal protei 99.0 1.8E-09 3.9E-14 76.4 7.7 67 187-258 1-72 (72)
98 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.0 1.4E-09 3.1E-14 80.9 7.1 69 186-260 4-81 (86)
99 cd04453 S1_RNase_E S1_RNase_E: 99.0 2.5E-09 5.3E-14 80.2 8.1 72 97-175 5-82 (88)
100 PLN00207 polyribonucleotide nu 99.0 1.2E-09 2.7E-14 110.9 8.5 85 93-185 747-836 (891)
101 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 3.8E-09 8.2E-14 77.9 8.3 72 98-177 5-77 (82)
102 cd04455 S1_NusA S1_NusA: N-uti 99.0 5.1E-09 1.1E-13 74.3 8.5 64 98-174 2-67 (67)
103 cd05702 S1_Rrp5_repeat_hs11_sc 98.9 4.6E-09 1E-13 75.1 7.8 63 100-168 1-65 (70)
104 cd04471 S1_RNase_R S1_RNase_R: 98.9 9.3E-09 2E-13 75.6 9.1 76 99-174 1-82 (83)
105 PRK09521 exosome complex RNA-b 98.9 7.1E-09 1.5E-13 88.7 9.7 93 161-260 41-143 (189)
106 cd04471 S1_RNase_R S1_RNase_R: 98.9 9E-09 2E-13 75.7 8.6 64 189-257 2-82 (83)
107 cd00164 S1_like S1_like: Ribos 98.9 4.3E-09 9.4E-14 72.9 6.4 64 103-173 1-65 (65)
108 PRK03987 translation initiatio 98.9 6.8E-09 1.5E-13 92.9 9.1 73 97-176 6-81 (262)
109 PRK11824 polynucleotide phosph 98.9 5.7E-09 1.2E-13 105.3 9.0 73 182-260 615-692 (693)
110 PRK12329 nusA transcription el 98.9 5.7E-09 1.2E-13 98.2 8.0 146 26-194 89-243 (449)
111 cd04453 S1_RNase_E S1_RNase_E: 98.9 8.8E-09 1.9E-13 77.2 7.5 70 185-259 4-83 (88)
112 TIGR02696 pppGpp_PNP guanosine 98.9 9.6E-09 2.1E-13 102.4 9.8 88 162-256 612-718 (719)
113 COG2183 Tex Transcriptional ac 98.9 3.4E-09 7.3E-14 105.2 6.4 78 182-264 652-734 (780)
114 COG1093 SUI2 Translation initi 98.8 3.2E-09 6.9E-14 92.8 5.0 73 97-176 9-84 (269)
115 COG2183 Tex Transcriptional ac 98.8 5.9E-09 1.3E-13 103.5 7.2 75 96-177 655-730 (780)
116 cd04473 S1_RecJ_like S1_RecJ_l 98.8 3.4E-08 7.4E-13 72.0 9.6 62 97-174 14-76 (77)
117 PRK11824 polynucleotide phosph 98.8 1.9E-08 4.2E-13 101.5 10.3 74 95-176 617-691 (693)
118 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 2.1E-08 4.6E-13 73.9 7.5 68 187-260 5-77 (82)
119 PRK09521 exosome complex RNA-b 98.8 2.9E-08 6.3E-13 84.9 9.1 104 41-177 26-143 (189)
120 cd04473 S1_RecJ_like S1_RecJ_l 98.8 4.2E-08 9.1E-13 71.6 8.5 62 182-257 10-76 (77)
121 TIGR02696 pppGpp_PNP guanosine 98.8 1.9E-08 4E-13 100.4 8.3 69 97-173 645-718 (719)
122 cd05702 S1_Rrp5_repeat_hs11_sc 98.7 3.6E-08 7.9E-13 70.4 6.3 58 189-251 1-65 (70)
123 cd00164 S1_like S1_like: Ribos 98.7 6.4E-08 1.4E-12 66.9 6.7 57 195-256 9-65 (65)
124 PRK09202 nusA transcription el 98.7 2.8E-08 6E-13 95.7 6.0 160 27-260 24-201 (470)
125 cd04460 S1_RpoE S1_RpoE: RpoE, 98.7 1.6E-07 3.4E-12 71.9 8.6 69 195-269 11-95 (99)
126 COG1185 Pnp Polyribonucleotide 98.6 6.6E-08 1.4E-12 94.8 7.8 92 163-261 587-691 (692)
127 cd04460 S1_RpoE S1_RpoE: RpoE, 98.6 1.7E-07 3.8E-12 71.6 8.5 71 101-177 1-86 (99)
128 TIGR03591 polynuc_phos polyrib 98.6 1.4E-07 3.1E-12 95.2 8.7 68 182-255 612-684 (684)
129 TIGR03591 polynuc_phos polyrib 98.5 2.3E-07 4.9E-12 93.7 8.2 70 94-171 613-683 (684)
130 TIGR00448 rpoE DNA-directed RN 98.5 7.3E-07 1.6E-11 75.6 9.2 80 98-177 80-168 (179)
131 COG1185 Pnp Polyribonucleotide 98.5 7.9E-07 1.7E-11 87.4 9.7 78 91-176 611-689 (692)
132 PRK04163 exosome complex RNA-b 98.4 7.6E-07 1.6E-11 78.7 7.2 70 185-260 60-138 (235)
133 COG1095 RPB7 DNA-directed RNA 98.3 3.2E-06 7E-11 70.7 8.0 80 98-177 80-168 (183)
134 TIGR02063 RNase_R ribonuclease 98.3 5.2E-06 1.1E-10 84.6 11.3 79 96-174 624-708 (709)
135 PRK04163 exosome complex RNA-b 98.3 3.3E-06 7.2E-11 74.7 8.4 73 98-177 62-138 (235)
136 cd04455 S1_NusA S1_NusA: N-uti 98.3 3.5E-06 7.6E-11 59.6 7.0 58 187-256 2-66 (67)
137 TIGR00448 rpoE DNA-directed RN 98.3 5.2E-06 1.1E-10 70.4 8.8 73 187-265 80-173 (179)
138 TIGR00358 3_prime_RNase VacB a 98.2 8.2E-06 1.8E-10 82.3 11.3 78 97-174 570-653 (654)
139 TIGR02063 RNase_R ribonuclease 98.2 4.1E-06 9E-11 85.3 8.8 70 183-257 622-708 (709)
140 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.2 6.4E-06 1.4E-10 58.7 7.1 69 100-175 1-72 (72)
141 KOG1067 Predicted RNA-binding 98.2 1.2E-06 2.6E-11 83.9 4.2 81 183-269 663-748 (760)
142 PRK11642 exoribonuclease R; Pr 98.2 7.3E-06 1.6E-10 84.2 10.0 79 98-176 642-726 (813)
143 COG1095 RPB7 DNA-directed RNA 98.1 7.5E-06 1.6E-10 68.6 7.2 76 187-268 80-178 (183)
144 PRK08563 DNA-directed RNA poly 98.1 1.6E-05 3.5E-10 67.8 9.5 80 98-177 80-168 (187)
145 PHA02858 EIF2a-like PKR inhibi 98.1 6.9E-06 1.5E-10 59.7 5.6 67 186-257 14-85 (86)
146 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.1 8.3E-06 1.8E-10 61.6 6.1 48 212-260 38-87 (92)
147 PRK08563 DNA-directed RNA poly 98.1 6E-05 1.3E-09 64.3 11.7 79 185-269 78-180 (187)
148 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.0 5.7E-05 1.2E-09 56.5 9.1 69 99-168 1-74 (88)
149 COG2996 Predicted RNA-bindinin 98.0 0.00012 2.6E-09 64.8 11.9 121 26-180 100-221 (287)
150 PRK11642 exoribonuclease R; Pr 98.0 2.9E-05 6.2E-10 79.9 8.9 70 187-260 642-727 (813)
151 TIGR00358 3_prime_RNase VacB a 97.9 3.5E-05 7.6E-10 77.8 8.4 69 185-257 569-653 (654)
152 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.9 5.3E-05 1.2E-09 57.1 7.2 72 98-177 5-87 (92)
153 PRK12327 nusA transcription el 97.9 1.2E-05 2.5E-10 75.2 4.0 96 150-257 87-198 (362)
154 KOG1067 Predicted RNA-binding 97.8 2E-05 4.3E-10 75.8 5.0 74 96-176 665-739 (760)
155 TIGR01953 NusA transcription t 97.8 3.2E-05 7E-10 71.8 5.2 98 149-260 83-199 (341)
156 PF13509 S1_2: S1 domain; PDB: 97.7 0.00018 3.9E-09 50.0 7.3 60 99-175 1-61 (61)
157 PTZ00162 DNA-directed RNA poly 97.7 0.00033 7.1E-09 59.2 9.2 79 98-177 80-166 (176)
158 KOG2916 Translation initiation 97.6 4.1E-05 9E-10 67.1 3.1 89 187-278 15-108 (304)
159 PRK05054 exoribonuclease II; P 97.5 0.00079 1.7E-08 67.9 11.4 77 98-174 558-643 (644)
160 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.5 0.00033 7.1E-09 50.0 5.6 63 189-258 1-72 (72)
161 PHA02858 EIF2a-like PKR inhibi 97.5 0.00031 6.6E-09 51.2 5.4 69 97-174 14-85 (86)
162 COG1096 Predicted RNA-binding 97.3 0.0024 5.2E-08 53.7 9.6 77 180-259 56-142 (188)
163 TIGR02062 RNase_B exoribonucle 97.2 0.0022 4.8E-08 64.7 10.2 76 98-173 554-638 (639)
164 TIGR00757 RNaseEG ribonuclease 97.2 0.0011 2.5E-08 63.2 7.4 59 98-162 24-96 (414)
165 COG1097 RRP4 RNA-binding prote 97.2 0.019 4.1E-07 50.3 14.2 86 98-194 63-152 (239)
166 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.1 0.0027 5.8E-08 47.5 7.5 59 188-252 1-75 (88)
167 PRK05054 exoribonuclease II; P 97.0 0.0024 5.1E-08 64.5 8.6 67 187-257 558-643 (644)
168 COG0557 VacB Exoribonuclease R 97.0 0.0042 9.1E-08 63.5 10.5 81 95-175 618-704 (706)
169 KOG1856 Transcription elongati 96.9 0.0012 2.6E-08 68.4 5.5 74 96-176 982-1059(1299)
170 COG1097 RRP4 RNA-binding prote 96.9 0.003 6.4E-08 55.3 6.7 69 186-260 62-139 (239)
171 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.7 0.012 2.7E-07 43.6 8.2 70 98-176 5-75 (86)
172 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.6 0.009 2E-07 44.4 6.8 67 187-260 5-76 (86)
173 PTZ00162 DNA-directed RNA poly 96.6 0.0099 2.1E-07 50.2 7.6 68 186-259 79-165 (176)
174 PF10447 EXOSC1: Exosome compo 96.3 0.0072 1.6E-07 44.5 4.7 76 151-246 3-82 (82)
175 KOG2916 Translation initiation 96.3 0.0031 6.7E-08 55.6 2.9 73 97-176 14-89 (304)
176 TIGR00757 RNaseEG ribonuclease 96.2 0.012 2.6E-07 56.3 6.6 58 184-246 21-97 (414)
177 TIGR02062 RNase_B exoribonucle 96.1 0.016 3.5E-07 58.5 7.5 66 187-256 554-638 (639)
178 COG1096 Predicted RNA-binding 96.0 0.074 1.6E-06 44.9 9.8 70 97-176 62-142 (188)
179 KOG1856 Transcription elongati 96.0 0.0056 1.2E-07 63.7 3.3 75 184-261 981-1061(1299)
180 KOG3298 DNA-directed RNA polym 95.9 0.075 1.6E-06 43.7 8.8 70 98-168 80-154 (170)
181 COG1107 Archaea-specific RecJ- 95.8 0.0076 1.6E-07 58.8 3.4 74 182-268 116-194 (715)
182 PRK12328 nusA transcription el 95.6 0.035 7.7E-07 52.0 7.0 61 187-259 137-206 (374)
183 COG0557 VacB Exoribonuclease R 95.4 0.046 9.9E-07 56.0 7.5 71 184-258 618-704 (706)
184 PF10447 EXOSC1: Exosome compo 95.3 0.054 1.2E-06 39.8 5.6 60 98-163 3-82 (82)
185 PRK10811 rne ribonuclease E; R 95.3 0.049 1.1E-06 56.4 7.1 62 98-166 37-110 (1068)
186 PF08292 RNA_pol_Rbc25: RNA po 95.2 0.13 2.7E-06 40.8 8.0 67 99-165 3-76 (122)
187 COG1107 Archaea-specific RecJ- 95.2 0.017 3.6E-07 56.5 3.3 68 95-175 118-186 (715)
188 PRK11712 ribonuclease G; Provi 94.6 0.095 2.1E-06 51.2 7.0 60 98-163 37-110 (489)
189 PF13509 S1_2: S1 domain; PDB: 93.8 0.27 5.8E-06 33.9 6.0 49 195-258 13-61 (61)
190 PRK12329 nusA transcription el 93.5 0.25 5.5E-06 47.3 7.2 66 187-258 151-224 (449)
191 KOG3409 Exosomal 3'-5' exoribo 92.8 0.65 1.4E-05 38.7 7.6 74 98-177 67-149 (193)
192 PF10246 MRP-S35: Mitochondria 90.9 1.4 3E-05 33.6 7.1 53 98-164 22-75 (104)
193 PRK10811 rne ribonuclease E; R 90.2 0.71 1.5E-05 48.2 6.5 60 187-251 37-112 (1068)
194 PRK11712 ribonuclease G; Provi 88.3 1.2 2.5E-05 43.8 6.2 59 184-247 34-111 (489)
195 COG1530 CafA Ribonucleases G a 87.7 0.9 2E-05 44.5 5.1 67 98-168 36-106 (487)
196 KOG3409 Exosomal 3'-5' exoribo 85.9 5.1 0.00011 33.6 7.7 78 152-258 68-147 (193)
197 KOG3298 DNA-directed RNA polym 85.8 4.4 9.6E-05 33.5 7.3 61 187-253 80-156 (170)
198 PRK12442 translation initiatio 84.7 8 0.00017 28.7 7.5 65 100-176 6-73 (87)
199 PF08292 RNA_pol_Rbc25: RNA po 82.1 6 0.00013 31.3 6.6 21 228-248 56-76 (122)
200 COG4148 ModC ABC-type molybdat 81.9 38 0.00083 31.1 12.2 114 98-247 230-349 (352)
201 TIGR00008 infA translation ini 81.5 13 0.00028 26.3 7.3 60 101-172 5-67 (68)
202 PRK10943 cold shock-like prote 77.3 12 0.00026 26.3 6.3 50 102-162 3-56 (69)
203 PF00313 CSD: 'Cold-shock' DNA 76.3 22 0.00047 24.3 7.5 49 103-162 1-53 (66)
204 COG3269 Predicted RNA-binding 75.5 27 0.00058 25.0 8.0 49 97-166 13-62 (73)
205 PRK15464 cold shock-like prote 74.6 12 0.00027 26.4 5.7 49 103-162 5-57 (70)
206 COG4148 ModC ABC-type molybdat 74.2 24 0.00051 32.4 8.6 107 15-164 239-349 (352)
207 PRK09507 cspE cold shock prote 73.6 19 0.00042 25.3 6.5 51 102-163 3-57 (69)
208 PF03459 TOBE: TOBE domain; I 73.0 12 0.00025 25.4 5.2 47 101-161 5-58 (64)
209 PRK15463 cold shock-like prote 72.7 15 0.00033 25.9 5.8 49 103-162 5-57 (70)
210 PRK09890 cold shock protein Cs 68.5 29 0.00064 24.4 6.5 49 103-162 5-57 (70)
211 PRK09937 stationary phase/star 68.4 22 0.00047 25.5 5.8 49 104-163 3-55 (74)
212 PF08206 OB_RNB: Ribonuclease 67.6 14 0.00031 24.9 4.6 42 105-162 1-44 (58)
213 COG1530 CafA Ribonucleases G a 67.4 8.1 0.00018 37.9 4.6 75 181-261 30-116 (487)
214 PRK10354 RNA chaperone/anti-te 66.1 32 0.0007 24.1 6.3 48 104-162 6-57 (70)
215 cd05700 S1_Rrp5_repeat_hs9 S1_ 65.7 8.3 0.00018 26.5 3.0 28 230-257 38-65 (65)
216 PRK12442 translation initiatio 64.0 36 0.00078 25.2 6.3 51 200-259 23-73 (87)
217 KOG3297 DNA-directed RNA polym 63.9 21 0.00045 30.3 5.6 66 98-164 80-157 (202)
218 PF01330 RuvA_N: RuvA N termin 62.7 29 0.00064 23.5 5.5 31 102-132 4-36 (61)
219 TIGR00008 infA translation ini 62.0 34 0.00073 24.2 5.6 46 200-254 21-66 (68)
220 PF09883 DUF2110: Uncharacteri 60.7 11 0.00024 32.7 3.6 84 88-175 61-147 (225)
221 COG0195 NusA Transcription elo 60.5 20 0.00043 30.6 5.2 60 122-194 2-62 (190)
222 PRK14998 cold shock-like prote 59.2 62 0.0013 23.0 7.0 49 104-163 3-55 (73)
223 TIGR02381 cspD cold shock doma 58.2 30 0.00064 24.2 4.9 49 104-163 3-55 (68)
224 COG1862 YajC Preprotein transl 58.0 58 0.0013 24.7 6.7 50 83-132 30-86 (97)
225 cd05700 S1_Rrp5_repeat_hs9 S1_ 57.5 40 0.00087 23.2 5.1 63 100-173 1-64 (65)
226 KOG1004 Exosomal 3'-5' exoribo 56.6 45 0.00097 29.0 6.5 60 98-165 64-124 (230)
227 PRK05886 yajC preprotein trans 56.2 76 0.0017 24.6 7.2 48 85-132 27-81 (109)
228 KOG1999 RNA polymerase II tran 52.4 1.1E+02 0.0025 32.4 9.7 52 186-242 408-469 (1024)
229 TIGR00739 yajC preprotein tran 52.1 82 0.0018 23.0 6.6 44 86-129 27-77 (84)
230 cd04458 CSP_CDS Cold-Shock Pro 51.9 72 0.0016 21.6 6.6 49 104-163 2-54 (65)
231 TIGR00638 Mop molybdenum-pteri 50.7 20 0.00043 24.5 3.1 47 101-161 7-60 (69)
232 KOG4078 Putative mitochondrial 48.7 52 0.0011 26.7 5.3 53 98-164 81-134 (173)
233 COG4776 Rnb Exoribonuclease II 45.8 6.2 0.00013 38.2 -0.3 76 97-172 559-641 (645)
234 COG0361 InfA Translation initi 45.7 1.1E+02 0.0024 22.0 7.6 65 99-175 5-72 (75)
235 PF10246 MRP-S35: Mitochondria 44.8 89 0.0019 23.9 5.8 50 187-248 22-76 (104)
236 COG4044 Uncharacterized protei 43.9 21 0.00045 30.9 2.6 85 89-174 63-156 (247)
237 KOG3013 Exosomal 3'-5' exoribo 43.1 79 0.0017 28.4 6.1 103 97-204 83-203 (301)
238 KOG1999 RNA polymerase II tran 41.9 4.7E+02 0.01 28.1 14.4 80 42-130 408-495 (1024)
239 PRK14605 ruvA Holliday junctio 41.3 71 0.0015 27.3 5.6 52 102-168 4-57 (194)
240 TIGR00084 ruvA Holliday juncti 40.7 75 0.0016 27.1 5.6 51 102-168 4-56 (191)
241 PF14604 SH3_9: Variant SH3 do 39.7 58 0.0013 20.9 3.8 32 97-129 15-46 (49)
242 PRK05585 yajC preprotein trans 38.5 1.5E+02 0.0033 22.7 6.5 48 85-132 41-95 (106)
243 PRK14604 ruvA Holliday junctio 38.0 84 0.0018 26.9 5.5 52 102-168 4-57 (195)
244 PF02599 CsrA: Global regulato 36.9 51 0.0011 22.1 3.2 34 229-264 8-41 (54)
245 KOG3754 Gamma-glutamylcysteine 36.5 38 0.00083 32.8 3.4 29 152-180 47-75 (640)
246 PF01835 A2M_N: MG2 domain; I 36.3 52 0.0011 24.2 3.6 32 231-262 9-47 (99)
247 PF06347 SH3_4: Bacterial SH3 32.8 1.3E+02 0.0028 19.5 4.8 38 181-222 16-54 (55)
248 PF00970 FAD_binding_6: Oxidor 32.3 89 0.0019 22.7 4.3 46 232-277 29-87 (99)
249 PRK01712 carbon storage regula 32.2 94 0.002 21.7 3.9 33 229-263 8-40 (64)
250 cd01716 Hfq Hfq, an abundant, 31.8 1.1E+02 0.0025 21.0 4.3 36 97-132 18-53 (61)
251 smart00357 CSP Cold shock prot 31.7 1.4E+02 0.003 19.4 4.9 47 105-163 2-50 (64)
252 PF09628 YvfG: YvfG protein; 31.4 30 0.00065 23.7 1.3 14 275-288 23-36 (68)
253 PRK14603 ruvA Holliday junctio 31.2 1.3E+02 0.0028 25.7 5.6 51 102-168 4-56 (197)
254 COG0195 NusA Transcription elo 31.1 85 0.0018 26.8 4.4 41 212-258 2-43 (190)
255 PRK14600 ruvA Holliday junctio 30.6 1.4E+02 0.003 25.3 5.6 46 102-163 4-51 (186)
256 PF01176 eIF-1a: Translation i 29.6 1.5E+02 0.0033 20.3 4.8 56 102-171 4-63 (65)
257 TIGR00074 hypC_hupF hydrogenas 28.7 1.8E+02 0.004 20.8 5.2 26 103-128 5-30 (76)
258 COG0335 RplS Ribosomal protein 28.5 90 0.002 24.3 3.7 23 232-254 20-42 (115)
259 PRK13901 ruvA Holliday junctio 28.5 1.6E+02 0.0035 25.3 5.6 50 102-167 4-55 (196)
260 PF01938 TRAM: TRAM domain; I 28.2 1.8E+02 0.004 19.2 6.5 49 98-165 3-53 (61)
261 PRK12336 translation initiatio 28.0 3.9E+02 0.0083 22.9 8.1 47 97-164 145-192 (201)
262 COG1545 Predicted nucleic-acid 27.7 3.2E+02 0.007 21.9 7.3 58 98-169 62-129 (140)
263 PF09465 LBR_tudor: Lamin-B re 27.5 1.5E+02 0.0034 19.9 4.2 28 38-65 2-40 (55)
264 PF00467 KOW: KOW motif; Inte 27.3 1.3E+02 0.0029 17.4 4.2 16 240-255 16-31 (32)
265 PRK00116 ruvA Holliday junctio 27.3 1.5E+02 0.0032 25.2 5.3 50 102-166 4-55 (192)
266 COG1278 CspC Cold shock protei 26.6 1.4E+02 0.003 21.0 4.1 48 104-162 3-54 (67)
267 smart00333 TUDOR Tudor domain. 26.6 1.1E+02 0.0024 19.8 3.6 35 98-132 14-51 (57)
268 COG0298 HypC Hydrogenase matur 26.4 2.6E+02 0.0057 20.4 5.6 43 103-160 5-49 (82)
269 TIGR02383 Hfq RNA chaperone Hf 26.0 1.6E+02 0.0034 20.3 4.2 32 97-128 22-53 (61)
270 PF07653 SH3_2: Variant SH3 do 26.0 1.4E+02 0.003 19.4 3.9 34 97-131 18-52 (55)
271 PRK00568 carbon storage regula 24.9 1.3E+02 0.0029 21.7 3.8 32 229-262 8-39 (76)
272 cd04474 RPA1_DBD_A RPA1_DBD_A: 24.7 1.6E+02 0.0034 22.2 4.5 40 152-193 33-72 (104)
273 COG4044 Uncharacterized protei 24.6 61 0.0013 28.1 2.3 73 182-255 69-154 (247)
274 PRK14601 ruvA Holliday junctio 24.4 1.8E+02 0.0039 24.6 5.2 50 102-167 4-56 (183)
275 PTZ00320 ribosomal protein L14 24.2 4.5E+02 0.0096 22.3 8.2 77 12-126 67-153 (188)
276 PF08605 Rad9_Rad53_bind: Fung 24.1 1.5E+02 0.0033 23.7 4.4 47 99-160 21-70 (131)
277 COG0250 NusG Transcription ant 24.1 1.4E+02 0.003 25.2 4.4 30 231-260 122-161 (178)
278 COG1551 CsrA RNA-binding globa 24.0 1.1E+02 0.0023 21.9 3.0 29 230-260 9-37 (73)
279 PF14444 S1-like: S1-like 23.3 2.5E+02 0.0055 19.1 5.1 15 102-116 3-18 (58)
280 cd05793 S1_IF1A S1_IF1A: Trans 23.2 2.9E+02 0.0062 19.8 6.6 61 103-177 2-66 (77)
281 COG2106 Uncharacterized conser 22.6 2E+02 0.0043 26.1 5.3 47 97-163 103-150 (272)
282 COG0632 RuvA Holliday junction 22.2 2.4E+02 0.0053 24.3 5.6 51 102-167 4-56 (201)
283 PRK14606 ruvA Holliday junctio 22.2 2E+02 0.0044 24.4 5.1 51 102-168 4-57 (188)
284 PF02237 BPL_C: Biotin protein 22.2 1.7E+02 0.0037 18.6 3.7 23 98-120 10-33 (48)
285 PRK00276 infA translation init 21.9 2.9E+02 0.0063 19.3 7.9 61 101-172 7-69 (72)
286 PRK14602 ruvA Holliday junctio 21.3 2.1E+02 0.0046 24.5 5.2 51 102-167 4-57 (203)
287 cd04480 RPA1_DBD_A_like RPA1_D 21.1 1.9E+02 0.0041 20.7 4.2 40 152-193 17-56 (86)
288 TIGR00202 csrA carbon storage 20.9 1.9E+02 0.0041 20.5 3.8 32 229-262 8-39 (69)
289 CHL00084 rpl19 ribosomal prote 20.8 1.2E+02 0.0025 23.9 3.0 23 232-254 22-44 (117)
290 PF09953 DUF2187: Uncharacteri 20.7 1.3E+02 0.0028 20.4 2.9 18 103-120 16-33 (57)
291 PF15057 DUF4537: Domain of un 20.3 3.2E+02 0.0069 21.4 5.6 92 98-221 10-109 (124)
292 PRK04012 translation initiatio 20.2 3.9E+02 0.0085 20.2 7.4 66 100-177 20-87 (100)
293 PRK10676 DNA-binding transcrip 20.1 4.5E+02 0.0097 23.4 7.2 49 100-162 199-254 (263)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-43 Score=337.22 Aligned_cols=248 Identities=25% Similarity=0.400 Sum_probs=233.1
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
|-.++|..|+||++.+. -+||++..+++..++.||++.|++||+|+|+|+++|++++|++||+|+..
T Consensus 198 G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~------------ 264 (541)
T COG0539 198 GVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLE------------ 264 (541)
T ss_pred EEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcc------------
Confidence 45688999999999999 99999999999999999999999999999999999999999999998432
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
+.+|+.+...+.+|+.+.|+|+.++++|+||++. |++||+|+|||+|.+. ..|.+.++ +||.|.|+|+
T Consensus 265 ----~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~-~~P~evv~------~Gq~V~V~Vl 333 (541)
T COG0539 265 ----EDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKK-NVPSEVVK------VGQEVEVKVL 333 (541)
T ss_pred ----cCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhccccc-CCHHHhcc------cCCEEEEEEE
Confidence 3589999999999999999999999999999999 9999999999999998 44999998 9999999999
Q ss_pred EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccccc
Q 022938 162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 233 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~ 233 (289)
++|++++||.||+|+ +||+...+.+++|+.++| +++|+||.++ +| ++|++|.++++|.....+...|
T Consensus 334 ~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le--~g---idG~vh~~d~sw~~~~~~~~~~ 408 (541)
T COG0539 334 DIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELE--GG---IDGLVHLSDLSWDRPGEEAEKY 408 (541)
T ss_pred eeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccC--CC---ccceEEHHhcCccccCcHHHhh
Confidence 999999999999997 589999999999999999 9999999996 55 9999999999999877776799
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938 234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279 (289)
Q Consensus 234 ~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~ 279 (289)
++||.++++|+.+|+++++|+|++|++.++||......++.|++.+
T Consensus 409 k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~ 454 (541)
T COG0539 409 KKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVK 454 (541)
T ss_pred ccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEE
Confidence 9999999999999999999999999999999999999999998754
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-40 Score=313.32 Aligned_cols=213 Identities=28% Similarity=0.432 Sum_probs=196.9
Q ss_pred ccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECC
Q 022938 42 ERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFS 121 (289)
Q Consensus 42 ~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~g 121 (289)
-.+|.++.++|+.+|.+++++.+|.+..+ ++.+....+++...+++|+++.|+|++++++|+||+++|
T Consensus 147 ~~~Gk~~~~kiie~d~~~n~vv~SrR~~~------------e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigG 214 (541)
T COG0539 147 PLIGKELEFKILELDKKRNNVVLSRRAVL------------EEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG 214 (541)
T ss_pred ccCCceEEEEEEEEccccCcEEEEhHHHh------------hHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecC
Confidence 46899999999999999999999987443 222233445567779999999999999999999999999
Q ss_pred EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec---chhhhcccccccccEEEe----
Q 022938 122 LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG---- 194 (289)
Q Consensus 122 v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G---- 194 (289)
++|++|++||||.+. .+|++.++ +||.|+|+|+++|.+++|+.||+|+ .||+.....+++|+.+.|
T Consensus 215 vdGLlHiseiS~~rv-~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~ 287 (541)
T COG0539 215 VDGLLHISEISWKRV-DHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTN 287 (541)
T ss_pred eeeEEehhhcccccc-CCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEE
Confidence 999999999999998 99999998 9999999999999999999999997 599999999999999999
Q ss_pred -eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhC
Q 022938 195 -RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVI 273 (289)
Q Consensus 195 -~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~ 273 (289)
++||+||++. +| ++||+|+|+|+|.+...|++.+++||.|.|+|+.||++++||+||+|++.+|||+.+.++|+
T Consensus 288 i~~~GafVei~--~G---vEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~ 362 (541)
T COG0539 288 LTDYGAFVEIE--EG---VEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHP 362 (541)
T ss_pred eecCcEEEEec--CC---ccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcC
Confidence 9999999997 66 99999999999999988999999999999999999999999999999999999999999999
Q ss_pred CCChH
Q 022938 274 PQGLE 278 (289)
Q Consensus 274 ~g~~~ 278 (289)
+|++.
T Consensus 363 ~g~~v 367 (541)
T COG0539 363 VGDVV 367 (541)
T ss_pred CCCeE
Confidence 99864
No 3
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=6.5e-39 Score=293.80 Aligned_cols=236 Identities=25% Similarity=0.391 Sum_probs=214.6
Q ss_pred cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938 4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ 83 (289)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~ 83 (289)
-+.++.+++|+++++.+..|+..+..+++....+|.+.|++|++++|.|++++++++++.+|+|+.
T Consensus 38 ~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~-------------- 103 (318)
T PRK07400 38 TVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRI-------------- 103 (318)
T ss_pred EEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhh--------------
Confidence 345688999999999999999999999999999999999999999999999999999999998732
Q ss_pred hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
.....|+.+.+.++.|++++|+|+++.++|+||+++|++||||.+++++.+. .+ ..+|+.++|+|+++
T Consensus 104 -~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~----~~-------~~vG~~i~~kVl~i 171 (318)
T PRK07400 104 -EYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKP----KE-------ELVGEELPLKFLEV 171 (318)
T ss_pred -hhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCC----cc-------ccCCCEEEEEEEEE
Confidence 2345799999999999999999999999999999999999999999998542 11 23999999999999
Q ss_pred ecCCcEEEEEeecchhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCE
Q 022938 164 NEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238 (289)
Q Consensus 164 d~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~ 238 (289)
|++++++.||+|.+.++..+.++++|+++.| +++|+||++ +| +.|++|+++++|.+..++.+.|++||.
T Consensus 172 d~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i---~g---v~Gllhisels~~~~~~~~~~~~vGd~ 245 (318)
T PRK07400 172 DEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI---GG---VSGLLHISEISHEHIETPHSVFNVNDE 245 (318)
T ss_pred EcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHcccccccChhhccCCCCE
Confidence 9999999999998777778889999999999 999999999 34 999999999999999999999999999
Q ss_pred EEEEEEEEeCCCCeEEEEEecCCCCchhHHhhh
Q 022938 239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271 (289)
Q Consensus 239 V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~ 271 (289)
|+|+|+++|.++++|.||+|++++|||+...+.
T Consensus 246 VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~ 278 (318)
T PRK07400 246 MKVMIIDLDAERGRISLSTKQLEPEPGDMLKDP 278 (318)
T ss_pred EEEEEEEEeCCCCEEEEEEeccccChhhhhhhH
Confidence 999999999999999999999999999876543
No 4
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=7.8e-38 Score=299.64 Aligned_cols=245 Identities=23% Similarity=0.383 Sum_probs=222.0
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
|-+.+|...+++++.+.+-.|+.-...++.....||.+.|++|++|+|.|++++..++++.||+++
T Consensus 41 G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~-------------- 106 (486)
T PRK07899 41 GTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKR-------------- 106 (486)
T ss_pred EEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehh--------------
Confidence 446778899999999999999999999999999999999999999999999999999999999873
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
+..+..|+.+.++++.|++++|+|+++.++|++|++ |++||||.+++++.+. .++.. ++|+.|+|+|++
T Consensus 107 -~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~-~~~~~--------~vGq~V~vkVle 175 (486)
T PRK07899 107 -AQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRV-RDLQP--------YIGQEIEAKIIE 175 (486)
T ss_pred -hcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhccccc-CChhh--------cCCCEEEEEEEE
Confidence 233468999999989999999999999999999999 7999999999998664 44322 499999999999
Q ss_pred EecCCcEEEEEeec-------chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcc
Q 022938 163 ANEEMKKLVFSEKD-------AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR 230 (289)
Q Consensus 163 vd~~~~ri~lS~k~-------~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~ 230 (289)
+|.+++++.+|+|. .+|+..+.++++|+++.| +++|+||+|+ | +.||||+++++|.++.++.
T Consensus 176 id~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg---g---v~Glv~~Sels~~~v~~~~ 249 (486)
T PRK07899 176 LDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG---G---VDGLVHVSELSWKHIDHPS 249 (486)
T ss_pred EECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC---C---EEEEEEHHHCCCcccCCHH
Confidence 99999999999985 357778889999999999 9999999994 4 9999999999999999999
Q ss_pred cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938 231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~ 278 (289)
+.|++||.|+|+|+++|++++||.||+|++.++||..+.+++..|+..
T Consensus 250 ~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv 297 (486)
T PRK07899 250 EVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIV 297 (486)
T ss_pred HhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEE
Confidence 999999999999999999999999999999999999999988888754
No 5
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=7e-38 Score=316.42 Aligned_cols=248 Identities=17% Similarity=0.241 Sum_probs=223.4
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
|-++++-.+++|+++. ...||++...++...+.+|++.|++||+++|+|+++|++++++.+|+|...
T Consensus 499 G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~------------ 565 (863)
T PRK12269 499 GVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQ------------ 565 (863)
T ss_pred EEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccc------------
Confidence 4467788899999994 578999999999999999999999999999999999999999999998431
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
+.+|+.+.+.+.+|++++|+|+++.++|+||+++ |++|++|.+|++|.....+|.+.|+ +||.|+|+|+
T Consensus 566 ----~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~k------vGd~V~vkVl 635 (863)
T PRK12269 566 ----PDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVK------IGDEVECMIL 635 (863)
T ss_pred ----cchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCC------CCCEEEEEEE
Confidence 2478888888999999999999999999999998 9999999999999432377887776 9999999999
Q ss_pred EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCcccc
Q 022938 162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDI 232 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~ 232 (289)
++|++++++.||+|+ +||+...+++++|+++.| +++|+||++. +| +.|++|.++++|.+. ..+...
T Consensus 636 ~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~--~g---V~GlIh~sels~~~~~~~~~~~ 710 (863)
T PRK12269 636 GYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEME--EG---IDGFLHVDDLSWVKRTRPADHE 710 (863)
T ss_pred EEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeC--CC---cEEEEEhHHhhccccccchhhc
Confidence 999999999999995 589999899999999999 9999999996 55 999999999999765 445568
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 233 ~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~ 278 (289)
|++||.|+|+|+++|++++||.||+|++.++||+.+.+++.+|+.-
T Consensus 711 ~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV 756 (863)
T PRK12269 711 LEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTV 756 (863)
T ss_pred cCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEE
Confidence 9999999999999999999999999999999999999999999764
No 6
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=4.5e-37 Score=297.28 Aligned_cols=241 Identities=18% Similarity=0.256 Sum_probs=216.6
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCC----CeEeeeeecccccCCcchh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNA----AKITPTTVNPILDDSSDAN 78 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~----~~i~ls~k~~l~~~~~~~~ 78 (289)
|-+.++..++|+++++....|++++..++.....+|.+.|++||.+.|+|+++|+++ .++.+|+|+.
T Consensus 208 G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~--------- 278 (491)
T PRK13806 208 GTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQA--------- 278 (491)
T ss_pred EEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhh---------
Confidence 345678899999999878899999999999999999999999999999999999986 4799998733
Q ss_pred hhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEE
Q 022938 79 NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS 157 (289)
Q Consensus 79 ~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~ 157 (289)
.+.+|+.+.+.+..|++++|+|+++.++|+||+++ |++||+|.++++|.....+|.+.++ +||.|+
T Consensus 279 -------~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~------~Gd~v~ 345 (491)
T PRK13806 279 -------GGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVA------PGDAVA 345 (491)
T ss_pred -------hcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCC------CCCEEE
Confidence 23468888888999999999999999999999998 9999999999998432266777776 999999
Q ss_pred EEEEEEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938 158 VKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 229 (289)
Q Consensus 158 vkVl~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~ 229 (289)
|+|+++|++++++.+|+|+ +||+...+++++|++++| ++||+||++. +| +.||||+++++|.+..++
T Consensus 346 vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~--~g---v~Gli~~se~s~~~~~~~ 420 (491)
T PRK13806 346 VKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLA--PG---VTGLLPASVISRAGKPAT 420 (491)
T ss_pred EEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcC--CC---cEEEEEHHHcCcccccch
Confidence 9999999999999999996 589999999999999999 9999999996 55 999999999999999999
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEecC-----CCCchhHHhh
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLE 270 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~-----~~~p~~~~~~ 270 (289)
.+.|++||.|+|+|+++|++++||+||+|++ ..+||.++..
T Consensus 421 ~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~~~~~~~~~~~~~~~~ 466 (491)
T PRK13806 421 YEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDDWKQFAP 466 (491)
T ss_pred hhcCCCCCEEEEEEEEEeCCCCEEEEEeehhhhhhhhhhHHHhhcc
Confidence 9999999999999999999999999999977 3589999854
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=6.2e-36 Score=289.37 Aligned_cols=247 Identities=22% Similarity=0.351 Sum_probs=214.4
Q ss_pred ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938 5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS 84 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~ 84 (289)
+.++-..++++++. ...|+.-...++.....+|... +|+++.|+|+.+|++++++.+|.+..+ +.
T Consensus 123 V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~~--vG~~i~~~V~~id~~~~~v~lSrk~~~------------~~ 187 (491)
T PRK13806 123 VTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPESY--VGQTFQFLITRVEENGRNIVVSRRALL------------ER 187 (491)
T ss_pred EEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHHc--CCCeEEEEEEEEECCCCeEEEEeehhh------------hh
Confidence 45566778888864 4566655555666667788753 999999999999999999999977332 22
Q ss_pred hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
.....|+.+...++.|++++|+|+++.++|+||+++ |+.||+|.++++|.+. .+|.+.++ +||.++|+|+++
T Consensus 188 ~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~-~~~~~~~~------vGd~i~vkVl~i 260 (491)
T PRK13806 188 EQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRV-QKADEAVS------VGDTVRVKVLGI 260 (491)
T ss_pred hhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccc-cChhHhcC------CCCEEEEEEEEE
Confidence 344678888888999999999999999999999997 9999999999999886 78887776 999999999999
Q ss_pred ecCC----cEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc-ccccCcc
Q 022938 164 NEEM----KKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIR 230 (289)
Q Consensus 164 d~~~----~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~-~~~~~~~ 230 (289)
|.++ +|+.||+|+ +||.....++++|+++.| .++|+||+++ +| +.||+|.++++| .++.++.
T Consensus 261 d~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~--~g---v~Glvh~sels~~~~~~~~~ 335 (491)
T PRK13806 261 ERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEIL--PG---IEGLVHVSEMSWTRRVNKPE 335 (491)
T ss_pred ecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeC--CC---cEEEEEHHHcCcccccCCHH
Confidence 9876 479999987 489999999999999999 9999999996 55 999999999998 4678888
Q ss_pred cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938 231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~ 278 (289)
+.|++||.|+|+|+++|+++++|.||+|++.++||+.+.+++.+|++.
T Consensus 336 ~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v 383 (491)
T PRK13806 336 DVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTV 383 (491)
T ss_pred HcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEE
Confidence 999999999999999999999999999999999999999999999754
No 8
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=8.6e-36 Score=281.68 Aligned_cols=247 Identities=22% Similarity=0.325 Sum_probs=222.0
Q ss_pred ccccccccceeEeCC-CCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhh
Q 022938 3 SLSSRIGSNTCLDAS-SCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQ 81 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~ 81 (289)
|-+.++..++|+++. +....|+....++++....+|.+.|++|++++|+|++++.+++++.+|+++
T Consensus 23 G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~------------- 89 (390)
T PRK06676 23 GEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR------------- 89 (390)
T ss_pred EEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHH-------------
Confidence 456788999999999 888999999999999899999999999999999999999998899999763
Q ss_pred hhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 82 SQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 82 ~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
......|+.+.++++.|++++|+|+++.++|++|+++|++||||.+++++.+. .+|.+ .+|+.++|+|+
T Consensus 90 --~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~-~~~~~--------~vG~~v~~~Vl 158 (390)
T PRK06676 90 --LEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFV-EDFSD--------FKGKTLEVKII 158 (390)
T ss_pred --hhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccC-CChHH--------cCCCEEEEEEE
Confidence 23345799999999999999999999999999999999999999999998765 44432 38999999999
Q ss_pred EEecCCcEEEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938 162 QANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 229 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~ 229 (289)
++|.+++++.+|+|.. +|...+.++++|+++.| .++|+||+++ | +.|++|.++++|.++.++
T Consensus 159 ~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~---~---v~g~v~~sels~~~~~~~ 232 (390)
T PRK06676 159 ELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG---G---VDGLVHISELSHERVEKP 232 (390)
T ss_pred EEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC---C---eEEEEEHHHcCccccCCH
Confidence 9999999999999963 45666788999999999 8999999993 4 999999999999999999
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~ 279 (289)
.+.|++||.|+|+|+++|+++++|.||+|++.++||+.+.+++..|+...
T Consensus 233 ~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~ 282 (390)
T PRK06676 233 SEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIE 282 (390)
T ss_pred HHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEE
Confidence 99999999999999999999999999999999999999998998887643
No 9
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.9e-35 Score=290.19 Aligned_cols=248 Identities=27% Similarity=0.428 Sum_probs=222.7
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
+-+.+|-.++|+++++ .-.|+++...++...+.+|++.|++||+|.|+|+++|++++++.+|++...
T Consensus 207 g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~------------ 273 (565)
T PRK06299 207 GVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLG------------ 273 (565)
T ss_pred EEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecc------------
Confidence 3457788999999997 788888888888888999999999999999999999999999999988321
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
+.+|+.+.+.++.|++++|+|+++.++|+||+++ |+.||+|.++++|.....+|.+.+. +||.|+|+|+
T Consensus 274 ----~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~------~G~~v~v~V~ 343 (565)
T PRK06299 274 ----EDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVS------VGQEVEVMVL 343 (565)
T ss_pred ----cChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcC------CCCEEEEEEE
Confidence 2479888888999999999999999999999998 9999999999998654356766665 9999999999
Q ss_pred EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCcccc
Q 022938 162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDI 232 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~ 232 (289)
++|++++++.||++. .||......+++|+++.| +++|+||+++ +| +.|++|.++++|.+. .++.+.
T Consensus 344 ~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---v~g~i~~s~l~~~~~~~~~~~~ 418 (565)
T PRK06299 344 EIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLE--GG---IDGLVHLSDISWDKKGEEAVEL 418 (565)
T ss_pred EEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECC--CC---CEEEEEHHHcCccccccChHhh
Confidence 999999999999985 488888888999999999 8999999995 45 999999999999876 788899
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 233 ~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~ 278 (289)
|++||.|+|+|+++|+++++|.||+|++..+||....+.+..|++.
T Consensus 419 ~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV 464 (565)
T PRK06299 419 YKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIV 464 (565)
T ss_pred CCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEE
Confidence 9999999999999999999999999999999999999888888764
No 10
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.6e-34 Score=271.54 Aligned_cols=240 Identities=22% Similarity=0.353 Sum_probs=210.5
Q ss_pred ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938 5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS 84 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~ 84 (289)
+..+..++|++++.. ..|+.....++.....+|... +|+++.|+|+++|++++++.+|++... ..
T Consensus 113 V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~------------~~ 177 (390)
T PRK06676 113 VTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVV------------EE 177 (390)
T ss_pred EEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHh------------hh
Confidence 456778899999943 388887777777777777653 999999999999999999999987321 12
Q ss_pred hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
.....|..+.+.++.|++++|+|+++.++|+||+++|++||||.+++++.+. .+|.+.++ +|+.++|+|+++|
T Consensus 178 ~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~-~~~~~~~~------vGd~i~~~Vl~vd 250 (390)
T PRK06676 178 ERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERV-EKPSEVVS------VGQEVEVKVLSID 250 (390)
T ss_pred hhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcccc-CCHHHhcC------CCCEEEEEEEEEe
Confidence 2335677777888999999999999999999999999999999999999876 77777665 9999999999999
Q ss_pred cCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCC
Q 022938 165 EEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEG 236 (289)
Q Consensus 165 ~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iG 236 (289)
++++++.+|+|. .||....+++++|+++.| .++|+||++. +| +.|++|.+++++.+..++.+.|++|
T Consensus 251 ~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~--~g---i~Glv~~se~~~~~~~~~~~~~~~G 325 (390)
T PRK06676 251 WETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVL--PG---VEGLVHISQISHKHIATPSEVLEEG 325 (390)
T ss_pred CCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEEC--CC---CeEEEEhHHcCccccCChhhccCCC
Confidence 999999999995 478888889999999999 8999999995 55 9999999999999888888999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhh
Q 022938 237 DEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271 (289)
Q Consensus 237 d~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~ 271 (289)
|.|+|+|+++|++++++.||+|++.++||.+..++
T Consensus 326 d~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~ 360 (390)
T PRK06676 326 QEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR 360 (390)
T ss_pred CEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence 99999999999999999999999999999998554
No 11
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.2e-34 Score=274.80 Aligned_cols=232 Identities=21% Similarity=0.302 Sum_probs=202.2
Q ss_pred ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938 5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS 84 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~ 84 (289)
+.++-..+|+++++ ..|+.....++.....++.. .+|+++.|+|+++|++++++.+|+|..+ +.
T Consensus 130 V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~~~~~ivLSrr~~l------------~~ 193 (486)
T PRK07899 130 VIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDKNRNNVVLSRRAWL------------EQ 193 (486)
T ss_pred EEEEECCeEEEEEC--CEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEECCCCEEEEEhHHHH------------Hh
Confidence 45677889999994 56777666565555556654 4999999999999999999999977322 11
Q ss_pred hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
.....|+.+...++.|++++|+|+++.++|+||+++|++||||.++++|.+. .+|.+.++ +||.|+|+|+++|
T Consensus 194 ~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v-~~~~~~~k------vGd~V~vkVl~iD 266 (486)
T PRK07899 194 TQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHI-DHPSEVVE------VGQEVTVEVLDVD 266 (486)
T ss_pred hhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCccc-CCHHHhcC------CCCEEEEEEEEEE
Confidence 2345788888889999999999999999999999999999999999999886 78887776 9999999999999
Q ss_pred cCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCC
Q 022938 165 EEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEG 236 (289)
Q Consensus 165 ~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iG 236 (289)
+++++|.||+|+ +||......+++|+++.| .++|+||++. +| +.||+|++++++.++.++.+.|++|
T Consensus 267 ~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~--~g---ieGLvh~SeLs~~~v~~~~~~~kvG 341 (486)
T PRK07899 267 MDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVE--EG---IEGLVHISELAERHVEVPEQVVQVG 341 (486)
T ss_pred CCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeC--CC---cEEEEEHHHcCcccccCccceeCCC
Confidence 999999999996 589888888999999999 9999999995 55 9999999999999998899999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEecCCCCc
Q 022938 237 DEVRVKVIKIDREKSRITLSIKQLEEDP 264 (289)
Q Consensus 237 d~V~vkV~~id~e~~ri~lSlK~~~~~p 264 (289)
|.|+|+|+++|++++||.||+|++.++-
T Consensus 342 d~V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 342 DEVFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred CEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence 9999999999999999999999986543
No 12
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=5.4e-34 Score=281.16 Aligned_cols=243 Identities=24% Similarity=0.379 Sum_probs=213.9
Q ss_pred cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938 4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ 83 (289)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~ 83 (289)
-+-++...+|+|+++.+..|+.-.-.+++ .++...|++|++++|.|+++++..+++.+|.+ +
T Consensus 37 ~V~~v~~~~~~Vdig~k~~g~lp~~e~~~---~~~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k---------------~ 98 (565)
T PRK06299 37 TVVAIDKDYVLVDVGLKSEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDGFGETVLSRE---------------K 98 (565)
T ss_pred EEEEEECCEEEEEeCCCeEEEEEHHHhcC---ccccccCCCCCEEEEEEEEEECCCCcEEEech---------------H
Confidence 35567789999999888888766555553 23456799999999999999999899999976 2
Q ss_pred hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
+.....|+++.++++.|++++|+|.++.++|++|+++|++||||.+++++.+. .++ .+++|++++|+|+++
T Consensus 99 ~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~-~~~--------~~~vG~~i~~~V~~~ 169 (565)
T PRK06299 99 AKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPV-RDT--------DPLEGKELEFKVIKL 169 (565)
T ss_pred HHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCC-CCh--------HHhCCCEEEEEEEEE
Confidence 34557899999999999999999999999999999999999999999998764 332 235999999999999
Q ss_pred ecCCcEEEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccc
Q 022938 164 NEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRD 231 (289)
Q Consensus 164 d~~~~ri~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~ 231 (289)
|.+++++.+|+|.. +|...+.++++|+++.| .++|+||+++ | +.|++|+++++|.++.++.+
T Consensus 170 d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~---g---~~glv~~se~s~~~~~~~~~ 243 (565)
T PRK06299 170 DKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG---G---VDGLLHITDISWKRVNHPSE 243 (565)
T ss_pred ECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC---C---EEEEEEHHHhcccccCCHhh
Confidence 99999999999963 46677889999999999 8999999994 4 99999999999999999999
Q ss_pred ccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938 232 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279 (289)
Q Consensus 232 ~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~ 279 (289)
.|++||.|+|+|+++|++++++.||+|.+.++||+.+.+.+.+|++..
T Consensus 244 ~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~ 291 (565)
T PRK06299 244 VVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVK 291 (565)
T ss_pred cCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEE
Confidence 999999999999999999999999999999999999998999988643
No 13
>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=4e-34 Score=279.34 Aligned_cols=248 Identities=23% Similarity=0.398 Sum_probs=218.4
Q ss_pred cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938 4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ 83 (289)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~ 83 (289)
-++++-.++++++++ ...|+.....++.....+|.+.|++|+++.|+|+++|++++++.+|++..
T Consensus 194 ~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~-------------- 258 (516)
T TIGR00717 194 VVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQL-------------- 258 (516)
T ss_pred EEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEec--------------
Confidence 356777899999985 47888888888888889999999999999999999999999999998732
Q ss_pred hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
...+|+.+.+.++.|++++|+|+++.++|+||+++ |+.||+|.+++++.+...+|.+.+. +||.++|+|++
T Consensus 259 --~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~------vG~~v~v~V~~ 330 (516)
T TIGR00717 259 --GEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVK------KGDEVEVMILD 330 (516)
T ss_pred --chhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhcc------CCCEEEEEEEE
Confidence 13478888888999999999999999999999998 9999999999997643355655565 99999999999
Q ss_pred EecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCccccc
Q 022938 163 ANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDIL 233 (289)
Q Consensus 163 vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~~ 233 (289)
+|++++++.||+++ .||....+.+++|+++.| +++|+||+++ +| +.|++|.++++|.+. .++...|
T Consensus 331 id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---v~glv~~s~ls~~~~~~~~~~~~ 405 (516)
T TIGR00717 331 IDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE--GG---IDGLIHLSDISWDKDGREADHLY 405 (516)
T ss_pred EcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECC--CC---CEEEEEHHHCcCcccCCCHhHcc
Confidence 99999999999986 588888888999999999 8999999996 55 999999999999754 4567889
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938 234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279 (289)
Q Consensus 234 ~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~ 279 (289)
++||.|.|+|+++|+++++|.||+|++.+|||....+.+..|+...
T Consensus 406 ~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~ 451 (516)
T TIGR00717 406 KKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVK 451 (516)
T ss_pred CCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEE
Confidence 9999999999999999999999999999999999988888887643
No 14
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=5.1e-34 Score=288.44 Aligned_cols=243 Identities=15% Similarity=0.283 Sum_probs=210.3
Q ss_pred cccccccceeEeCCCCCCccceeEeeccc-ccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 4 LSSRIGSNTCLDASSCTHSSLSLSLSLSS-LVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
-+.+|..+++|+.+.....||++...++. ....+|.+.|++||+|+|+|+++|+++++++||+|+..
T Consensus 585 ~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~------------ 652 (863)
T PRK12269 585 RVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVT------------ 652 (863)
T ss_pred EEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcc------------
Confidence 45788899999999988999999888886 46889999999999999999999999999999987321
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
..+|+.+.+.+.+|++++|+|++++++|+||+++ |++||||.++++|.....++.+.|+ +||.|+|+|+
T Consensus 653 ----~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~k------vGq~VkvkVl 722 (863)
T PRK12269 653 ----ANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELE------VGKEIECMVI 722 (863)
T ss_pred ----cCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccC------CCCEEEEEEE
Confidence 2379999899999999999999999999999998 9999999999998664233334454 9999999999
Q ss_pred EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc---c
Q 022938 162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---R 230 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~---~ 230 (289)
++|++++++.||+|+ +||+.+...+++|+++.| +++|+||++. +| +.|++|.++++|++..++ .
T Consensus 723 ~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~--~g---VeGlI~~s~lsdd~~~~~~~~~ 797 (863)
T PRK12269 723 ECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVP--GG---VEGLVRKQHLVENRDGDPGEAL 797 (863)
T ss_pred EEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcC--CC---eEEEEEHHHcCCcccccchhhc
Confidence 999999999999995 589988888999999999 9999999995 55 999999999999875443 3
Q ss_pred cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhC
Q 022938 231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVI 273 (289)
Q Consensus 231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~ 273 (289)
..|++||.|+|+|+++|+++++|.||+|+.+..--.+.+++|.
T Consensus 798 ~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~~~~~~~~~~~~~~~ 840 (863)
T PRK12269 798 RKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQRDELSRYM 840 (863)
T ss_pred cccCCCCEEEEEEEEEEcCCCEEEEEEechhhHHHHHHHHHhh
Confidence 4599999999999999999999999999876544444455553
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=1.1e-33 Score=281.87 Aligned_cols=246 Identities=24% Similarity=0.371 Sum_probs=221.8
Q ss_pred ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
|-+.++...+++++++.+..|+.-...+++....+|.+.|++|++++|+|++++.+++++.+|+++.
T Consensus 308 G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~------------- 374 (647)
T PRK00087 308 GTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEA------------- 374 (647)
T ss_pred EEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehh-------------
Confidence 4567889999999999999999999999999999999999999999999999999999999998743
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.....|+.+.++++.|++++|+|+++.++|+||+++|++||||.+++++.+. .+|.+ ++|+.++|+|++
T Consensus 375 --~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gfiP~sel~~~~~-~d~~~--------~vG~~v~v~Vl~ 443 (647)
T PRK00087 375 --DREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYV-EDLSE--------YKGQELEVKIIE 443 (647)
T ss_pred --cchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHhCcccc-CCHHH--------hCCCEEEEEEEE
Confidence 2345799999999999999999999999999999999999999999998775 55432 389999999999
Q ss_pred EecCCcE-EEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938 163 ANEEMKK-LVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 229 (289)
Q Consensus 163 vd~~~~r-i~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~ 229 (289)
+|+++++ +.+|+|.. ++...++++++|+++.| .++|+||++ +| +.|++|.++++|.++.++
T Consensus 444 vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l---~g---v~Gll~~sels~~~~~~~ 517 (647)
T PRK00087 444 FNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI---GG---VDGLLHVSEISWGRVEKP 517 (647)
T ss_pred EEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE---CC---EEEEEEHHHcCccccCCH
Confidence 9999988 99999874 34566788999999999 899999999 34 999999999999999999
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~ 278 (289)
.+.|++||.|+|+|+++|++++++.||+|++.++||....+++..|+..
T Consensus 518 ~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v 566 (647)
T PRK00087 518 SDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIV 566 (647)
T ss_pred HHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEE
Confidence 9999999999999999999999999999999999999999888888754
No 16
>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=2.8e-32 Score=266.41 Aligned_cols=228 Identities=21% Similarity=0.331 Sum_probs=202.8
Q ss_pred cccccccceeEeCCCCCCccceeEeecccc-cccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938 4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSL-VCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS 82 (289)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~ 82 (289)
-+.++..++|++++.+...|++....++.. ...+|.+.|++||.+.|+|+++|++++++.+|++...
T Consensus 279 ~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~------------ 346 (516)
T TIGR00717 279 RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCK------------ 346 (516)
T ss_pred EEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcc------------
Confidence 356788999999999888898887777743 4667888899999999999999999999999987321
Q ss_pred hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
..+|..+.+.+++|++++|+|+++.++|+||+++ |++||+|.++++|.+...++...++ +|+.|.|+|+
T Consensus 347 ----~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~------~G~~V~~~Vl 416 (516)
T TIGR00717 347 ----ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYK------KGDEIEAVVL 416 (516)
T ss_pred ----cCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccC------CCCEEEEEEE
Confidence 2468888888899999999999999999999999 9999999999998764345555554 9999999999
Q ss_pred EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccccc
Q 022938 162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 233 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~ 233 (289)
++|++++++.+|+|. +||....+++++|+++.| +++|+||++. +| +.|+||.+++++++..++.+.|
T Consensus 417 ~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---~~Glv~~s~l~~~~~~~~~~~~ 491 (516)
T TIGR00717 417 AVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELP--GG---VEGLIRNSELSENRDEDKTDEI 491 (516)
T ss_pred EEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcC--CC---eEEEEEHHHcCccccccccccC
Confidence 999999999999997 588888888999999999 9999999995 54 9999999999999999999999
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 234 NEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 234 ~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
++||.|+++|+++|++++++.||+|
T Consensus 492 ~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 492 KVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred CCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 9999999999999999999999987
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.98 E-value=4.4e-31 Score=263.31 Aligned_cols=233 Identities=25% Similarity=0.393 Sum_probs=203.0
Q ss_pred ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCe-EeeeeecccccCCcchhhhhhh
Q 022938 5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAK-ITPTTVNPILDDSSDANNRQSQ 83 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~-i~ls~k~~l~~~~~~~~~~~~~ 83 (289)
+.++...+|+++++. .+|+.....++.....+|.+ + +|+++.|+|+++|+++++ +.+|++..+ +
T Consensus 397 V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~-~-vG~~v~v~Vl~vd~e~~~~l~lS~k~~~------------~ 461 (647)
T PRK00087 397 VKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE-Y-KGQELEVKIIEFNRKRRKKVVLSRKAIL------------E 461 (647)
T ss_pred EEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH-h-CCCEEEEEEEEEEcCCCcEEEEEeHHHh------------h
Confidence 345678899999985 78887777777777777764 3 999999999999999998 999987432 1
Q ss_pred hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
..+...|....+.++.|+++.|+|+++.++|+||+++|++||+|.++++|.+. .+|.+.|+ +||.++|+|+++
T Consensus 462 ~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~-~~~~~~~~------vGd~V~vkV~~i 534 (647)
T PRK00087 462 EEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRV-EKPSDVLK------VGDEIKVYILDI 534 (647)
T ss_pred hhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcccc-CCHHHhcC------CCCEEEEEEEEE
Confidence 11233455555668999999999999999999999999999999999999886 77777665 999999999999
Q ss_pred ecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCC
Q 022938 164 NEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE 235 (289)
Q Consensus 164 d~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~i 235 (289)
|++++++.+|+|. +||.....++++|+++.| .++|+||++. +| +.|++|.+++++.+..++.+.|++
T Consensus 535 d~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~--~~---i~Gli~~sel~~~~~~~~~~~~kv 609 (647)
T PRK00087 535 DKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELE--PG---VDGLVHISQISWKRIDKPEDVLSE 609 (647)
T ss_pred ECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEhhhcCccccCCHhhcCCC
Confidence 9999999999996 578888888999999999 8999999995 55 999999999999999999999999
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEecCCCCc
Q 022938 236 GDEVRVKVIKIDREKSRITLSIKQLEEDP 264 (289)
Q Consensus 236 Gd~V~vkV~~id~e~~ri~lSlK~~~~~p 264 (289)
||.|+|+|+++|++++++.||+|++.++|
T Consensus 610 Gd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 610 GEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred CCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 99999999999999999999999999999
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.91 E-value=9.3e-24 Score=193.75 Aligned_cols=174 Identities=17% Similarity=0.291 Sum_probs=146.1
Q ss_pred hhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 86 SSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 86 ~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
....|++...+++.|++++|+|+++.++|++|++| +.+||||.+|+++.+. .+|.+.++ +|+.++|+|++++
T Consensus 18 f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~-~~~~~~~~------~G~~v~~~Vi~~~ 90 (318)
T PRK07400 18 FAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRV-EGPEEVLQ------PNETREFFILSDE 90 (318)
T ss_pred HHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccc-cCHHHccC------CCCEEEEEEEEEe
Confidence 33445554455899999999999999999999999 6999999999999886 77877776 9999999999999
Q ss_pred cCCcEEEEEeec----chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCC
Q 022938 165 EEMKKLVFSEKD----AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE 235 (289)
Q Consensus 165 ~~~~ri~lS~k~----~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~i 235 (289)
.+++++.||+|. .+|+......+.|+++.| .++|+||++ +| +.||+|.|+++|.+.. +. .+
T Consensus 91 ~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l---~G---v~gfip~s~ls~~~~~---~~-~v 160 (318)
T PRK07400 91 NEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRI---EG---LRGFIPGSHISTRKPK---EE-LV 160 (318)
T ss_pred CCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHcCccCCc---cc-cC
Confidence 999999999996 367776667778999999 889999999 35 9999999999986433 33 39
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938 236 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279 (289)
Q Consensus 236 Gd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~ 279 (289)
|+.++|+|+++|+++++|.||+|....+ ...+++..|++..
T Consensus 161 G~~i~~kVl~id~~~~~i~lS~K~~~~~---~~~~~~k~G~vv~ 201 (318)
T PRK07400 161 GEELPLKFLEVDEERNRLVLSHRRALVE---RKMNRLEVGEVVV 201 (318)
T ss_pred CCEEEEEEEEEEcccCEEEEEhhHhhhh---hhhccCCCCCEEE
Confidence 9999999999999999999999976543 3456777777643
No 19
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.78 E-value=1.3e-18 Score=176.95 Aligned_cols=193 Identities=22% Similarity=0.298 Sum_probs=169.4
Q ss_pred cccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC
Q 022938 41 IERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF 120 (289)
Q Consensus 41 ~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~ 120 (289)
.|++|.++.||++++.+..+.+.++..+++......... .++.|+.+.|+|.++.+.|+.|.+-
T Consensus 467 ~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~n----------------DI~iG~~V~~~I~~vt~~Gv~v~v~ 530 (1710)
T KOG1070|consen 467 IYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVN----------------DIEIGQLVPGVIRKVTPQGVEVLVT 530 (1710)
T ss_pred ceecCCcccCccceecccCcEEEEEEehHhhcccccccc----------------cccccceeeeEEEEecCCcEEEEEe
Confidence 589999999999999999999999999888776653222 1689999999999999999999876
Q ss_pred -C-EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc------hhhhcccccccccEE
Q 022938 121 -S-LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA------VWNKYSSRVNVEDIF 192 (289)
Q Consensus 121 -g-v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~------~~~~~~~~~~~G~iv 192 (289)
| +.|++|.+++++.+. .-|...| .+|..+++||+.++.+.+++.+++|.+ |....+.+..+|+++
T Consensus 531 ~~ni~g~lp~~hlsd~~~-~~p~~~f------~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~ 603 (1710)
T KOG1070|consen 531 FGNIKGVLPKEHLSDHPL-QPPLRDF------KVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKIT 603 (1710)
T ss_pred cCceeeecChHhhhhccc-cccccee------eeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceE
Confidence 4 999999999999875 4454444 488888999999999999999999974 444567788999999
Q ss_pred Ee-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 193 VG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 193 ~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
.| .++||||.+- +| ++||.|.+++++.++.+.++.|.+||+|.|+|.++|++++||.+++|+..
T Consensus 604 ~G~l~~~~~~g~~V~F~--g~---lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~ 672 (1710)
T KOG1070|consen 604 KGTLCAIKENGAFVTFT--GG---LSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS 672 (1710)
T ss_pred EEEEeeeccCCeEEEec--Cc---cccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence 99 8999999993 54 99999999999999999999999999999999999999999999999975
No 20
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.75 E-value=1.7e-17 Score=168.95 Aligned_cols=230 Identities=22% Similarity=0.244 Sum_probs=192.2
Q ss_pred eEeCCCCCCccceeEe-ecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHH
Q 022938 13 CLDASSCTHSSLSLSL-SLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWK 91 (289)
Q Consensus 13 ~~~~~~~~~~~~~~~~-~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~ 91 (289)
-.+++..+-.|=+..+ .+++..-.+|...|..++.+.+.++.++..+..+.++++.+.-.... .. ....-=
T Consensus 1083 ~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~-~~-------~kd~~i 1154 (1710)
T KOG1070|consen 1083 LILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITP-VD-------SKDGSI 1154 (1710)
T ss_pred eEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEecccccceeecccccccCcc-cc-------ccCCcc
Confidence 4677778888855555 99999999999999999999999999999888899998855432111 00 000000
Q ss_pred HHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938 92 AARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL 170 (289)
Q Consensus 92 ~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri 170 (289)
...++++.|++++|.|..+.+.|+|+.++ ++.||+|++++++.+. ..|...|. +|+.+..+|++++...+|+
T Consensus 1155 ks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~-k~w~k~~~------~gklv~~rv~~ve~~s~ri 1227 (1710)
T KOG1070|consen 1155 KSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFE-KEWEKHLP------VGKLVTGRVLSVEEDSKRI 1227 (1710)
T ss_pred cchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchh-hhhhccCC------ccceeeeEEEEeeccCceE
Confidence 12445799999999999999999999999 9999999999999886 77777776 9999999999999999999
Q ss_pred EEEeecch------hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEE
Q 022938 171 VFSEKDAV------WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEV 239 (289)
Q Consensus 171 ~lS~k~~~------~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V 239 (289)
.+|++... .......++.|+...| .++|.|+++.. .+ ++.|++|.++.++.+..+....+..|+.|
T Consensus 1228 el~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~-tv--~~~g~~~~~e~~d~~~e~it~~~~~~~~V 1304 (1710)
T KOG1070|consen 1228 ELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDV-TV--NMVGLCHISEEADDRGENITALYYAGDRV 1304 (1710)
T ss_pred EEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecC-cc--eecccccceeecchhhhhcccceecccee
Confidence 99999742 2345678899999999 89999999962 22 58999999999999999999999999999
Q ss_pred EEEEEEEeCCCCeEEEEEecC
Q 022938 240 RVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 240 ~vkV~~id~e~~ri~lSlK~~ 260 (289)
+|.++..+.++++|.+.+|..
T Consensus 1305 ~a~~lk~~~ek~rIsl~~k~s 1325 (1710)
T KOG1070|consen 1305 KACVLKEDSEKKRISLGLKSS 1325 (1710)
T ss_pred eeEeeeccchhhhhhhhhhhh
Confidence 999999999999999998875
No 21
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.64 E-value=5.5e-16 Score=140.66 Aligned_cols=92 Identities=25% Similarity=0.376 Sum_probs=83.5
Q ss_pred cccc-cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 184 SRVN-VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 184 ~~~~-~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
..++ +|++|.| .+||+||.|...+ ++.||+|+|++||.++.++++.+++||.|.|+|+++|+++++|.||+
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 3455 7999988 8999999994222 49999999999999999999999999999999999999999999999
Q ss_pred ecCCCCchhHHhhhhCCCChH
Q 022938 258 KQLEEDPLLETLEKVIPQGLE 278 (289)
Q Consensus 258 K~~~~~p~~~~~~~~~~g~~~ 278 (289)
|++.++||..+.++|..|...
T Consensus 89 K~v~~~pw~~~~e~~~~g~~v 109 (319)
T PTZ00248 89 KRVSPEDIEACEEKFSKSKKV 109 (319)
T ss_pred eecccchHHHHHHhCcCCCEE
Confidence 999999999999999998654
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=2e-16 Score=122.36 Aligned_cols=76 Identities=46% Similarity=0.778 Sum_probs=70.5
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
.+++|+++.| ++||+||+|. +| -+||+|+|+++.++++++.+.+++||.|.|+|+++|. +++|+||+|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~--~g---~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELE--GG---KTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEec--CC---CcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence 5789999988 9999999995 55 8999999999999999999999999999999999997 9999999999
Q ss_pred CCCCchh
Q 022938 260 LEEDPLL 266 (289)
Q Consensus 260 ~~~~p~~ 266 (289)
++..|-.
T Consensus 76 ~~e~pe~ 82 (129)
T COG1098 76 LEEEPEK 82 (129)
T ss_pred hhhCccc
Confidence 9887754
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.61 E-value=3.2e-16 Score=142.19 Aligned_cols=135 Identities=13% Similarity=0.176 Sum_probs=116.6
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
++|+++.|+|+++.++|+||++. |++||||.|+++|.+. .+|.+.++ +||.+.|+|+++|+++++|.||.
T Consensus 16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri-~~i~d~vk------vGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRI-RSINKLIR------VGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccccc-CCHHHhcC------CCCEEEEEEEEEeCCCCEEEEEe
Confidence 37999999999999999999994 8999999999999887 88998887 99999999999999999999999
Q ss_pred ec---chhhhcccccccccEEEe------eeeeEEEE------EecCCCceeEEEEEEccCcCcccccCcccccC---CC
Q 022938 175 KD---AVWNKYSSRVNVEDIFVG------RDYGAFIH------LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EG 236 (289)
Q Consensus 175 k~---~~~~~~~~~~~~G~iv~G------~~~G~fV~------i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~---iG 236 (289)
|+ .+|......++.|+++.| ..+|+|++ .. ++ ..++.|..++....+.++.+.|. ++
T Consensus 89 K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~--pl---~~~~gh~y~af~~~v~~~~evl~~l~i~ 163 (319)
T PTZ00248 89 KRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIW--PL---YKKYGHALDALKEALTNPDNVFEGLDIP 163 (319)
T ss_pred eecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHH--HH---HHhcCCHHHHHHHHhcCchhhhccCCCC
Confidence 96 489999999999999999 56999997 33 33 78888988887777777766665 67
Q ss_pred CEEEEEEE
Q 022938 237 DEVRVKVI 244 (289)
Q Consensus 237 d~V~vkV~ 244 (289)
+.+...++
T Consensus 164 ~ev~~~l~ 171 (319)
T PTZ00248 164 EEVKESLL 171 (319)
T ss_pred HHHHHHHH
Confidence 66655554
No 24
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.60 E-value=1.1e-13 Score=121.07 Aligned_cols=174 Identities=15% Similarity=0.147 Sum_probs=138.5
Q ss_pred ccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEE-cCcEEEE
Q 022938 40 IIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFN-GGGLLVR 118 (289)
Q Consensus 40 ~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~-~~G~~V~ 118 (289)
.-.++||+|++.|. -..++++.+|++.+. .++|+.-+++|+.+. +-|+||+
T Consensus 42 ~e~evGdev~vFiY--~D~~~rl~aTt~~p~--------------------------~tvg~~g~~~Vv~v~~~lGaFlD 93 (287)
T COG2996 42 DELEVGDEVTVFIY--VDSEDRLIATTREPK--------------------------ATVGEYGWLKVVEVNKDLGAFLD 93 (287)
T ss_pred CccccCcEEEEEEE--ECCCCceeheeecce--------------------------EeecceeEEEEEEEcCCcceEEe
Confidence 35899999999984 345589999988654 478999999999999 7899999
Q ss_pred EC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecchh-hhccccccc---ccEEE
Q 022938 119 FF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVW-NKYSSRVNV---EDIFV 193 (289)
Q Consensus 119 l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~~~-~~~~~~~~~---G~iv~ 193 (289)
+| .-+.++|.++++.... .+| .+|+++-|.+. +|. ++|+...++...+ +........ ++.+.
T Consensus 94 ~Gl~KDl~vp~~elp~~~~-~wp----------q~Gd~l~v~l~-~Dk-k~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~ 160 (287)
T COG2996 94 WGLPKDLLVPLDELPTLKS-LWP----------QKGDKLLVYLY-VDK-KGRIWGTLAIEKILENLATPAYNNLKNQEVD 160 (287)
T ss_pred cCCCcceeeehhhcccccc-cCC----------CCCCEEEEEEE-Ecc-CCcEEEEecchhHHHhcCCccchhhhcCeee
Confidence 99 9999999999976431 234 29999999985 885 4588888876533 344444444 77777
Q ss_pred e-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHH
Q 022938 194 G-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET 268 (289)
Q Consensus 194 G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~ 268 (289)
| ...|.||-++ +| +.|++|.||.. ..++.||.++++|+.+.+ +++|.||++.+..+-.++-
T Consensus 161 ~tVYr~~~~G~fv~~e--~~---~~GfIh~sEr~--------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l~~d 226 (287)
T COG2996 161 ATVYRLLESGTFVITE--NG---YLGFIHKSERF--------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEMLDED 226 (287)
T ss_pred eEEEEEeccceEEEEc--CC---eEEEEcchhhc--------ccccCCceEEEEEEEEcc-CCeeecccccccHHhhhhh
Confidence 7 8899999885 54 99999999875 457899999999999997 9999999999866554443
No 25
>PRK08582 hypothetical protein; Provisional
Probab=99.54 E-value=6.4e-14 Score=113.76 Aligned_cols=97 Identities=36% Similarity=0.617 Sum_probs=82.6
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
.+++|++|.| +++|+||+|. +| +.|+||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~--~~---~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELP--EG---KTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 3688999998 9999999995 54 9999999999999999999999999999999999997 5999999999
Q ss_pred CCCCchhHHhh-----------h-hCCCChHHHHHHHhhh
Q 022938 260 LEEDPLLETLE-----------K-VIPQGLEPYLKSFYKK 287 (289)
Q Consensus 260 ~~~~p~~~~~~-----------~-~~~g~~~~~~~~~~~~ 287 (289)
+.++||.+... . -...+.+.-|+.|+|.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~~l~~flk~ 115 (139)
T PRK08582 76 AKDRPKRQHDRPRHEDNRGGGNDVAPKEDFEQKMSRFLKD 115 (139)
T ss_pred cccCchhhccccccccccccccccccccCHHHHHHHHHHH
Confidence 99999975221 0 1125788888888874
No 26
>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=99.52 E-value=1e-13 Score=100.34 Aligned_cols=72 Identities=28% Similarity=0.497 Sum_probs=66.7
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
++.|++++|+|.+++++|+||+++ +++||||.+++++.+. .+|.+.+. +||+++|+|+++|.+++++.+|+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRI-DDPSEVYK------IGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEE-SSSHGTCE------TTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccc-cccccccC------CCCEEEEEEEEEECCCCeEEEEEC
Confidence 579999999999999999999999 9999999999998865 66777766 999999999999999999999986
No 27
>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=99.49 E-value=1.2e-13 Score=100.25 Aligned_cols=70 Identities=23% Similarity=0.439 Sum_probs=62.4
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcc---cchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQ---KSIHEIAKGLTGSIISVKVIQANEEMKKLVF 172 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~---~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l 172 (289)
+++|+++.|+|+++.++|+||+++ +++|++|.++++|.+. .+|. +.|+ +||.++|+|+++|++++++.|
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~-~~~~~~~~~~~------~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFV-SDPSLYNKYLP------EGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccc-cChhhHhcccC------CCCEEEEEEEEEECCCCEEec
Confidence 368999999999999999999998 9999999999999885 5543 4554 999999999999999999987
Q ss_pred E
Q 022938 173 S 173 (289)
Q Consensus 173 S 173 (289)
|
T Consensus 74 S 74 (74)
T cd05705 74 S 74 (74)
T ss_pred C
Confidence 6
No 28
>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=99.45 E-value=1.8e-13 Score=99.28 Aligned_cols=66 Identities=26% Similarity=0.446 Sum_probs=59.7
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~---~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
+++|+++.| +++|+||+++ +| +.|++|+++++|.++.++ .+.|++||.|+|+|+++|+++++|.||
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 IKEGQLLRGYVSSVTKQGVFFRLS--SS---IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeC--CC---CEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 478999999 9999999996 55 999999999999986664 588999999999999999999999886
No 29
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=99.45 E-value=2.1e-13 Score=130.69 Aligned_cols=142 Identities=15% Similarity=0.222 Sum_probs=111.6
Q ss_pred eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhc--CCCEE
Q 022938 26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKE--SGFIY 103 (289)
Q Consensus 26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~G~iv 103 (289)
..++|+++.-.+|. +++|+.+.+.|...+. +|+.++..+.. +.+.+ ++..++.+++.++ .|+++
T Consensus 73 ~eI~L~eAk~~~~~--~~vGD~ie~~I~~~~f--gRia~q~aKq~------i~Qki----re~ere~i~~eyk~~~GeIV 138 (470)
T PRK09202 73 KEISLEEARKIDPD--AEVGDYIEEEIESVDF--GRIAAQTAKQV------IVQKI----REAERERVYEEYKDRVGEII 138 (470)
T ss_pred ceeeHHHHhhhCcc--ccCCCeEEEEEccccC--ChHHHHHHHHH------HHHHH----HHHHHHHHHHHHHhhcCCEE
Confidence 56778888777775 8999999999977663 66666643222 23333 4445556666665 99999
Q ss_pred EEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEeecchhhh
Q 022938 104 EGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSEKDAVWNK 181 (289)
Q Consensus 104 ~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~k~~~~~~ 181 (289)
+|+|.++.++|++|+++|++||||.++++ |.+.++ +|++++|+|++++++++ ++.|||+...+..
T Consensus 139 ~G~V~ri~~~giiVDLggvea~LP~sE~i-------p~E~~~------~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l~ 205 (470)
T PRK09202 139 TGVVKRVERGNIIVDLGRAEAILPRKEQI-------PRENFR------PGDRVRAYVYEVRKEARGPQIILSRTHPEFLK 205 (470)
T ss_pred EEEEEEEecCCEEEEECCeEEEecHHHcC-------CCccCC------CCCEEEEEEEEEecCCCCCeEEEEeCcHHHHH
Confidence 99999999999999999999999999985 444454 99999999999998877 9999999987777
Q ss_pred cccccccccEEEe
Q 022938 182 YSSRVNVEDIFVG 194 (289)
Q Consensus 182 ~~~~~~~G~iv~G 194 (289)
.+...++-++..|
T Consensus 206 ~Lf~~EVPEI~~G 218 (470)
T PRK09202 206 KLFEQEVPEIADG 218 (470)
T ss_pred HHHHHhCcccccC
Confidence 7777777777766
No 30
>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=99.44 E-value=6.1e-13 Score=96.26 Aligned_cols=70 Identities=20% Similarity=0.310 Sum_probs=62.5
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCc-cCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~-~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|++++|+|+++.++|+||.++ +++|+||.+++++.. ...+|.+.|+ +||.++|+|+++|++++++.||.+
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFP------IGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCC------CCCEEEEEEEEEeCCCCEEEEEec
Confidence 789999999999999999998 999999999999763 1256666665 999999999999999999999986
No 31
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.43 E-value=1.3e-13 Score=106.94 Aligned_cols=73 Identities=22% Similarity=0.365 Sum_probs=68.8
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
+++|.+++|+|+++.+||+||++. |-+|++|+||+++.++ +|..+.+. +||.|.|+|+++|. ++++.||+|
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fV-kdI~d~L~------vG~eV~vKVl~ide-~GKisLSIr 74 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFV-KDIHDHLK------VGQEVKVKVLDIDE-NGKISLSIR 74 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhH-HhHHHHhc------CCCEEEEEEEeecc-CCCcceehH
Confidence 579999999999999999999999 8999999999999998 88888887 99999999999996 999999999
Q ss_pred cc
Q 022938 176 DA 177 (289)
Q Consensus 176 ~~ 177 (289)
..
T Consensus 75 ~~ 76 (129)
T COG1098 75 KL 76 (129)
T ss_pred Hh
Confidence 74
No 32
>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=99.42 E-value=7.5e-13 Score=98.12 Aligned_cols=72 Identities=22% Similarity=0.448 Sum_probs=66.4
Q ss_pred hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
.++.|+++.|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++ +||.++|+|.++|.+++++.+|+
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~-~~~~~~~~------~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-TDPSFGFK------KGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccc-cCHHHhcC------CCCEEEEEEEEEcCCCCEEEEeC
Confidence 3789999999999999999999998 8999999999999876 67777776 99999999999999999999985
No 33
>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=99.42 E-value=7.9e-13 Score=94.60 Aligned_cols=69 Identities=30% Similarity=0.618 Sum_probs=63.3
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|++++|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++ +||.++|+|+++|++++++.||++
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFI-KDPEEHFR------VGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhc-CCHHHccc------CCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999998 8999999999998775 67776665 999999999999999999999985
No 34
>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=99.40 E-value=6.8e-13 Score=98.34 Aligned_cols=74 Identities=31% Similarity=0.434 Sum_probs=67.5
Q ss_pred hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 022938 179 WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI 253 (289)
Q Consensus 179 ~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri 253 (289)
....+.++++|+++.| .++|+||+++ +| +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++
T Consensus 5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~--~~---~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i 79 (83)
T cd04461 5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFL--GG---LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79 (83)
T ss_pred chhhHHhCCCCCEEEEEEEEEeeceEEEEcC--CC---CEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence 3445677999999999 9999999995 54 999999999999999999999999999999999999999999
Q ss_pred EEEE
Q 022938 254 TLSI 257 (289)
Q Consensus 254 ~lSl 257 (289)
.||+
T Consensus 80 ~lsl 83 (83)
T cd04461 80 LLSL 83 (83)
T ss_pred EEeC
Confidence 9985
No 35
>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=99.40 E-value=1.5e-12 Score=93.00 Aligned_cols=68 Identities=24% Similarity=0.490 Sum_probs=61.8
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
|++++|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++ +||.++|+|+++|.+++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL-KHPEKKFK------PGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccc-cCHHHcCC------CCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999998 8999999999998775 66666665 99999999999999999999985
No 36
>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=99.40 E-value=2.4e-12 Score=93.37 Aligned_cols=68 Identities=15% Similarity=0.297 Sum_probs=61.0
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
++.|++++|+|++++++|+||+++ |++||+|.+++++. +.+ .+||.+.|+|+++|++++++.||+
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~-------~~~------~~Gq~v~~~V~~vd~~~~~v~ls~ 68 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKL------KVGQLLLCVVEKVKDDGRVVSLSA 68 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc-------ccc------CCCCEEEEEEEEEECCCCEEEEEE
Confidence 478999999999999999999997 79999999999864 223 399999999999999999999999
Q ss_pred ecc
Q 022938 175 KDA 177 (289)
Q Consensus 175 k~~ 177 (289)
++.
T Consensus 69 k~~ 71 (74)
T cd05694 69 DPS 71 (74)
T ss_pred eec
Confidence 864
No 37
>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=99.39 E-value=1.2e-12 Score=94.59 Aligned_cols=69 Identities=45% Similarity=0.776 Sum_probs=63.7
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
++++|+++.| .++|+||+++ +| +.|++|.+++++.+..++...|++||+++|+|+++|++++++.||+|
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~--~~---~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG--NG---IEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES--TS---SEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC--Cc---EEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 3688999999 8899999996 44 99999999999999999999999999999999999999999999986
No 38
>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=99.39 E-value=2.4e-12 Score=93.33 Aligned_cols=68 Identities=18% Similarity=0.212 Sum_probs=60.9
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
+++.|+++.| .++|+||+++ .+| +.||+|.++++|. +.+++||.+.|+|+++|++++++.||+|+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g-~~g---v~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIG-IPG---TTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeC-CCC---cEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 4688999999 9999999995 234 9999999999976 67999999999999999999999999999
Q ss_pred CCC
Q 022938 260 LEE 262 (289)
Q Consensus 260 ~~~ 262 (289)
+.+
T Consensus 71 ~~~ 73 (74)
T cd05694 71 SKV 73 (74)
T ss_pred ccc
Confidence 765
No 39
>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=99.38 E-value=1.4e-12 Score=94.32 Aligned_cols=65 Identities=17% Similarity=0.331 Sum_probs=59.3
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
|+++.| .++|+||.++ +| +.|++|.+++++.. .+++.+.|++||.|+|+|+++|+++++|.||+|
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 GQEVTGFVNNVSKEFVWLTIS--PD---VKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CC---cEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 677777 8999999996 55 99999999999864 788999999999999999999999999999987
No 40
>PRK05807 hypothetical protein; Provisional
Probab=99.38 E-value=3.6e-12 Score=103.17 Aligned_cols=96 Identities=40% Similarity=0.611 Sum_probs=78.4
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
.+++|+++.| +++|+||++ +| ..|++|++++++.++.++.+.|++||.|+|+|+++|+ +++|.||+|.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L---~~---~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~ 74 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV---EG---KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ 74 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 4678999998 999999999 34 8999999999999999999999999999999999998 7999999999
Q ss_pred CC-CCc--------hhHHhhhhCCCChHHHHHHHhhh
Q 022938 260 LE-EDP--------LLETLEKVIPQGLEPYLKSFYKK 287 (289)
Q Consensus 260 ~~-~~p--------~~~~~~~~~~g~~~~~~~~~~~~ 287 (289)
+. +.| |.....+....+.+.-|..|++.
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 111 (136)
T PRK05807 75 AMKQKKSVKPAEIDWQKEKNKNNNGNFEDRLSKFLKD 111 (136)
T ss_pred ccccccccCccccccccccccCCCcCHHHHHHHHHHH
Confidence 86 222 12111222335888889998874
No 41
>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=99.37 E-value=3.8e-12 Score=90.38 Aligned_cols=67 Identities=28% Similarity=0.469 Sum_probs=59.6
Q ss_pred CCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|++++|+|+++.++|++|+++|++||||.+++++.+. .+|.+ .+||.++|+|+++|.+++++.+|++
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPV-EDLDE--------YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCccc-CChHH--------hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 7899999999999999999999999999999997664 44422 3899999999999999999999985
No 42
>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=99.37 E-value=6.3e-12 Score=90.67 Aligned_cols=71 Identities=18% Similarity=0.201 Sum_probs=64.1
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
+.|+++.|+|+++.++|+||+++ +++|++|.+++++.+. .++.+.++ +||.++|+|+++|.+++++.||.+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~-~~~~~~~~------~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYS-EALPYKFK------KNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccc-cccccccC------CCCEEEEEEEEEeCCCCEEEEEEC
Confidence 58999999999999999999999 9999999999998774 55656565 999999999999999999999974
No 43
>PRK07252 hypothetical protein; Provisional
Probab=99.36 E-value=2.4e-12 Score=101.95 Aligned_cols=72 Identities=39% Similarity=0.753 Sum_probs=66.3
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
++|+++.| .++|+||++. +| +.|++|.+++++.++.++.+.|++||.|+|+|+++|++++++.||+|.++
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~--~~---~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE--NG---TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC--CC---CEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 57888888 8999999995 44 99999999999999989989999999999999999999999999999997
Q ss_pred CC
Q 022938 262 ED 263 (289)
Q Consensus 262 ~~ 263 (289)
++
T Consensus 77 ~~ 78 (120)
T PRK07252 77 EE 78 (120)
T ss_pred cC
Confidence 63
No 44
>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=4e-12 Score=91.46 Aligned_cols=68 Identities=16% Similarity=0.239 Sum_probs=60.9
Q ss_pred CCEEE-EEEEEE-EcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 100 GFIYE-GKIQGF-NGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 100 G~iv~-g~V~~v-~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
|++++ |+|+++ .++|+||++. |++||+|.+++++.+. .++.+.++ +||.++|+|+++|+.++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKV-PSDTGPFK------AGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchh-cCcccccC------CCCEEEEEEEEEeCCCCEEEEeC
Confidence 78899 999999 6999999998 9999999999998775 55666665 99999999999999999999985
No 45
>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=99.34 E-value=2.8e-12 Score=92.56 Aligned_cols=66 Identities=21% Similarity=0.299 Sum_probs=59.5
Q ss_pred cccccEEEe-----e-eeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 186 VNVEDIFVG-----R-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 186 ~~~G~iv~G-----~-~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
+++|+++.| . ++|+|+++. +| ..|++|++++++++..++.+.|++||.|+|+|+++|. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~--~~---~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLP--FG---KTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECC--CC---CEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 468999999 4 489999995 55 9999999999999999999999999999999999984 89999986
No 46
>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=99.34 E-value=7.3e-12 Score=90.91 Aligned_cols=70 Identities=34% Similarity=0.518 Sum_probs=63.1
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
++|+++.| .++|+||++...+| +.|++|.+++++.+..++.+.|++||.|+|+|.++|.+++++.||+|+
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~---~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGN---IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCC---eEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 57888888 89999999952223 899999999999999999999999999999999999999999999985
No 47
>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=99.34 E-value=4.4e-12 Score=90.30 Aligned_cols=67 Identities=15% Similarity=0.299 Sum_probs=61.2
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
|+++.|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++ +||.++|+|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYL-KDWKKRFK------VGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhh-cCHhhccC------CCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998 8999999999998876 67776665 9999999999999999999876
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.33 E-value=2.9e-12 Score=129.71 Aligned_cols=84 Identities=30% Similarity=0.491 Sum_probs=76.0
Q ss_pred cccccccccEEE-e-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938 182 YSSRVNVEDIFV-G-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255 (289)
Q Consensus 182 ~~~~~~~G~iv~-G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l 255 (289)
.....++|+++. | .+||+||+|. +| ++||||+|+++|+++.++.+.|++||.|+|+|+++|+ ++||.|
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~--~g---~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~L 820 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIA--PG---REGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRL 820 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeC--CC---CEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEE
Confidence 344578999995 4 9999999996 55 9999999999999999999999999999999999997 899999
Q ss_pred EEecCCCCchhHHhhh
Q 022938 256 SIKQLEEDPLLETLEK 271 (289)
Q Consensus 256 SlK~~~~~p~~~~~~~ 271 (289)
|+|++.++||++...+
T Consensus 821 SlK~l~~~Pw~~~~~~ 836 (891)
T PLN00207 821 SRRALLPEANSEKSSQ 836 (891)
T ss_pred EEeccccCchhhhhhh
Confidence 9999999999998763
No 49
>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=99.33 E-value=5.2e-12 Score=91.13 Aligned_cols=69 Identities=20% Similarity=0.347 Sum_probs=62.4
Q ss_pred cCCCEEEEEEEEEEc-CcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 98 ESGFIYEGKIQGFNG-GGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~-~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
++|+++.|+|+++.+ +|+||+++ |.+|++|.+++++.+. .+|.+.++ +||.++|+|+++|. +++.||++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~-~~~~~~~~------~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYT-ENPLEGFK------PGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCccc-CCHHHhCC------CCCEEEEEEEEecC--CEEEEEeC
Confidence 589999999999986 89999999 9999999999999886 77777676 99999999999974 89999985
No 50
>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=99.32 E-value=8.8e-12 Score=89.91 Aligned_cols=68 Identities=25% Similarity=0.406 Sum_probs=62.0
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
+++|+++.| .++|+||++. +| +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++.||+|
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 LKVGDILPGRVTKVNDRYVLVQLG--NK---VTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeC--CC---cEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 468999988 8999999996 55 99999999999988778888999999999999999999999999985
No 51
>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=99.32 E-value=1.1e-11 Score=89.63 Aligned_cols=69 Identities=22% Similarity=0.314 Sum_probs=62.1
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
+.|++++|+|+++.++|+||++.| .+||+|.+++++.+. .+|.+.++ +||+++|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~-~~~~~~~~------~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRV-DDPSEVVD------VGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcc-cCHhhEEC------CCCEEEEEEEEECCCC-cEEEEe
Confidence 479999999999999999999975 799999999999876 77777776 9999999999999876 888886
No 52
>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=99.32 E-value=9.5e-12 Score=89.00 Aligned_cols=69 Identities=20% Similarity=0.392 Sum_probs=63.5
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|++++|+|.++.++|++|+++ +.+|++|.+++++.+. .+|.+.++ +||.++|+|+++|++++++.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~-~~~~~~~~------~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPI-ENGEDEVK------VGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcccc-CCHhHcCC------CCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999998 8999999999998876 77777776 999999999999988899999985
No 53
>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=99.32 E-value=4.8e-12 Score=90.51 Aligned_cols=65 Identities=29% Similarity=0.425 Sum_probs=59.4
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
|+++.| .++|+||++. +| +.||+|.+++++++..++.+.|++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFY--NN---VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC--CC---CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 567777 8999999995 44 99999999999998889999999999999999999999999999986
No 54
>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=99.31 E-value=4.7e-12 Score=116.97 Aligned_cols=143 Identities=19% Similarity=0.248 Sum_probs=106.3
Q ss_pred eeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhh--cCCCE
Q 022938 25 SLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYK--ESGFI 102 (289)
Q Consensus 25 ~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~G~i 102 (289)
...++|+++.-.+|+ +++||.+.+.+...+ -+|+.++..+.+ +.+.++++ .++.+++.+ +.|++
T Consensus 69 ~~ei~l~~A~~~d~~--~~vGD~I~~~I~~~~--fgR~aaq~aKqv------i~Qkire~----ere~i~~ey~~k~Gei 134 (341)
T TIGR01953 69 SLEISLEDAREIDPD--VQIGDEVKKEIPPEN--FGRIAAQTAKQV------ILQKIREA----ERERVYDEFSSKEGEI 134 (341)
T ss_pred cccccHHHHHhhccc--cccCCEEEEEecccC--CCHHHHHHHHHH------HHHHHHHH----HHHHHHHHHHhhcCCE
Confidence 356888999888885 999999999884332 256555543322 33344444 455555555 59999
Q ss_pred EEEEEEEEEcCc-EEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC--cEEEEEeecchh
Q 022938 103 YEGKIQGFNGGG-LLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM--KKLVFSEKDAVW 179 (289)
Q Consensus 103 v~g~V~~v~~~G-~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~--~ri~lS~k~~~~ 179 (289)
++|+|.++.++| ++|++|+++||||.+|+.. .+.+. +|++++|.|++++.+. .++.+|++.+.+
T Consensus 135 V~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip-------~E~~~------~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~ 201 (341)
T TIGR01953 135 ISGTVKRVNRRGNLYVELGKTEGILPKKEQIP-------GEKFR------IGDRIKAYVYEVRKTAKGPQIILSRTHPEF 201 (341)
T ss_pred EEEEEEEEecCCcEEEEECCeEEEecHHHcCC-------CcCCC------CCCEEEEEEEEEEcCCCCCeEEEEeCcHHH
Confidence 999999999988 6999999999999999763 33343 9999999999999553 589999999877
Q ss_pred hhcccccccccEEEe
Q 022938 180 NKYSSRVNVEDIFVG 194 (289)
Q Consensus 180 ~~~~~~~~~G~iv~G 194 (289)
...+.+.++-++..|
T Consensus 202 v~~Lfe~EVPEI~dG 216 (341)
T TIGR01953 202 VKELLKLEVPEIADG 216 (341)
T ss_pred HHHHHHHhCccccCC
Confidence 766666666666665
No 55
>PRK08059 general stress protein 13; Validated
Probab=99.30 E-value=1.1e-11 Score=98.68 Aligned_cols=77 Identities=45% Similarity=0.809 Sum_probs=71.1
Q ss_pred ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
++++++|+++.| .++|+||++. ++ +.|++|.+++++.+..++.+.|++||.|+|+|.++|++++++.||+
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~--~~---~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lsl 76 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALD--EE---TQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEEC--CC---CEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEE
Confidence 456889999999 8999999996 54 9999999999999888888899999999999999999999999999
Q ss_pred ecCCCCc
Q 022938 258 KQLEEDP 264 (289)
Q Consensus 258 K~~~~~p 264 (289)
|.+..+|
T Consensus 77 k~~~~~~ 83 (123)
T PRK08059 77 RATEEAP 83 (123)
T ss_pred EEcccCc
Confidence 9999888
No 56
>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=99.29 E-value=8.8e-12 Score=89.67 Aligned_cols=58 Identities=29% Similarity=0.479 Sum_probs=54.0
Q ss_pred eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
.++|+||++. +| +.||+|.|++++.+.+++.+.|++||.++|+|+++|++++++.||+
T Consensus 14 ~~~G~~V~l~--~g---v~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 14 PDLGAVFELK--DG---LLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred cCceEEEEeC--CC---CEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 4799999995 55 9999999999999988899999999999999999999999999995
No 57
>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=99.29 E-value=1.4e-11 Score=89.07 Aligned_cols=66 Identities=35% Similarity=0.615 Sum_probs=58.6
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
+.|+++.| .+||+||++. | +..+||+|++++++.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~---~-~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIP---G-CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEEC---C-CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 47888888 9999999993 2 12699999999999999999999999999999999999965 999986
No 58
>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=99.29 E-value=2.7e-11 Score=87.93 Aligned_cols=72 Identities=21% Similarity=0.320 Sum_probs=65.1
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
+.|+++.|+|+++.++|+||++. |++|++|.+++++.+. .+|.+.++ +||.++|+|.++|.+.+++.+|+
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~-~~~~~~~~------~Gd~v~vkv~~~d~~~~~i~ls~ 74 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRI-RSIRKLVK------VGRKEVVKVIRVDKEKGYIDLSK 74 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCccc-CCHHHeeC------CCCEEEEEEEEEECCCCEEEEEE
Confidence 47999999999999999999995 4999999999998876 77777776 99999999999999899999998
Q ss_pred ec
Q 022938 175 KD 176 (289)
Q Consensus 175 k~ 176 (289)
++
T Consensus 75 k~ 76 (76)
T cd04452 75 KR 76 (76)
T ss_pred cC
Confidence 74
No 59
>PHA02945 interferon resistance protein; Provisional
Probab=99.29 E-value=1.8e-11 Score=89.57 Aligned_cols=72 Identities=31% Similarity=0.409 Sum_probs=64.5
Q ss_pred ccccEEEe----eeeeEEEEEecCCCceeEEEEEEccCc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 187 NVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 187 ~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~sel--s~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
++|+++.| .++|+||.+...+ +..||+|+|+. +..++++ ++.+ .||++.|+|+.+|+.++.|.||+|+.
T Consensus 10 ~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 10 NVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 67888888 8999999996444 49999999955 9999999 9999 99999999999999999999999998
Q ss_pred CCC
Q 022938 261 EED 263 (289)
Q Consensus 261 ~~~ 263 (289)
..+
T Consensus 85 ~~~ 87 (88)
T PHA02945 85 CRH 87 (88)
T ss_pred ccC
Confidence 654
No 60
>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=1.2e-11 Score=88.32 Aligned_cols=64 Identities=23% Similarity=0.463 Sum_probs=58.3
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
|+++.| .++|+||+++ +| +.|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLS--DH---IKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec--CC---cEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 566777 8999999995 55 9999999999999888888999999999999999999999999985
No 61
>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=99.28 E-value=2.3e-11 Score=87.50 Aligned_cols=70 Identities=21% Similarity=0.397 Sum_probs=64.3
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
|+++.|+|+++.++|++|+++ +++|++|.+++++.+. .+|.+.++ +||.++|+|+++|.+++++.+|++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~-~~~~~~~~------~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRV-EDATERFK------VGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccc-cCHHHccC------CCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 789999999999999999998 8999999999998875 67777766 9999999999999999999999986
No 62
>PRK07252 hypothetical protein; Provisional
Probab=99.27 E-value=3e-11 Score=95.63 Aligned_cols=73 Identities=18% Similarity=0.272 Sum_probs=66.7
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
+.|+++.|+|+++.++|+||+++ ++.|++|.+++++.+. .++.+.++ +||.|+|+|+++|.+.+++.+|++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~-~~~~~~~~------vGD~V~VkI~~iD~~~~ri~lSlk~ 74 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFI-DNIHQLLK------VGEEVLVQVVDFDEYTGKASLSLRT 74 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccc-cChhhccC------CCCEEEEEEEEEeCCCCEEEEEEee
Confidence 57999999999999999999998 8999999999998876 66666665 9999999999999999999999997
Q ss_pred c
Q 022938 177 A 177 (289)
Q Consensus 177 ~ 177 (289)
.
T Consensus 75 ~ 75 (120)
T PRK07252 75 L 75 (120)
T ss_pred c
Confidence 5
No 63
>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=99.26 E-value=2e-11 Score=86.89 Aligned_cols=68 Identities=18% Similarity=0.377 Sum_probs=59.5
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
|+++.|+|+++.++|+||+++ +++|++|.++++|.....+|.+.++ +||.|+|+|.++|.+++++.+|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~------~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYK------KGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEEC------CCCEEEEEEEEEECCcCEEeCC
Confidence 789999999999999999998 8999999999996432366666665 9999999999999999998774
No 64
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=99.26 E-value=1.2e-11 Score=114.92 Aligned_cols=144 Identities=19% Similarity=0.222 Sum_probs=109.5
Q ss_pred eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938 26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG 105 (289)
Q Consensus 26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g 105 (289)
..++|+++.-.+|+ .++|+.+...+...+. +|+.+.. ++..+.+.++++.+...|+++.+ +.|++++|
T Consensus 73 ~eisL~eAk~i~~~--~~vGD~i~~~I~~~~f--gR~aaq~------akqvI~Qkire~ere~v~~ef~~--k~GeiV~G 140 (362)
T PRK12327 73 LEISLEDALAINPA--YELGDVIEIEVTPKDF--GRIAAQT------AKQVIMQRLREAEREIIYNEFSE--REGDIVTG 140 (362)
T ss_pred ccccHHHHhhhCcc--ccCCCEEEEecCcCCC--ChHHHHH------HHHHHHHHHHHHHHHHHHHHHHH--hcCCEEEE
Confidence 45678888777774 9999999998854443 4544442 23335566777777777766555 69999999
Q ss_pred EEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEeecchhhhcc
Q 022938 106 KIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSEKDAVWNKYS 183 (289)
Q Consensus 106 ~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~k~~~~~~~~ 183 (289)
+|.++.++|++|++|+++||||.+++. |++.++ +|++++|.|.+++.+.+ ++.+||..+.+...+
T Consensus 141 ~V~~~~~~~~~Vdlg~vEa~LP~~E~i-------p~e~~~------~Gd~Ika~V~~V~~~~kgp~IivSRt~p~~v~~L 207 (362)
T PRK12327 141 VVQRRDNRFVYVNLGKIEAVLPPAEQI-------PGETYK------HGDRIKVYVVKVEKTTKGPQIFVSRTHPGLVKRL 207 (362)
T ss_pred EEEEEeCCcEEEEeCCeEEEecHHHcC-------CCCCCC------CCCEEEEEEEEEecCCCCCeEEEEeCCHHHHHHH
Confidence 999999999999999999999988864 334444 99999999999996543 799999988776666
Q ss_pred cccccccEEEe
Q 022938 184 SRVNVEDIFVG 194 (289)
Q Consensus 184 ~~~~~G~iv~G 194 (289)
...++-++..|
T Consensus 208 fe~EVPEI~~G 218 (362)
T PRK12327 208 FELEVPEIYDG 218 (362)
T ss_pred HHHhCccccCC
Confidence 66666666665
No 65
>PRK08582 hypothetical protein; Provisional
Probab=99.26 E-value=3.7e-11 Score=97.59 Aligned_cols=73 Identities=23% Similarity=0.361 Sum_probs=66.3
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
++.|+++.|+|++++++|+||+++ +++|+||.+++++.+. .++.+.++ +||.|+|+|+++|. .++|.||++
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v-~~~~~~l~------vGD~VkvkV~~id~-~gkI~LSlk 74 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV-KDINDHLK------VGDEVEVKVLNVED-DGKIGLSIK 74 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccc-cccccccC------CCCEEEEEEEEECC-CCcEEEEEE
Confidence 579999999999999999999999 8999999999999886 67766665 99999999999996 489999999
Q ss_pred cc
Q 022938 176 DA 177 (289)
Q Consensus 176 ~~ 177 (289)
+.
T Consensus 75 ~~ 76 (139)
T PRK08582 75 KA 76 (139)
T ss_pred ec
Confidence 74
No 66
>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=99.25 E-value=2.8e-11 Score=86.98 Aligned_cols=68 Identities=37% Similarity=0.624 Sum_probs=61.5
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
|+++.| .++|+||++. ++ +.|++|.+++++++..++.+.|++||.++|+|+++|++++++.||+|..+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~--~~---~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~ 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG--DG---VEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC--CC---CEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 566666 8999999996 44 99999999999999889999999999999999999999999999999863
No 67
>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=99.25 E-value=3.3e-11 Score=87.47 Aligned_cols=70 Identities=41% Similarity=0.675 Sum_probs=62.8
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
++|+++.| .++|+||++. +. +..|++|.+++++++..++.+.|++||.|+|+|.++|++++++.||+|..
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 KVGQKIDGTVRRVEDYGVFIDID--GT--NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEEC--CC--CeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 35788888 9999999995 21 39999999999999888888999999999999999999999999999975
No 68
>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=99.25 E-value=6.1e-11 Score=86.09 Aligned_cols=72 Identities=17% Similarity=0.327 Sum_probs=65.0
Q ss_pred CCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
.|+++.|+|+++.++|+||++. +..|++|.+++++.+. .+|.+.++ +||.|+|+|.++|.+.+++.+|++.
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~-~~~~~~~~------~Gd~v~v~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRV-ADASKLFR------VGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCcc-CCHhHeec------CCCEEEEEEEEEeCCCCEEEEEEEe
Confidence 6999999999999999999997 5999999999998775 66666665 9999999999999999999999987
Q ss_pred c
Q 022938 177 A 177 (289)
Q Consensus 177 ~ 177 (289)
+
T Consensus 75 ~ 75 (77)
T cd05708 75 S 75 (77)
T ss_pred e
Confidence 4
No 69
>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=99.24 E-value=1.9e-11 Score=87.01 Aligned_cols=63 Identities=30% Similarity=0.534 Sum_probs=57.3
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
|+++.| .++|+||++. +| +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLG--RG---VDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC--CC---CEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 566666 8999999995 44 999999999999999999999999999999999999999999886
No 70
>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=99.22 E-value=5.7e-11 Score=84.20 Aligned_cols=65 Identities=18% Similarity=0.459 Sum_probs=56.2
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
|++++|+|+++.++|++|++. +++||+|.++++..+. . .+.+ .+|+.++|+|+++|++++++.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS-S--KSTY------KEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC-c--ccCc------CCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999997 8999999999975442 1 3334 49999999999999999998876
No 71
>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=99.22 E-value=3.2e-11 Score=85.84 Aligned_cols=63 Identities=38% Similarity=0.796 Sum_probs=55.5
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~-~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
|+++.| .++|+||++. +| ++|++|.++++| .+..++.+.|++||.|+|+|+++|+++++|.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~--~~---~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD--GG---IDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC--CC---CEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 556666 9999999996 54 999999999997 467788889999999999999999999999875
No 72
>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=99.22 E-value=6.6e-11 Score=85.06 Aligned_cols=70 Identities=20% Similarity=0.356 Sum_probs=60.0
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.+|+++.|+|+++.++|+||+++ +++|++|.+++++.....++.+.++ +||.++|+|.++|.+++++.++
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~------~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVS------LGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeC------CCCEEEEEEEEeeCCcCEEeCC
Confidence 58999999999999999999998 8999999999986522235555555 9999999999999998888764
No 73
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=1.1e-11 Score=108.16 Aligned_cols=83 Identities=34% Similarity=0.623 Sum_probs=73.8
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
.+|++|-| .+||+||.|...+| +.||+|+||++..++++++++++.||.+-|+|+++|++++.|.||+|.+.
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g---~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~ 86 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPG---KEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT 86 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCC---eeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence 67888888 89999999986665 99999999999999999999999999999999999999999999999998
Q ss_pred CCchhHHhhhh
Q 022938 262 EDPLLETLEKV 272 (289)
Q Consensus 262 ~~p~~~~~~~~ 272 (289)
++.-.+.++.+
T Consensus 87 ~~q~~~k~~~w 97 (269)
T COG1093 87 EHQRRKKIQEW 97 (269)
T ss_pred HHHHHHHHHHH
Confidence 76655544443
No 74
>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=99.21 E-value=9.6e-11 Score=85.88 Aligned_cols=71 Identities=35% Similarity=0.665 Sum_probs=61.0
Q ss_pred ccEEEe-----eeeeEEEEEecC-CCceeEEEEEEccCcCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 189 EDIFVG-----RDYGAFIHLRFP-DGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~-~G~~~i~Glv~~sels~~~~-~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
|+++.| .++|+||+++.. +| ..|++|.+++++.+. .++.+.|++||.|+|+|.++| ++++.+|+|+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~---~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~ 75 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGR---KEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVD 75 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCC---cEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecc
Confidence 456666 899999999511 13 899999999999986 888899999999999999999 799999999988
Q ss_pred CCc
Q 022938 262 EDP 264 (289)
Q Consensus 262 ~~p 264 (289)
++.
T Consensus 76 ~~~ 78 (79)
T cd05684 76 QDT 78 (79)
T ss_pred cCC
Confidence 753
No 75
>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=99.18 E-value=1.2e-10 Score=82.33 Aligned_cols=68 Identities=21% Similarity=0.381 Sum_probs=61.1
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|+++.|+|+++.++|+||+++ +..||+|.+++++.+. .+|.+.++ +||.++++|.++|. .+++.+|++
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRV-KDVKDVLK------EGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCccc-CCHHHccC------CCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999999 9999999999998775 66666565 99999999999998 889999875
No 76
>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=99.18 E-value=1.1e-10 Score=82.42 Aligned_cols=68 Identities=25% Similarity=0.444 Sum_probs=60.8
Q ss_pred CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.|++++|+|.++.++|++|++++.+|++|.+++++.+. .+|.+.++ +||.++|+|.++|.+++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRV-KHPSEVVN------VGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccc-cCHhHEEC------CCCEEEEEEEEEECCCCEEecC
Confidence 48999999999999999999999999999999997665 66666665 9999999999999988998875
No 77
>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=99.17 E-value=1.1e-10 Score=83.44 Aligned_cols=65 Identities=31% Similarity=0.468 Sum_probs=59.1
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
|+++.| .++|+||+++ .+ ..|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~--~~---~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG--YK---SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CC---ceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 667777 7899999995 43 89999999999999999999999999999999999988999999986
No 78
>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=99.17 E-value=5.2e-11 Score=91.39 Aligned_cols=74 Identities=16% Similarity=0.377 Sum_probs=63.3
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc------------------CcCcccchhcccccCCCCEEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS------------------CKEPQKSIHEIAKGLTGSIISV 158 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~------------------~~~p~~~~~~~~~~~vG~~V~v 158 (289)
+.|+++.|+|+++.++|++|.++ |++||+|.+++++.+. ..++.+.| .+||.|+|
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f------~vGd~V~~ 75 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLF------SVGQLVRC 75 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhc------cCCCEEEE
Confidence 68999999999999999999999 9999999999998652 02244444 49999999
Q ss_pred EEEEEecC---CcEEEEEeecc
Q 022938 159 KVIQANEE---MKKLVFSEKDA 177 (289)
Q Consensus 159 kVl~vd~~---~~ri~lS~k~~ 177 (289)
+|+++|++ ++++.||++.+
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHH
Confidence 99999987 78999999874
No 79
>PRK05807 hypothetical protein; Provisional
Probab=99.17 E-value=2.2e-10 Score=92.78 Aligned_cols=73 Identities=22% Similarity=0.335 Sum_probs=66.3
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
+++|++++|+|+++.++|+||++++..|++|.+++++.+. .++.+.++ +||.|+|+|+++|. .++|.||++.
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v-~~~~~~~k------vGd~V~VkV~~id~-~gkI~LSlk~ 74 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYV-KDIREHLK------EQDKVKVKVISIDD-NGKISLSIKQ 74 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccc-cCccccCC------CCCEEEEEEEEECC-CCcEEEEEEe
Confidence 4789999999999999999999998999999999999886 67666665 99999999999997 7999999987
Q ss_pred c
Q 022938 177 A 177 (289)
Q Consensus 177 ~ 177 (289)
.
T Consensus 75 ~ 75 (136)
T PRK05807 75 A 75 (136)
T ss_pred c
Confidence 4
No 80
>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=99.16 E-value=1.2e-10 Score=82.11 Aligned_cols=67 Identities=25% Similarity=0.454 Sum_probs=59.7
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
|+++.|+|+++.++|+||+++ +..|++|.+++++.+. .+|.+.++ +||.++|+|.++|.+.+++.+|
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~-~~~~~~~~------~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFV-SHPSDVVS------VGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccc-cCHHHhcC------CCCEEEEEEEEEECCCCEEecC
Confidence 688999999999999999999 8999999999998765 56665555 9999999999999988888875
No 81
>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=99.14 E-value=1.7e-10 Score=82.96 Aligned_cols=66 Identities=41% Similarity=0.727 Sum_probs=57.3
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~-~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
+++|+++.| +++|+||++. +| ++|++|.++++|. +..++.+.|++||.|+|+|.++|++++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~--~~---~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE--EG---VEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC--CC---CEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 467888888 9999999995 55 9999999999875 44467788999999999999999999999874
No 82
>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=99.14 E-value=2e-10 Score=81.21 Aligned_cols=64 Identities=45% Similarity=0.908 Sum_probs=57.6
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
|+++.| .++|+||+++ ++ ..|++|.+++++.+..++.+.|++||.++|+|.++|+ ++++.||+|
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 GSVVEGTVTRLKPFGAFVELG--GG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--CC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 556666 8999999996 44 8999999999999888888999999999999999998 899999986
No 83
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.13 E-value=3.3e-10 Score=80.20 Aligned_cols=70 Identities=26% Similarity=0.495 Sum_probs=61.9
Q ss_pred CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
.|+++.|+|.++.++|++|+++ ++.|++|.+++++.+. .++.+.++ +||.++|+|.+++.+++++.+|++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~-~~~~~~~~------~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRV-KDPEEVLK------VGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcccc-CCHHHeec------CCCEEEEEEEEEeCCCCEEEEEeC
Confidence 6999999999999999999999 9999999999998763 44544454 999999999999998899999874
No 84
>PRK08059 general stress protein 13; Validated
Probab=99.12 E-value=3.1e-10 Score=90.41 Aligned_cols=74 Identities=23% Similarity=0.377 Sum_probs=67.1
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
++.|+++.|+|+++.++|+||+++ +..|++|.+++++.+. .++.+.++ +||.|+|+|.++|.+.+++.+|++
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~-~~~~~~~~------vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFV-KDIHDFLS------VGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccc-cCHHHcCC------CCCEEEEEEEEEECCCCeEEEEEE
Confidence 678999999999999999999999 8999999999998765 56655555 999999999999999999999999
Q ss_pred cc
Q 022938 176 DA 177 (289)
Q Consensus 176 ~~ 177 (289)
..
T Consensus 78 ~~ 79 (123)
T PRK08059 78 AT 79 (123)
T ss_pred Ec
Confidence 75
No 85
>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=99.11 E-value=5.9e-10 Score=81.67 Aligned_cols=69 Identities=29% Similarity=0.424 Sum_probs=60.5
Q ss_pred CCEEEEEEEEEEcCcEEEEEC----CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF----SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~----gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
|+++.|+|+++.++|+||+++ +..||+|.+++++.+...++.+.|+ +||.|+|+|.++| .+++.+|++
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 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVK------RGQKVKVKVISIQ--NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeC------CCCEEEEEEEEEe--CCEEEEEEE
Confidence 789999999999999999998 6899999999998763146666665 9999999999999 789999998
Q ss_pred c
Q 022938 176 D 176 (289)
Q Consensus 176 ~ 176 (289)
+
T Consensus 73 ~ 73 (79)
T cd05684 73 D 73 (79)
T ss_pred e
Confidence 6
No 86
>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=99.11 E-value=3.9e-10 Score=79.71 Aligned_cols=67 Identities=24% Similarity=0.457 Sum_probs=59.8
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
|+++.|+|+++.++|+||+++ +..||+|.+++++.+. .++.+.++ +||.++|+|.++|+ ++++.+|+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERV-EKVEDVLK------VGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccc-cCHHHccC------CCCEEEEEEEEECC-CCcEEeeC
Confidence 688999999999999999998 8999999999998765 56665555 99999999999998 88998885
No 87
>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=99.10 E-value=1.2e-10 Score=89.37 Aligned_cols=70 Identities=31% Similarity=0.533 Sum_probs=61.2
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-------------------cCcccccCCCCEEEE
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV 241 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-------------------~~~~~~~~iGd~V~v 241 (289)
+++|+++.| .++|+||.+. +| +.|++|+++++|.+. .++.+.|++||.|+|
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~--~g---~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~ 75 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLP--NG---LTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC 75 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECC--CC---cEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence 478999999 8999999994 44 999999999998652 347788999999999
Q ss_pred EEEEEeCC---CCeEEEEEecC
Q 022938 242 KVIKIDRE---KSRITLSIKQL 260 (289)
Q Consensus 242 kV~~id~e---~~ri~lSlK~~ 260 (289)
+|+++|++ +++|.||+|..
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHH
Confidence 99999997 79999999974
No 88
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.09 E-value=4.4e-10 Score=100.52 Aligned_cols=84 Identities=36% Similarity=0.621 Sum_probs=71.2
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
++|+++.| .++|+||++...+| +.|++|.++++++++.++.+.|++||.|.|+|+++|+++++|.||+|.+.
T Consensus 7 ~~GdiV~G~V~~I~~~G~fV~L~e~~g---ieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~ 83 (262)
T PRK03987 7 EEGELVVGTVKEVKDFGAFVTLDEYPG---KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVN 83 (262)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCC---cEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecc
Confidence 67888888 89999999952224 99999999999999999999999999999999999999999999999987
Q ss_pred CCchhHHhhhhC
Q 022938 262 EDPLLETLEKVI 273 (289)
Q Consensus 262 ~~p~~~~~~~~~ 273 (289)
++.-.+.++++.
T Consensus 84 ~~e~~~~~~~~~ 95 (262)
T PRK03987 84 EHQRREKIQEWK 95 (262)
T ss_pred cchHHHHHHHHH
Confidence 665334333333
No 89
>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=99.08 E-value=3.4e-10 Score=80.22 Aligned_cols=61 Identities=18% Similarity=0.312 Sum_probs=52.7
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
|+++.| .++|+||++. +| +.|++|.++++..+.. .+.|++||.++|+|+++|+++++|.||
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 GMLVNARVKKVLSNGLILDFL--SS---FTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc--CC---ceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 567777 8999999995 44 9999999999765444 677999999999999999999999886
No 90
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=99.08 E-value=3e-10 Score=105.20 Aligned_cols=145 Identities=11% Similarity=0.139 Sum_probs=113.5
Q ss_pred eeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEE
Q 022938 25 SLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYE 104 (289)
Q Consensus 25 ~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~ 104 (289)
...++|+++.-.+|. +++|+.+...+---+. +|+.+..- +..+.+.++++.++..++++.+ +.|++++
T Consensus 76 ~~eI~L~eAk~i~~~--~~vGd~i~~~i~~~~f--gRiaaq~a------kq~i~Qkir~~er~~i~~ey~~--~~Geiv~ 143 (374)
T PRK12328 76 EKFISLSEAKEIDPS--VEIGDELTYELSLENM--GRTAANTL------FKELEYHIQRLLEESIFEKYKK--KVGKIVF 143 (374)
T ss_pred cceeeHHHHHhhCCC--CCCCCEEEEecChhhC--CHHHHHHH------HHHHHHHHHHHHHHHHHHHHHH--hcCcEEE
Confidence 356888999888874 9999999887743222 57666643 3335667777777777877766 5999999
Q ss_pred EEEEEEEc-CcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc---EEEEEeecchhh
Q 022938 105 GKIQGFNG-GGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK---KLVFSEKDAVWN 180 (289)
Q Consensus 105 g~V~~v~~-~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~---ri~lS~k~~~~~ 180 (289)
|+|.++.. .+++|++++++|+||.+++. |.+.|+ +|++++|.|.+|+...+ ++.|||..+.+.
T Consensus 144 g~V~r~~~~~~i~vdlg~~ea~LP~~eqi-------p~E~~~------~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v 210 (374)
T PRK12328 144 GTVVRVDNEENTFIEIDEIRAVLPMKNRI-------KGEKFK------VGDVVKAVLKRVKIDKNNGILIELSRTSPKFL 210 (374)
T ss_pred EEEEEEecCCCEEEEcCCeEEEeCHHHcC-------CCCcCC------CCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH
Confidence 99999997 46999999999999999854 555555 99999999999998755 899999998777
Q ss_pred hcccccccccEEEe
Q 022938 181 KYSSRVNVEDIFVG 194 (289)
Q Consensus 181 ~~~~~~~~G~iv~G 194 (289)
..+.+.++-++..|
T Consensus 211 ~~Lfe~EVPEI~dG 224 (374)
T PRK12328 211 EALLELEVPEIKDG 224 (374)
T ss_pred HHHHHHhCccccCC
Confidence 66666677776666
No 91
>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=99.05 E-value=4.7e-10 Score=79.07 Aligned_cols=63 Identities=38% Similarity=0.661 Sum_probs=56.0
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
|+++.| +++|+||+++ ++ ..|++|.+++++.+..++.+.|++||.++|+|.++|++++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~--~~---~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG--VK---QDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC--CC---CEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 455666 8999999996 44 999999999999888888889999999999999999999999876
No 92
>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=99.03 E-value=1.1e-09 Score=77.21 Aligned_cols=63 Identities=46% Similarity=0.907 Sum_probs=56.7
Q ss_pred cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
+|+++.| .++|+||+++ + +.|++|.+++++.+..++.+.|++||.|+|+|.++|++++++.||
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---G---VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC---C---eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 3677777 8999999994 3 899999999998888888899999999999999999999999876
No 93
>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=99.02 E-value=1.2e-09 Score=81.27 Aligned_cols=73 Identities=12% Similarity=0.184 Sum_probs=61.0
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
+.|+++.|+|+++.++|++|+++ +.+|++|.+++++... ..+..+.+ .+||.+.|+|++++++ +++.||
T Consensus 5 ~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l------~vGd~i~~~V~~~~~~-~~i~LS 77 (86)
T cd05789 5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYL------DEGDLIVAEVQSVDSD-GSVSLH 77 (86)
T ss_pred CCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhC------CCCCEEEEEEEEECCC-CCEEEE
Confidence 68999999999999999999999 8999999999985321 12333334 3999999999999876 899999
Q ss_pred eecc
Q 022938 174 EKDA 177 (289)
Q Consensus 174 ~k~~ 177 (289)
++..
T Consensus 78 ~~~~ 81 (86)
T cd05789 78 TRSL 81 (86)
T ss_pred eCcc
Confidence 9874
No 94
>PHA02945 interferon resistance protein; Provisional
Probab=99.01 E-value=2.3e-09 Score=78.55 Aligned_cols=71 Identities=21% Similarity=0.248 Sum_probs=61.8
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCC--CCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQM--SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sel--s~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
.++|+++-|+|.. .++|+||.+. |.+||+|.++. +..+. ++ .+.+ .||++-|+|+++|+.++.|-
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wv-K~-rd~l-------~GqkvV~KVirVd~~kg~ID 78 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYF-KY-RDKL-------VGKTVKVKVIRVDYTKGYID 78 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceE-ee-eeEe-------cCCEEEEEEEEECCCCCEEE
Confidence 3799999999999 9999999985 79999999965 87776 54 4433 89999999999999999999
Q ss_pred EEeecc
Q 022938 172 FSEKDA 177 (289)
Q Consensus 172 lS~k~~ 177 (289)
+|+|..
T Consensus 79 lSlK~V 84 (88)
T PHA02945 79 VNYKRM 84 (88)
T ss_pred eEeeEc
Confidence 999863
No 95
>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=99.01 E-value=1.4e-09 Score=76.76 Aligned_cols=63 Identities=46% Similarity=0.838 Sum_probs=55.8
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
|+++.| .++|+||+++ ++ ..|++|.+++++.+..++.+.|++||.|+|+|.++|+ ++++.||+
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 GKIYEGKVVKIKDFGAFVEIL--PG---KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC--CC---CEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 455666 8999999995 44 8999999999999888888899999999999999999 89999984
No 96
>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=99.00 E-value=1.7e-09 Score=76.69 Aligned_cols=62 Identities=29% Similarity=0.572 Sum_probs=54.1
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
|+++.| .++|+||++ +| +.||+|.+++++.+..++.+ .+||.++|+|+++|++++++.||+|
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---EG---VRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 566777 899999999 34 99999999999887777665 3899999999999999999999975
No 97
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.00 E-value=1.8e-09 Score=76.37 Aligned_cols=67 Identities=45% Similarity=0.783 Sum_probs=59.7
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
++|+++.| .++|+||+++ ++ +.|++|.+++++.+..++...|++||.++|+|.+++++++++.+|++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG--NG---VEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeC--CC---CEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 35888888 8899999995 44 99999999999887777888899999999999999998899999975
No 98
>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=98.99 E-value=1.4e-09 Score=80.91 Aligned_cols=69 Identities=22% Similarity=0.362 Sum_probs=60.0
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~----~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.++|++|.| .++|++|+++ ++ +.|++|.+++++ .+..++.+.+++||.++|+|+++|++ +++.||
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~--~~---~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS 77 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDIN--SP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLH 77 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECC--CC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEE
Confidence 478999998 8999999995 44 999999999986 34567778899999999999999985 999999
Q ss_pred EecC
Q 022938 257 IKQL 260 (289)
Q Consensus 257 lK~~ 260 (289)
+|+.
T Consensus 78 ~~~~ 81 (86)
T cd05789 78 TRSL 81 (86)
T ss_pred eCcc
Confidence 9884
No 99
>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=98.98 E-value=2.5e-09 Score=80.17 Aligned_cols=72 Identities=24% Similarity=0.331 Sum_probs=59.2
Q ss_pred hcCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCC---CccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938 97 KESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSP---SHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL 170 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~---~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri 170 (289)
++.|+++.|+|+++.++ |+||+++ |.+||||.++++| .+. .++.+.++ +||.|.|+|++.....+..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v-~~~~~~~~------~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKH-KKIAKLLK------EGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhcccc-CCHHHcCC------CCCEEEEEEEEecCCCCCc
Confidence 47999999999999996 9999999 8999999999998 333 55666665 9999999999877666555
Q ss_pred EEEee
Q 022938 171 VFSEK 175 (289)
Q Consensus 171 ~lS~k 175 (289)
.+|..
T Consensus 78 ~lt~~ 82 (88)
T cd04453 78 RLTTN 82 (88)
T ss_pred eEEEE
Confidence 55543
No 100
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.98 E-value=1.2e-09 Score=110.88 Aligned_cols=85 Identities=22% Similarity=0.323 Sum_probs=73.7
Q ss_pred HHHhhcCCCEEE-EEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938 93 ARAYKESGFIYE-GKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL 170 (289)
Q Consensus 93 l~~~~~~G~iv~-g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri 170 (289)
+....+.|++++ |+|+++.++|+||++. |++||||+++++|.++ .++.+.++ +||.|+|+|+++|. .+++
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv-~~~~dv~k------vGD~V~VkVi~ID~-~grI 818 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWL-AKPEDAFK------VGDRIDVKLIEVND-KGQL 818 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccc-cCHHHhcC------CCCEEEEEEEEECC-CCcE
Confidence 334468999996 6999999999999998 9999999999999886 78877776 99999999999996 7899
Q ss_pred EEEeec---chhhhcccc
Q 022938 171 VFSEKD---AVWNKYSSR 185 (289)
Q Consensus 171 ~lS~k~---~~~~~~~~~ 185 (289)
.||+|. +||+...+.
T Consensus 819 ~LSlK~l~~~Pw~~~~~~ 836 (891)
T PLN00207 819 RLSRRALLPEANSEKSSQ 836 (891)
T ss_pred EEEEeccccCchhhhhhh
Confidence 999986 588866443
No 101
>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=98.96 E-value=3.8e-09 Score=77.94 Aligned_cols=72 Identities=22% Similarity=0.272 Sum_probs=62.9
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
+.|+++.|+|+++.+.+++|+++ +.+|++|.++++..+. .++.+.++ +||.+.|+|+++|.+ +++.||.+.
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~-~~~~~~~~------~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDK-KEIRKSLQ------PGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcch-HHHHhcCC------CCCEEEEEEEEeCCC-CCEEEEECC
Confidence 68999999999999999999999 8999999999987654 44445554 999999999999976 899999886
Q ss_pred c
Q 022938 177 A 177 (289)
Q Consensus 177 ~ 177 (289)
.
T Consensus 77 ~ 77 (82)
T cd04454 77 N 77 (82)
T ss_pred C
Confidence 4
No 102
>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=98.95 E-value=5.1e-09 Score=74.31 Aligned_cols=64 Identities=20% Similarity=0.373 Sum_probs=54.6
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC--cEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM--KKLVFSE 174 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~--~ri~lS~ 174 (289)
..|++++|+|.++.++|++|++++.+||||.+|++. .+.++ +|+++++.|.+++.++ .++.+|+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~-------~~~~~------~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP-------GESYR------PGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC-------CCcCC------CCCEEEEEEEEEecCCCCCEEEEeC
Confidence 479999999999999999999999999999999863 22233 9999999999999654 4788885
No 103
>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=98.94 E-value=4.6e-09 Score=75.14 Aligned_cols=63 Identities=17% Similarity=0.281 Sum_probs=54.7
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCc-cCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~-~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
|+++.|+|+++.++|++|+++ |++|++|.+++++.+ ...+|.+.|+ +||.++|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~------~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFK------IGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCC------CCCEEEEEEEEEeCccc
Confidence 789999999999999999999 999999999999875 2266666665 99999999999987553
No 104
>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=98.92 E-value=9.3e-09 Score=75.64 Aligned_cols=76 Identities=17% Similarity=0.245 Sum_probs=58.3
Q ss_pred CCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchh----cccccCCCCEEEEEEEEEecCCcEEEE
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIH----EIAKGLTGSIISVKVIQANEEMKKLVF 172 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~----~~~~~~vG~~V~vkVl~vd~~~~ri~l 172 (289)
.|++++|+|+++.++|+||+++ |++|++|.+++++.+...++..... ....+.+||.|+|+|.++|.+++++.+
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 3889999999999999999999 6999999999986543222211000 001234999999999999998899988
Q ss_pred Ee
Q 022938 173 SE 174 (289)
Q Consensus 173 S~ 174 (289)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 75
No 105
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.92 E-value=7.1e-09 Score=88.68 Aligned_cols=93 Identities=23% Similarity=0.320 Sum_probs=75.5
Q ss_pred EEEecCCcEEEEEeecchhhhcccccccccEEEe-----eeeeEEEEEecCC--C---ceeEEEEEEccCcCcccccCcc
Q 022938 161 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPD--G---LYHLTGLVHVSEVSWDLIQDIR 230 (289)
Q Consensus 161 l~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~--G---~~~i~Glv~~sels~~~~~~~~ 230 (289)
+++|.+++++.+ .||.......++|++|.| .++|+||+|...+ + ...+.|++|.+++++.+..++.
T Consensus 41 ~~id~~~~~Isv----~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~ 116 (189)
T PRK09521 41 VFIDDINRKISV----IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT 116 (189)
T ss_pred EEEcCCCCEEEE----ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence 345666777777 467776778899999999 8999999995210 0 0028899999999998888888
Q ss_pred cccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 231 DILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
+.|++||.|.|+|++++ +++.||+|+.
T Consensus 117 ~~~~~GD~V~akV~~i~---~~i~LS~k~~ 143 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT---DPLQLSTKGK 143 (189)
T ss_pred hccCCCCEEEEEEEecC---CcEEEEEecC
Confidence 99999999999999998 7899999974
No 106
>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=98.90 E-value=9e-09 Score=75.70 Aligned_cols=64 Identities=30% Similarity=0.644 Sum_probs=54.2
Q ss_pred ccEEEe-----eeeeEEEEEecCC-CceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeCCCC
Q 022938 189 EDIFVG-----RDYGAFIHLRFPD-GLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS 251 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~-G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~e~~ 251 (289)
|+++.| +++|+||++. + | +.|++|.+++++++.. .....|++||.|+|+|.++|++++
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~--~~~---~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~ 76 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELD--NLT---VEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR 76 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEec--CCC---EEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence 667777 9999999996 3 5 9999999999876422 345789999999999999999999
Q ss_pred eEEEEE
Q 022938 252 RITLSI 257 (289)
Q Consensus 252 ri~lSl 257 (289)
++.+++
T Consensus 77 ~i~~~l 82 (83)
T cd04471 77 KIDFEL 82 (83)
T ss_pred EEEEEE
Confidence 999986
No 107
>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=98.90 E-value=4.3e-09 Score=72.90 Aligned_cols=64 Identities=22% Similarity=0.435 Sum_probs=56.0
Q ss_pred EEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 103 YEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 103 v~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
+.|+|+++.++|++|+++ +.+|++|.+++++.+. .++.+.++ +||.++|+|.++|++.+++.+|
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~-~~~~~~~~------~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-KDPSEVFK------VGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccc-cCHhhEeC------CCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999999 9999999999998765 55655555 9999999999999988888775
No 108
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.89 E-value=6.8e-09 Score=92.90 Aligned_cols=73 Identities=19% Similarity=0.307 Sum_probs=66.2
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.+.|+++.|+|+++.++|+||++. |++||+|.+++++.+. .++.+.++ +||.+.|+|+++|.+++++.||
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i-~~i~~~~k------vGd~V~vkVi~VD~~k~~I~LS 78 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWV-KNIRDHVK------EGQKVVCKVIRVDPRKGHIDLS 78 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccc-cCHHHhCC------CCCEEEEEEEEEecccCeEEEE
Confidence 468999999999999999999995 6999999999998876 66766665 9999999999999999999999
Q ss_pred eec
Q 022938 174 EKD 176 (289)
Q Consensus 174 ~k~ 176 (289)
++.
T Consensus 79 lK~ 81 (262)
T PRK03987 79 LKR 81 (262)
T ss_pred EEe
Confidence 984
No 109
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.88 E-value=5.7e-09 Score=105.33 Aligned_cols=73 Identities=42% Similarity=0.776 Sum_probs=67.3
Q ss_pred cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.....++|+++.| .++|+||++. +| ..|++|+|++++.++.++.+.|++||.|+|+|+++|++ +++.||
T Consensus 615 ~~~~~~vG~v~~G~V~~I~~fGafVei~--~~---~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS 688 (693)
T PRK11824 615 ITAEPEVGEIYEGKVVRIVDFGAFVEIL--PG---KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLS 688 (693)
T ss_pred hcccCcCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEE
Confidence 3456899999999 9999999996 55 99999999999999999999999999999999999986 999999
Q ss_pred EecC
Q 022938 257 IKQL 260 (289)
Q Consensus 257 lK~~ 260 (289)
+|.+
T Consensus 689 ~k~~ 692 (693)
T PRK11824 689 RKAV 692 (693)
T ss_pred EEec
Confidence 9976
No 110
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=98.87 E-value=5.7e-09 Score=98.23 Aligned_cols=146 Identities=12% Similarity=0.109 Sum_probs=110.9
Q ss_pred eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938 26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG 105 (289)
Q Consensus 26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g 105 (289)
..++|+++.-.+|. +++|+.+...|.-...+-+|+.+..-+ ..+.+.++.+++...++++.+ +.|++++|
T Consensus 89 ~eIsL~eAk~i~~~--~~iGD~v~~~v~~~~~~fgRiAAq~aK------Qvi~Qkire~ER~~i~~ef~~--~~GeIV~G 158 (449)
T PRK12329 89 HQISLAEVQQVADE--AQLGDTVVLDVTPEQEDFGRMAAIQTK------QVLAQKLRDQQRKMIQEEFQD--LEDTVLTA 158 (449)
T ss_pred ccccHHHHHhhCCC--CcCCCEEEEecCccccchhHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH--hcCcEEEE
Confidence 45778888877774 999999987762110133677776443 336677888888888888777 59999999
Q ss_pred EEEEEEcCcEEEEE----C--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC---cEEEEEeec
Q 022938 106 KIQGFNGGGLLVRF----F--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM---KKLVFSEKD 176 (289)
Q Consensus 106 ~V~~v~~~G~~V~l----~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~---~ri~lS~k~ 176 (289)
+|.++.+.+++|++ | +++|+||.++.. |++.|+ +|++++|.|.+|+... -++.|||..
T Consensus 159 ~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi-------p~E~y~------~Gdrika~i~~V~~~~~kGpqIilSRt~ 225 (449)
T PRK12329 159 RVLRFERQSVIMAVSSGFGQPEVEAELPKREQL-------PNDNYR------ANATFKVFLKEVSEGPRRGPQLFVSRAN 225 (449)
T ss_pred EEEEEcCCCEEEEecccCCCcceEEEecHHHcC-------CCCcCC------CCCEEEEEEEEeecCCCCCCEEEEEcCC
Confidence 99999999999998 4 299999999854 555565 9999999999998753 389999998
Q ss_pred chhhhcccccccccEEEe
Q 022938 177 AVWNKYSSRVNVEDIFVG 194 (289)
Q Consensus 177 ~~~~~~~~~~~~G~iv~G 194 (289)
..+...+...++-++..|
T Consensus 226 p~lv~~Lfe~EVPEI~dG 243 (449)
T PRK12329 226 AGLVVYLFENEVPEIEEG 243 (449)
T ss_pred HHHHHHHHHhhCcccccC
Confidence 777666666666666555
No 111
>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=98.87 E-value=8.8e-09 Score=77.17 Aligned_cols=70 Identities=26% Similarity=0.383 Sum_probs=59.7
Q ss_pred ccccccEEEe-----eee--eEEEEEecCCCceeEEEEEEccCcCc---ccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 022938 185 RVNVEDIFVG-----RDY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT 254 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~--G~fV~i~~~~G~~~i~Glv~~sels~---~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~ 254 (289)
.+++|+++.| .++ |+||+++ +| .+||+|.++++| .++.++.+.+++||.|.|+|+......+--.
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~--~g---~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~ 78 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIG--LG---KNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR 78 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeC--CC---CEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence 5678999999 665 9999996 55 899999999999 5678888999999999999999887777777
Q ss_pred EEEec
Q 022938 255 LSIKQ 259 (289)
Q Consensus 255 lSlK~ 259 (289)
||.+-
T Consensus 79 lt~~~ 83 (88)
T cd04453 79 LTTNI 83 (88)
T ss_pred EEEEE
Confidence 77654
No 112
>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=98.86 E-value=9.6e-09 Score=102.44 Aligned_cols=88 Identities=24% Similarity=0.523 Sum_probs=69.6
Q ss_pred EEecCCcEEEEEeecch--------hhhccc--ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcC----
Q 022938 162 QANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVS---- 222 (289)
Q Consensus 162 ~vd~~~~ri~lS~k~~~--------~~~~~~--~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels---- 222 (289)
+++ +.+.+.++-.... ...... ..++|+++.| .+||+||+|. +| +.||+|+|+++
T Consensus 612 di~-d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~--~G---~eGLvHISeisdls~ 685 (719)
T TIGR02696 612 SIE-DDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL--PG---KDGLLHISQIRKLAG 685 (719)
T ss_pred EEe-cCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec--CC---ceEEEEhhhcccccc
Confidence 355 3567776655421 112223 4799999999 9999999996 55 99999999996
Q ss_pred cccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 223 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 223 ~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
+.++.++.+.|++||.|+|+|+++|+ ++||.|+
T Consensus 686 ~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 686 GKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred ccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 46889999999999999999999995 8899886
No 113
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.86 E-value=3.4e-09 Score=105.22 Aligned_cols=78 Identities=36% Similarity=0.604 Sum_probs=71.4
Q ss_pred cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.++++++|+++.| .+||+||+|+ - +..|++|+|++++.++.+|.+.+++||.|+|+|+++|..++||.||
T Consensus 652 ~i~dLk~Gm~leg~Vrnv~~fgafVdIg--v---~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Ls 726 (780)
T COG2183 652 SITDLKPGMILEGTVRNVVDFGAFVDIG--V---HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALS 726 (780)
T ss_pred hHhhccCCCEEEEEEEEeeeccceEEec--c---ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeE
Confidence 3678999999999 9999999997 3 3899999999999999999999999999999999999999999999
Q ss_pred EecCCCCc
Q 022938 257 IKQLEEDP 264 (289)
Q Consensus 257 lK~~~~~p 264 (289)
|+..+..+
T Consensus 727 mr~~~~~~ 734 (780)
T COG2183 727 MRLDEEEG 734 (780)
T ss_pred eeccCCcc
Confidence 99875433
No 114
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.84 E-value=3.2e-09 Score=92.81 Aligned_cols=73 Identities=19% Similarity=0.295 Sum_probs=68.0
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.++|+++-|+|..|.++|+||.+. |++||+|.||++..++ .+..++++ +||.+-|+|++||+.++.+-||
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wV-knIrd~vk------egqkvV~kVlrVd~~rg~IDLS 81 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWV-KNIRDYVK------EGQKVVAKVLRVDPKRGHIDLS 81 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHH-HHHHHHhh------cCCeEEEEEEEEcCCCCeEeee
Confidence 369999999999999999999985 7999999999999887 88888887 9999999999999999999999
Q ss_pred eec
Q 022938 174 EKD 176 (289)
Q Consensus 174 ~k~ 176 (289)
+|.
T Consensus 82 lkr 84 (269)
T COG1093 82 LKR 84 (269)
T ss_pred hhh
Confidence 986
No 115
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.84 E-value=5.9e-09 Score=103.54 Aligned_cols=75 Identities=25% Similarity=0.416 Sum_probs=71.7
Q ss_pred hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
.+++|++++|+|+++.++|+||++| ..+|++|++++++.++ .+|.+.+. +||.|+|+|+++|..+++|.||+
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv-~~P~~vv~------vGdiV~v~V~~vD~~r~rI~Lsm 727 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFV-KDPNEVVK------VGDIVKVKVIEVDTARKRIALSM 727 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhc-CChHHhcc------cCCEEEEEEEEEecccCeeeeEe
Confidence 5799999999999999999999999 9999999999999998 99998887 99999999999999999999999
Q ss_pred ecc
Q 022938 175 KDA 177 (289)
Q Consensus 175 k~~ 177 (289)
+..
T Consensus 728 r~~ 730 (780)
T COG2183 728 RLD 730 (780)
T ss_pred ecc
Confidence 974
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=98.84 E-value=3.4e-08 Score=72.04 Aligned_cols=62 Identities=21% Similarity=0.330 Sum_probs=55.3
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
++.|+.++|+|.++.++|+||++. +..|++|.+++... + .+||.++++|.++ .+.+++.+|+
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~~~---------~------~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD---------Y------EVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCc---------C------CCCCEEEEEEEEE-CCCCcEEEEE
Confidence 689999999999999999999999 89999999997432 2 3999999999999 7889998875
No 117
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.81 E-value=1.9e-08 Score=101.53 Aligned_cols=74 Identities=23% Similarity=0.401 Sum_probs=68.3
Q ss_pred HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
...+.|+++.|+|+++.++|+||++. |.+|++|++++++.+. .++.+.++ +||.|+|+|+++|.+ +++.||
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v-~~~~~v~k------vGD~V~VkV~~iD~~-grI~LS 688 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERV-EKVEDVLK------EGDEVKVKVLEIDKR-GRIRLS 688 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccc-cCccceeC------CCCEEEEEEEEECCC-CcEEEE
Confidence 44689999999999999999999998 9999999999999886 78888776 999999999999977 999999
Q ss_pred eec
Q 022938 174 EKD 176 (289)
Q Consensus 174 ~k~ 176 (289)
+|.
T Consensus 689 ~k~ 691 (693)
T PRK11824 689 RKA 691 (693)
T ss_pred EEe
Confidence 986
No 118
>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=98.80 E-value=2.1e-08 Score=73.93 Aligned_cols=68 Identities=22% Similarity=0.245 Sum_probs=61.0
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
++|+++.| .+.+++|+++ . ...|++|.++++.....++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~--~---~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDIL--S---RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeC--C---CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 68888888 8999999996 3 399999999999887888889999999999999999986 8999999873
No 119
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.79 E-value=2.9e-08 Score=84.89 Aligned_cols=104 Identities=20% Similarity=0.209 Sum_probs=77.3
Q ss_pred cccCCCeEEEEEEEE---eCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEE
Q 022938 41 IERICQRNLCPVGKF---STNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLV 117 (289)
Q Consensus 41 ~~~vG~~v~~~Vl~~---d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V 117 (289)
.|..+..+.+.+... |.++.++++. +|.......+.|+++.|+|+++.++|++|
T Consensus 26 ty~~~~~i~as~~G~~~id~~~~~Isv~-----------------------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V 82 (189)
T PRK09521 26 TYEDNGEVYASVVGKVFIDDINRKISVI-----------------------PFKKTPPLLKKGDIVYGRVVDVKEQRALV 82 (189)
T ss_pred EEeeCCEEEEEeeEEEEEcCCCCEEEEe-----------------------cCcCCCCCCCCCCEEEEEEEEEcCCeEEE
Confidence 455666777766654 4555566553 12221223579999999999999999999
Q ss_pred EEC-----------CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc
Q 022938 118 RFF-----------SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA 177 (289)
Q Consensus 118 ~l~-----------gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~ 177 (289)
+++ +..|++|.+++++.+. .++.+.|+ +||.|.|+|++++ +++.||.+..
T Consensus 83 ~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~-~~~~~~~~------~GD~V~akV~~i~---~~i~LS~k~~ 143 (189)
T PRK09521 83 RIVSIEGSERELATSKLAYIHISQVSDGYV-ESLTDAFK------IGDIVRAKVISYT---DPLQLSTKGK 143 (189)
T ss_pred EEEEecccccccCCCceeeEEhhHcChhhh-hhHHhccC------CCCEEEEEEEecC---CcEEEEEecC
Confidence 985 5789999999988664 44555555 9999999999997 7899999863
No 120
>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=98.78 E-value=4.2e-08 Score=71.57 Aligned_cols=62 Identities=34% Similarity=0.542 Sum_probs=54.2
Q ss_pred cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.+.+++.|+.+.| +++|+||++. ++ ..|++|.+++. +.+++||.++++|.++ .+++++.+|
T Consensus 10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~--~~---~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~ 75 (77)
T cd04473 10 TMEDLEVGKLYKGKVNGVAKYGVFVDLN--DH---VRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLI 75 (77)
T ss_pred chhhCCCCCEEEEEEEeEecceEEEEEC--CC---cEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEE
Confidence 4556889999999 9999999996 44 99999999864 5699999999999999 789999998
Q ss_pred E
Q 022938 257 I 257 (289)
Q Consensus 257 l 257 (289)
+
T Consensus 76 ~ 76 (77)
T cd04473 76 P 76 (77)
T ss_pred E
Confidence 5
No 121
>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=98.77 E-value=1.9e-08 Score=100.42 Aligned_cols=69 Identities=19% Similarity=0.295 Sum_probs=61.2
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCC---C-CccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMS---P-SHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels---~-~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
.+.|++++|+|+++.++|+||++. |++||+|+||++ | .+. .+|.+.++ +||.|+|+|+++|. ++|+.
T Consensus 645 ~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv-~~~~dv~k------vGd~V~VKVl~ID~-~gKI~ 716 (719)
T TIGR02696 645 PEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRV-ENVEDVLS------VGQKIQVEIADIDD-RGKLS 716 (719)
T ss_pred CCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCc-CCHHHcCC------CCCEEEEEEEEECC-CCCee
Confidence 579999999999999999999998 999999999996 3 444 77888776 99999999999994 77888
Q ss_pred EE
Q 022938 172 FS 173 (289)
Q Consensus 172 lS 173 (289)
|+
T Consensus 717 L~ 718 (719)
T TIGR02696 717 LV 718 (719)
T ss_pred ec
Confidence 76
No 122
>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=98.72 E-value=3.6e-08 Score=70.45 Aligned_cols=58 Identities=22% Similarity=0.298 Sum_probs=50.0
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKS 251 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~~~~~~iGd~V~vkV~~id~e~~ 251 (289)
|+++.| .++|+||++. +| ++|++|.+++++.+ ..++.+.|++||.|+|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~--~~---i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA--DN---VHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC--CC---cEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 566777 8899999995 55 99999999999884 77888899999999999999998543
No 123
>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=98.69 E-value=6.4e-08 Score=66.92 Aligned_cols=57 Identities=47% Similarity=0.857 Sum_probs=51.7
Q ss_pred eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.++|+||+++ +| ..|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
T Consensus 9 ~~~g~~v~l~--~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 9 TKFGVFVELE--DG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred EeeeEEEEec--CC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 7899999996 44 999999999998877788889999999999999999999998875
No 124
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.67 E-value=2.8e-08 Score=95.68 Aligned_cols=160 Identities=13% Similarity=0.137 Sum_probs=111.0
Q ss_pred EeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEE
Q 022938 27 SLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGK 106 (289)
Q Consensus 27 ~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~ 106 (289)
+-.+++++.....+.|.....+.+. +|+++|.+.+-....+++.
T Consensus 24 ~~~le~al~~a~~k~~~~~~~~~v~---id~~~g~~~~~~~~~vV~~--------------------------------- 67 (470)
T PRK09202 24 IEALEEALATAYKKKYGPEANIRVE---IDRKTGDIEVFRRWEVVEE--------------------------------- 67 (470)
T ss_pred HHHHHHHHHHHHHhhcCCcccEEEE---EeCCCCeEEEEEEEEEecc---------------------------------
Confidence 3445666666666777555555554 4888887777654333211
Q ss_pred EEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee-c--------c
Q 022938 107 IQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK-D--------A 177 (289)
Q Consensus 107 V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k-~--------~ 177 (289)
+..-.+.+|.++... .+| ...+|+.+.+.|...+ .+|+.++.. + .
T Consensus 68 ------------v~~~~~eI~L~eAk~----~~~--------~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ 121 (470)
T PRK09202 68 ------------VEDPTKEISLEEARK----IDP--------DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREA 121 (470)
T ss_pred ------------ccCCcceeeHHHHhh----hCc--------cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHH
Confidence 112235666666532 122 2349999999998775 444443322 2 2
Q ss_pred hhhhcccccc--cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC
Q 022938 178 VWNKYSSRVN--VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK 250 (289)
Q Consensus 178 ~~~~~~~~~~--~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~ 250 (289)
.++..++.++ .|+++.| .++|+||+++ | +.|++|.++++ |.+.|++||.|+|+|+++++++
T Consensus 122 ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg---g---vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~ 189 (470)
T PRK09202 122 ERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG---R---AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEA 189 (470)
T ss_pred HHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC---C---eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCC
Confidence 3446678887 9999999 8899999994 4 99999999985 6688999999999999999987
Q ss_pred C--eEEEEEecC
Q 022938 251 S--RITLSIKQL 260 (289)
Q Consensus 251 ~--ri~lSlK~~ 260 (289)
+ .|.||.+..
T Consensus 190 kg~qIilSRt~p 201 (470)
T PRK09202 190 RGPQIILSRTHP 201 (470)
T ss_pred CCCeEEEEeCcH
Confidence 7 899998763
No 125
>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=98.65 E-value=1.6e-07 Score=71.88 Aligned_cols=69 Identities=29% Similarity=0.501 Sum_probs=58.6
Q ss_pred eeeeEEEEEecCCCceeEEEEEEccCcCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 022938 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIK 258 (289)
Q Consensus 195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~-----------~~~~~~iGd~V~vkV~~id~e~-----~ri~lSlK 258 (289)
.++|+||++. + +.|++|.+++++++... ....|++||.|+|+|.++|.+. .++.||+|
T Consensus 11 ~~~GifV~l~---~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k 84 (99)
T cd04460 11 VDFGAFVRIG---P---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMR 84 (99)
T ss_pred EeccEEEEEc---C---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEe
Confidence 8999999994 3 89999999998776543 3477999999999999999864 58999999
Q ss_pred cCCCCchhHHh
Q 022938 259 QLEEDPLLETL 269 (289)
Q Consensus 259 ~~~~~p~~~~~ 269 (289)
+....||+-+.
T Consensus 85 ~~~~g~~~~~~ 95 (99)
T cd04460 85 QPGLGKLEWIE 95 (99)
T ss_pred cCCCCcHHHhh
Confidence 99888887654
No 126
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.65 E-value=6.6e-08 Score=94.82 Aligned_cols=92 Identities=37% Similarity=0.658 Sum_probs=77.2
Q ss_pred EecCCcEEEEEeecc--------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938 163 ANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 229 (289)
Q Consensus 163 vd~~~~ri~lS~k~~--------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~ 229 (289)
++ +.+.+.++-... .......++++|+++.| .+||+||.+. +| -.|+||+|++++.++...
T Consensus 587 ie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~--~g---kdgl~hiS~~~~~rv~kv 660 (692)
T COG1185 587 IE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL--PG---KDGLVHISQLAKERVEKV 660 (692)
T ss_pred ec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec--CC---cceeEEehhhhhhhhhcc
Confidence 44 556666655432 23345688999999999 8999999995 65 899999999999999999
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
.+.++.||.|.||+..+|+ ++|+.||+|..+
T Consensus 661 ~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~ 691 (692)
T COG1185 661 EDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL 691 (692)
T ss_pred cceeecCceEEEEEeeecc-cCCccceehhcc
Confidence 9999999999999999997 899999999764
No 127
>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=98.64 E-value=1.7e-07 Score=71.63 Aligned_cols=71 Identities=15% Similarity=0.311 Sum_probs=58.5
Q ss_pred CEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCc----------ccchhcccccCCCCEEEEEEEEEecCC---
Q 022938 101 FIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEP----------QKSIHEIAKGLTGSIISVKVIQANEEM--- 167 (289)
Q Consensus 101 ~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p----------~~~~~~~~~~~vG~~V~vkVl~vd~~~--- 167 (289)
+++.|+|+++.++|+||+++++.|++|.+++++.+...++ ...+ .+||.++|+|.++|.+.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~------~~Gd~v~vkI~~vd~~~~~~ 74 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVL------KVGDVVRARIVAVSLKERRP 74 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEE------CCCCEEEEEEEEEeHHHCcC
Confidence 4789999999999999999999999999999876542221 2333 49999999999999764
Q ss_pred --cEEEEEeecc
Q 022938 168 --KKLVFSEKDA 177 (289)
Q Consensus 168 --~ri~lS~k~~ 177 (289)
.++.||++..
T Consensus 75 ~~~~i~ls~k~~ 86 (99)
T cd04460 75 RESKIGLTMRQP 86 (99)
T ss_pred CCceEEEEEecC
Confidence 5899999975
No 128
>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=98.59 E-value=1.4e-07 Score=95.17 Aligned_cols=68 Identities=43% Similarity=0.815 Sum_probs=61.1
Q ss_pred cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938 182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255 (289)
Q Consensus 182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l 255 (289)
.....++|+++.| .++|+||++. +| ..||+|+|++++.++.++.+.|++||.|+|+|+++|+ ++++.|
T Consensus 612 ~~~~~~~G~i~~G~V~~I~~~GafVei~--~g---~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 612 ITAEPEVGKIYEGKVVRIMDFGAFVEIL--PG---KDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred hhcccccCcEEEEEEEEEeCCEEEEEEC--CC---cEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 3456799999999 9999999995 55 9999999999999999999999999999999999997 777754
No 129
>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=98.53 E-value=2.3e-07 Score=93.70 Aligned_cols=70 Identities=21% Similarity=0.384 Sum_probs=62.0
Q ss_pred HHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938 94 RAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 94 ~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
....+.|+++.|+|+++.++|+||++. |.+||+|.+++++.+. .++.+.++ +||.|+|+|+++|. ++++.
T Consensus 613 ~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v-~~~~~~~k------vGD~V~VkVi~id~-~gki~ 683 (684)
T TIGR03591 613 TAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERV-EKVEDVLK------EGDEVKVKVLEIDK-QGRIK 683 (684)
T ss_pred hcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcc-cChhhccC------CCCEEEEEEEEECC-CCCcc
Confidence 344689999999999999999999998 8999999999999886 77887776 99999999999996 56654
No 130
>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=98.49 E-value=7.3e-07 Score=75.60 Aligned_cols=80 Identities=18% Similarity=0.234 Sum_probs=62.4
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccch----hcccccCCCCEEEEEEEEEe-----cCCc
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSI----HEIAKGLTGSIISVKVIQAN-----EEMK 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~----~~~~~~~vG~~V~vkVl~vd-----~~~~ 168 (289)
..|++++|+|++++++|+||+++.++|++|.+++.+.+..-++.+.. .....+.+|+.|+++|.+++ ++..
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 159 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGS 159 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcc
Confidence 58999999999999999999998899999999998655322222100 00123459999999999998 5567
Q ss_pred EEEEEeecc
Q 022938 169 KLVFSEKDA 177 (289)
Q Consensus 169 ri~lS~k~~ 177 (289)
++.+|+|++
T Consensus 160 ~I~lt~k~~ 168 (179)
T TIGR00448 160 KIGLTMRQP 168 (179)
T ss_pred eEEEEeccC
Confidence 999999985
No 131
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.46 E-value=7.9e-07 Score=87.39 Aligned_cols=78 Identities=22% Similarity=0.353 Sum_probs=68.9
Q ss_pred HHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcE
Q 022938 91 KAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKK 169 (289)
Q Consensus 91 ~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~r 169 (289)
+.+....++|+++.|+|+++.++|+||.+. |-+|++|.+++++.++ ...++.++ +||.+.|++..+| ..+|
T Consensus 611 ~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv-~kv~dvlk------~Gd~v~Vkv~~iD-~~Gr 682 (692)
T COG1185 611 EAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERV-EKVEDVLK------EGDEVKVKVIEID-KQGR 682 (692)
T ss_pred HHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhh-hcccceee------cCceEEEEEeeec-ccCC
Confidence 345566799999999999999999999998 9999999999999876 66667766 9999999999999 5789
Q ss_pred EEEEeec
Q 022938 170 LVFSEKD 176 (289)
Q Consensus 170 i~lS~k~ 176 (289)
+.+|++.
T Consensus 683 i~ls~~~ 689 (692)
T COG1185 683 IRLSIKA 689 (692)
T ss_pred ccceehh
Confidence 9999875
No 132
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.39 E-value=7.6e-07 Score=78.70 Aligned_cols=70 Identities=27% Similarity=0.364 Sum_probs=60.9
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRITL 255 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----~~~~~~~~iGd~V~vkV~~id~e~~ri~l 255 (289)
..++||+|.| .++|+||+|+ .+ ..|++|.+++++.+. .++.+.|++||.|.|+|++++++ +.+.|
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~--~~---~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~L 133 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDIN--SP---YKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVL 133 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeC--CC---ceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEE
Confidence 3488999999 8999999996 33 899999999999876 78888999999999999999974 46999
Q ss_pred EEecC
Q 022938 256 SIKQL 260 (289)
Q Consensus 256 SlK~~ 260 (289)
|+|+.
T Consensus 134 S~k~~ 138 (235)
T PRK04163 134 TLKGK 138 (235)
T ss_pred EEcCC
Confidence 99874
No 133
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.29 E-value=3.2e-06 Score=70.75 Aligned_cols=80 Identities=16% Similarity=0.162 Sum_probs=61.8
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcc--cchhcc--cccCCCCEEEEEEEEEecCC-----c
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQ--KSIHEI--AKGLTGSIISVKVIQANEEM-----K 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~--~~~~~~--~~~~vG~~V~vkVl~vd~~~-----~ 168 (289)
..|+++.|.|+++.++|+||.++-.+||+|.+++.+.+...++. ....+. ..+.+|+.|++||..+.... .
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~ 159 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRES 159 (183)
T ss_pred ccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccc
Confidence 57999999999999999999999999999999999874422221 111110 12349999999999887655 4
Q ss_pred EEEEEeecc
Q 022938 169 KLVFSEKDA 177 (289)
Q Consensus 169 ri~lS~k~~ 177 (289)
++.++++++
T Consensus 160 ~I~lTmrq~ 168 (183)
T COG1095 160 KIGLTMRQP 168 (183)
T ss_pred eEEEEeccc
Confidence 788999985
No 134
>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=98.28 E-value=5.2e-06 Score=84.56 Aligned_cols=79 Identities=20% Similarity=0.286 Sum_probs=60.6
Q ss_pred hhcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCccc-ch-hc--ccccCCCCEEEEEEEEEecCCcE
Q 022938 96 YKESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQK-SI-HE--IAKGLTGSIISVKVIQANEEMKK 169 (289)
Q Consensus 96 ~~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~-~~-~~--~~~~~vG~~V~vkVl~vd~~~~r 169 (289)
..+.|++++|+|++++++|+||++. |++|++|.+++++.+..-+... .+ .+ ...+.+||.|+|+|.++|..+++
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 3478999999999999999999997 6999999999986543111110 00 00 01245999999999999999999
Q ss_pred EEEEe
Q 022938 170 LVFSE 174 (289)
Q Consensus 170 i~lS~ 174 (289)
+.+++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99875
No 135
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.28 E-value=3.3e-06 Score=74.65 Aligned_cols=73 Identities=19% Similarity=0.278 Sum_probs=61.5
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
+.|+++.|+|+++.++|++|+++ +..|++|.+++++.+. ..++.+.|+ +||.|.|+|++++++ +.+.||
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~------~GDlV~akV~~i~~~-~~~~LS 134 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLD------IGDYIIAKVKDVDRT-RDVVLT 134 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCC------CCCEEEEEEEEECCC-CcEEEE
Confidence 79999999999999999999999 8999999999998653 134444454 999999999999854 458999
Q ss_pred eecc
Q 022938 174 EKDA 177 (289)
Q Consensus 174 ~k~~ 177 (289)
.+..
T Consensus 135 ~k~~ 138 (235)
T PRK04163 135 LKGK 138 (235)
T ss_pred EcCC
Confidence 8764
No 136
>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=98.27 E-value=3.5e-06 Score=59.63 Aligned_cols=58 Identities=17% Similarity=0.302 Sum_probs=47.6
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEE
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLS 256 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~--~ri~lS 256 (289)
..|++++| .++|+||+++ + ++|++|.++++. .+.|++||.|++.|.+++.++ ..|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig---~---~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG---K---VEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC---C---eEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 46888888 7899999994 3 899999999863 356899999999999999654 457776
No 137
>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=98.25 E-value=5.2e-06 Score=70.40 Aligned_cols=73 Identities=34% Similarity=0.626 Sum_probs=58.7
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEe---
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID--- 247 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id--- 247 (289)
.+|+++.| +++|+||+++ + +.|++|.+++.+++.. +....+++||.|+++|.++|
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg--~----~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLG--P----FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeC--C----ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccC
Confidence 46888888 9999999995 2 8999999998865431 23467999999999999998
Q ss_pred --CCCCeEEEEEecCCCCch
Q 022938 248 --REKSRITLSIKQLEEDPL 265 (289)
Q Consensus 248 --~e~~ri~lSlK~~~~~p~ 265 (289)
++..+|.+|+|+----|+
T Consensus 154 ~~~~~~~I~lt~k~~~LG~~ 173 (179)
T TIGR00448 154 RRPEGSKIGLTMRQPLLGKL 173 (179)
T ss_pred CCCCcceEEEEeccCcCCcc
Confidence 678899999998544443
No 138
>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=98.24 E-value=8.2e-06 Score=82.31 Aligned_cols=78 Identities=18% Similarity=0.302 Sum_probs=60.8
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccc-h-hc--ccccCCCCEEEEEEEEEecCCcEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKS-I-HE--IAKGLTGSIISVKVIQANEEMKKL 170 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~-~-~~--~~~~~vG~~V~vkVl~vd~~~~ri 170 (289)
-+.|++++|+|++++++|+||++. +++|++|.+++.+.+..-++... + .+ ...+.+||+|+|+|.++|.++++|
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 378999999999999999999997 79999999999876431222110 0 00 023459999999999999999999
Q ss_pred EEEe
Q 022938 171 VFSE 174 (289)
Q Consensus 171 ~lS~ 174 (289)
.+++
T Consensus 650 ~f~l 653 (654)
T TIGR00358 650 IFEL 653 (654)
T ss_pred EEEE
Confidence 8875
No 139
>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=98.22 E-value=4.1e-06 Score=85.29 Aligned_cols=70 Identities=27% Similarity=0.562 Sum_probs=58.7
Q ss_pred ccccccccEEEe-----eeeeEEEEEecCC-CceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEE
Q 022938 183 SSRVNVEDIFVG-----RDYGAFIHLRFPD-GLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIK 245 (289)
Q Consensus 183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~-G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~ 245 (289)
+..-++|+++.| +++|+||++. + | ++|++|++++++++. .+....|++||.|+|+|.+
T Consensus 622 yl~~~iG~~~~g~V~~v~~fGifV~L~--~~~---~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~ 696 (709)
T TIGR02063 622 YMSEKIGEEFEGVISGVTSFGLFVELE--NNT---IEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVK 696 (709)
T ss_pred hhhccCCcEEEEEEEEEEeCCEEEEec--CCc---eEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEE
Confidence 334578999999 8999999995 3 4 999999999986543 2344679999999999999
Q ss_pred EeCCCCeEEEEE
Q 022938 246 IDREKSRITLSI 257 (289)
Q Consensus 246 id~e~~ri~lSl 257 (289)
+|.++++|.+++
T Consensus 697 vd~~~~~I~~~l 708 (709)
T TIGR02063 697 ADLDTGKIDFEL 708 (709)
T ss_pred EecccCeEEEEE
Confidence 999999999986
No 140
>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=98.22 E-value=6.4e-06 Score=58.75 Aligned_cols=69 Identities=19% Similarity=0.301 Sum_probs=56.4
Q ss_pred CCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEE-EEEEEEEecCCcEEEEEee
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSII-SVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V-~vkVl~vd~~~~ri~lS~k 175 (289)
|++++|+|..-++.+++|++. |+.|++|..++++ ...+++. .+ .+.++||++ ++.|+ +...+.+.+|.|
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-HVSNCPL-LW---HCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHH-HH---hhhhcCCCccceEEE--eccccEEEEecC
Confidence 689999999999999999998 7999999999999 5434432 22 245699999 99998 777888888865
No 141
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.20 E-value=1.2e-06 Score=83.88 Aligned_cols=81 Identities=28% Similarity=0.443 Sum_probs=70.6
Q ss_pred ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
..++..|-+++| .++|+||++- +| ..||+|.++|+..++.+|++.+.+||.|.++.+..|+ .+.+.+|.
T Consensus 663 ~~~l~~g~vy~~tIt~~rd~G~~V~l~--p~---~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ 736 (760)
T KOG1067|consen 663 VQDLEFGGVYTATITEIRDTGVMVELY--PM---QQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSS 736 (760)
T ss_pred ccceEeeeEEEEEEeeecccceEEEec--CC---chhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehh
Confidence 346777777777 8999999995 55 9999999999999999999999999999999999998 67788888
Q ss_pred ecCCCCchhHHh
Q 022938 258 KQLEEDPLLETL 269 (289)
Q Consensus 258 K~~~~~p~~~~~ 269 (289)
|.+.++|-...-
T Consensus 737 ralLp~p~~~~~ 748 (760)
T KOG1067|consen 737 RALLPDPATKES 748 (760)
T ss_pred hhhcCCcccCCc
Confidence 888999976543
No 142
>PRK11642 exoribonuclease R; Provisional
Probab=98.19 E-value=7.3e-06 Score=84.23 Aligned_cols=79 Identities=22% Similarity=0.277 Sum_probs=61.6
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcc--cchhc--ccccCCCCEEEEEEEEEecCCcEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQ--KSIHE--IAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~--~~~~~--~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
+.|++++|+|++++++|+||++. +++|++|.+++++.++.-+.. ....+ ...+.+||.|+|+|.++|.+.++|.
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 68999999999999999999997 499999999998764312211 00000 0124599999999999999999999
Q ss_pred EEeec
Q 022938 172 FSEKD 176 (289)
Q Consensus 172 lS~k~ 176 (289)
+++..
T Consensus 722 f~l~~ 726 (813)
T PRK11642 722 FSLIS 726 (813)
T ss_pred EEEec
Confidence 99854
No 143
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.14 E-value=7.5e-06 Score=68.55 Aligned_cols=76 Identities=30% Similarity=0.566 Sum_probs=56.5
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----------cC-cccccCCCCEEEEEEEEEeCCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK 250 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----------~~-~~~~~~iGd~V~vkV~~id~e~ 250 (289)
..|+++.| .++|+||.++ + .+||+|.+++.++++ -. -...+++||.|++||+.+....
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~ig--p----~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIG--P----LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred ccccEEEEEEEEEeecceEEEec--c----ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEeccc
Confidence 34555555 9999999997 4 899999999988732 11 2336999999999999987544
Q ss_pred -----CeEEEEEecC--CCCchhHH
Q 022938 251 -----SRITLSIKQL--EEDPLLET 268 (289)
Q Consensus 251 -----~ri~lSlK~~--~~~p~~~~ 268 (289)
-+|.++||+. -.-+|-+.
T Consensus 154 ~~~~~~~I~lTmrq~~LGklew~~~ 178 (183)
T COG1095 154 RRPRESKIGLTMRQPGLGKLEWIEE 178 (183)
T ss_pred CccccceEEEEeccccCCcchhhhh
Confidence 6789999984 34455543
No 144
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.14 E-value=1.6e-05 Score=67.79 Aligned_cols=80 Identities=15% Similarity=0.228 Sum_probs=60.4
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc-ch-h--cccccCCCCEEEEEEEEEecCC-----c
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK-SI-H--EIAKGLTGSIISVKVIQANEEM-----K 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~-~~-~--~~~~~~vG~~V~vkVl~vd~~~-----~ 168 (289)
..|+++.|+|++++++|++|+++.++|+++.+++.+.+..-++.+ .+ . ....+.+|+.|+|+|.+++.+. .
T Consensus 80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~ 159 (187)
T PRK08563 80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS 159 (187)
T ss_pred cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence 589999999999999999999999999999999976543111110 00 0 0012349999999999998754 3
Q ss_pred EEEEEeecc
Q 022938 169 KLVFSEKDA 177 (289)
Q Consensus 169 ri~lS~k~~ 177 (289)
++.+|++.+
T Consensus 160 ~I~ls~~~~ 168 (187)
T PRK08563 160 KIGLTMRQP 168 (187)
T ss_pred EEEEEecCC
Confidence 788899975
No 145
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.11 E-value=6.9e-06 Score=59.72 Aligned_cols=67 Identities=25% Similarity=0.399 Sum_probs=59.9
Q ss_pred cccccEEEe----eeeeEEEEEecCCCceeEEEEEE-ccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 186 VNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 186 ~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~-~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
-++|+++.| .+.|+||.+- .|+++|++. .++++..++.++.+.+ +|-+..|+|+.+|++++-|.||.
T Consensus 14 P~v~dvv~~Vv~i~d~~~YV~Ll----eY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 14 PNINEVTKGIVFVKDNIFYVKLI----DYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCCeEEEEEEEEeccEEEEEEe----cCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 367888878 8999999995 256999998 8999999999999989 99999999999999999999984
No 146
>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=98.10 E-value=8.3e-06 Score=61.56 Aligned_cols=48 Identities=23% Similarity=0.335 Sum_probs=41.0
Q ss_pred EEEEEEccCcCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 212 LTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 212 i~Glv~~sels~~~~~--~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
..|++|.+++...+.. ++.+.|++||.|+|+|++++. ...+.||++.-
T Consensus 38 ~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~Lst~~~ 87 (92)
T cd05791 38 FRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYLSTAEN 87 (92)
T ss_pred cccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEEEecCC
Confidence 7899999998877665 688999999999999999985 46799998763
No 147
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.07 E-value=6e-05 Score=64.27 Aligned_cols=79 Identities=25% Similarity=0.544 Sum_probs=61.0
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeC
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~ 248 (289)
.-.+|+++.| .++|+||+++ + +.|++|.+++.+++.. +....+++||.|+++|.+++.
T Consensus 78 ~P~~GEVv~g~V~~v~~~Gi~V~lg--~----~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~ 151 (187)
T PRK08563 78 KPELQEVVEGEVVEVVEFGAFVRIG--P----VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSL 151 (187)
T ss_pred eccCCCEEEEEEEEEEccEEEEEEe--C----ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEc
Confidence 3457999999 8999999996 2 8999999999866432 345679999999999999997
Q ss_pred CC-----CeEEEEEecCC---CCchhHHh
Q 022938 249 EK-----SRITLSIKQLE---EDPLLETL 269 (289)
Q Consensus 249 e~-----~ri~lSlK~~~---~~p~~~~~ 269 (289)
+. .+|.+|+|+-- -+.|.+..
T Consensus 152 ~~~~~~~~~I~ls~~~~~LG~~~w~~~~~ 180 (187)
T PRK08563 152 KERRPRGSKIGLTMRQPGLGKLEWIEEEK 180 (187)
T ss_pred ccCCCCCCEEEEEecCCCCCcHHHHHHHH
Confidence 54 38999999842 34455433
No 148
>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=98.01 E-value=5.7e-05 Score=56.49 Aligned_cols=69 Identities=13% Similarity=0.175 Sum_probs=53.2
Q ss_pred CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc---chh--cccccCCCCEEEEEEEEEecCCc
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK---SIH--EIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~---~~~--~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
.|+++.|+|+++++.|+||.+|.+++|++..++.+... .+|.+ .+. .......|+.|++||..+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~-~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDME-FDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccce-ECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 48999999999999999999999999999999976654 34421 121 12345689999999998876544
No 149
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=97.98 E-value=0.00012 Score=64.76 Aligned_cols=121 Identities=14% Similarity=0.126 Sum_probs=83.4
Q ss_pred eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938 26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG 105 (289)
Q Consensus 26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g 105 (289)
+++++++.+-..+ -=.++||.+-|.+. +|.. +|+..+++.. ..++.+. ....+. -.++.++|
T Consensus 100 l~vp~~elp~~~~-~wpq~Gd~l~v~l~-~Dkk-~Ri~g~~a~~------~~l~~l~----~~~~~~-----l~nq~v~~ 161 (287)
T COG2996 100 LLVPLDELPTLKS-LWPQKGDKLLVYLY-VDKK-GRIWGTLAIE------KILENLA----TPAYNN-----LKNQEVDA 161 (287)
T ss_pred eeeehhhcccccc-cCCCCCCEEEEEEE-EccC-CcEEEEecch------hHHHhcC----Cccchh-----hhcCeeee
Confidence 3455555543211 12689999999873 4544 6999987622 0111100 001111 14899999
Q ss_pred EEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecchhh
Q 022938 106 KIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN 180 (289)
Q Consensus 106 ~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~~~~ 180 (289)
+|-+....|.||-.. +..||||.||.-..+ +.|+++.++|+.+.. .+++.||++....+
T Consensus 162 tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p---------------rlG~~l~~rVi~~re-Dg~lnLSl~p~~~E 221 (287)
T COG2996 162 TVYRLLESGTFVITENGYLGFIHKSERFAEP---------------RLGERLTARVIGVRE-DGKLNLSLRPRAHE 221 (287)
T ss_pred EEEEEeccceEEEEcCCeEEEEcchhhcccc---------------cCCceEEEEEEEEcc-CCeeecccccccHH
Confidence 999999999999999 899999999864332 399999999999985 89999999875443
No 150
>PRK11642 exoribonuclease R; Provisional
Probab=97.96 E-value=2.9e-05 Score=79.91 Aligned_cols=70 Identities=30% Similarity=0.532 Sum_probs=58.8
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeCCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK 250 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~e~ 250 (289)
++|+++.| +++|+||+|. ++ .++|+||.+++.+++.. +....|++||.|+|+|.++|.++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~--~~--~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~ 717 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLD--DL--FIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE 717 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEEC--CC--CeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence 78999999 9999999995 32 49999999999876321 23467999999999999999999
Q ss_pred CeEEEEEecC
Q 022938 251 SRITLSIKQL 260 (289)
Q Consensus 251 ~ri~lSlK~~ 260 (289)
++|.+++-..
T Consensus 718 rkI~f~l~~~ 727 (813)
T PRK11642 718 RKIDFSLISS 727 (813)
T ss_pred CeEEEEEecc
Confidence 9999998543
No 151
>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=97.91 E-value=3.5e-05 Score=77.80 Aligned_cols=69 Identities=26% Similarity=0.482 Sum_probs=57.3
Q ss_pred ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEEeC
Q 022938 185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~id~ 248 (289)
+-++|+++.| +++|+||++.. . +++|++|.+++.+++. ++....|++||.|+|+|.++|+
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~-~---~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~ 644 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDD-N---GIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNM 644 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecC-C---ceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEec
Confidence 3367999888 99999999951 3 4999999999987641 2234679999999999999999
Q ss_pred CCCeEEEEE
Q 022938 249 EKSRITLSI 257 (289)
Q Consensus 249 e~~ri~lSl 257 (289)
++++|.+++
T Consensus 645 ~~~~I~f~l 653 (654)
T TIGR00358 645 ETRSIIFEL 653 (654)
T ss_pred ccCeEEEEE
Confidence 999999985
No 152
>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=97.89 E-value=5.3e-05 Score=57.12 Aligned_cols=72 Identities=19% Similarity=0.233 Sum_probs=57.9
Q ss_pred cCCCEEEEEEEEEEcCcEEEEE--------C-CEEEEeecCCCCCCccCc--CcccchhcccccCCCCEEEEEEEEEecC
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRF--------F-SLVGFLPFPQMSPSHSCK--EPQKSIHEIAKGLTGSIISVKVIQANEE 166 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l--------~-gv~g~ip~sels~~~~~~--~p~~~~~~~~~~~vG~~V~vkVl~vd~~ 166 (289)
+.|+++.|+|+++....+.|++ . ...|++|.+++...+. . +..+.| .+||.|+++|.+++.
T Consensus 5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~-d~~~~~~~f------~~GDiV~AkVis~~~- 76 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEK-DKVEMYKCF------RPGDIVRAKVISLGD- 76 (92)
T ss_pred CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcccccc-chHHHHhhc------CCCCEEEEEEEEcCC-
Confidence 6899999999999999999999 6 6899999999876553 2 233334 499999999999974
Q ss_pred CcEEEEEeecc
Q 022938 167 MKKLVFSEKDA 177 (289)
Q Consensus 167 ~~ri~lS~k~~ 177 (289)
.+.+.||.+..
T Consensus 77 ~~~~~Lst~~~ 87 (92)
T cd05791 77 ASSYYLSTAEN 87 (92)
T ss_pred CCCcEEEecCC
Confidence 35688887754
No 153
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.87 E-value=1.2e-05 Score=75.24 Aligned_cols=96 Identities=17% Similarity=0.242 Sum_probs=68.9
Q ss_pred cCCCCEEEEEEEEEecCCcEEEEEe-------ecchhhhccccc--ccccEEEe-----eeeeEEEEEecCCCceeEEEE
Q 022938 150 GLTGSIISVKVIQANEEMKKLVFSE-------KDAVWNKYSSRV--NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGL 215 (289)
Q Consensus 150 ~~vG~~V~vkVl~vd~~~~ri~lS~-------k~~~~~~~~~~~--~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Gl 215 (289)
..+|+.+.+.+...+..+..+..+. ++...+..++++ +.|+++.| .+.|+||+++ | +.|+
T Consensus 87 ~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg---~---vEa~ 160 (362)
T PRK12327 87 YELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG---K---IEAV 160 (362)
T ss_pred ccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC---C---eEEE
Confidence 3489999998865442221111111 112345667788 99999999 7789999994 3 9999
Q ss_pred EEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCe--EEEEE
Q 022938 216 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR--ITLSI 257 (289)
Q Consensus 216 v~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~r--i~lSl 257 (289)
+|.+++. +.+.|++||.++|.|.+++.+++. |.||.
T Consensus 161 LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSR 198 (362)
T PRK12327 161 LPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSR 198 (362)
T ss_pred ecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence 9988774 357799999999999999976654 55554
No 154
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.84 E-value=2e-05 Score=75.78 Aligned_cols=74 Identities=22% Similarity=0.307 Sum_probs=64.2
Q ss_pred hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938 96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174 (289)
Q Consensus 96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~ 174 (289)
.+..|-+++|+|+++.++|+||++. +..|++|.+|++..++ ..|++.+. +||.+.++..+.|+..+...+|+
T Consensus 665 ~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~i-akpsd~le------vGq~I~vk~ie~d~~g~~~ls~r 737 (760)
T KOG1067|consen 665 DLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKI-AKPSDLLE------VGQEIQVKYIERDPRGGIMLSSR 737 (760)
T ss_pred ceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccc-cChHHHHh------hcceeEEEEEeecCccceeehhh
Confidence 3567889999999999999999999 8999999999999987 88988876 99999999999997666555555
Q ss_pred ec
Q 022938 175 KD 176 (289)
Q Consensus 175 k~ 176 (289)
+-
T Consensus 738 al 739 (760)
T KOG1067|consen 738 AL 739 (760)
T ss_pred hh
Confidence 43
No 155
>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=97.77 E-value=3.2e-05 Score=71.83 Aligned_cols=98 Identities=16% Similarity=0.263 Sum_probs=71.4
Q ss_pred ccCCCCEEEEEEEEEecCCcEEEEEe-ec--------chhhhccccc--ccccEEEe-----eeee-EEEEEecCCCcee
Q 022938 149 KGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVG-----RDYG-AFIHLRFPDGLYH 211 (289)
Q Consensus 149 ~~~vG~~V~vkVl~vd~~~~ri~lS~-k~--------~~~~~~~~~~--~~G~iv~G-----~~~G-~fV~i~~~~G~~~ 211 (289)
++.+|+.+.+.+...+ .+|+.++. |+ ..++..++++ +.|++++| .+.| +||+++ |
T Consensus 83 ~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG---~--- 154 (341)
T TIGR01953 83 DVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG---K--- 154 (341)
T ss_pred ccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC---C---
Confidence 3459999999885432 34433332 22 2455667777 59999999 5556 699994 3
Q ss_pred EEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEEecC
Q 022938 212 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSIKQL 260 (289)
Q Consensus 212 i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~--~ri~lSlK~~ 260 (289)
+.|++|.++.. +.+.|++||.++|.|.+++.+. ..|.||.+..
T Consensus 155 ~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 155 TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 99999999886 3466999999999999999543 5689998763
No 156
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.74 E-value=0.00018 Score=49.97 Aligned_cols=60 Identities=22% Similarity=0.144 Sum_probs=36.3
Q ss_pred CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
.|++.+.+|...++.|+|++.+ +-+.++|.+++.... .+|+.|.|.|. .| ..+|+.+|++
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~---------------~~Gd~v~VFvY-~D-~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPL---------------KVGDEVEVFVY-LD-KEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG---------------------TTSEEEEEEE-E--TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCC---------------CCCCEEEEEEE-EC-CCCCEEEecC
Confidence 3888899999999999999999 699999999975332 29999999996 56 3558888764
No 157
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.66 E-value=0.00033 Score=59.23 Aligned_cols=79 Identities=6% Similarity=0.062 Sum_probs=57.5
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc---ch-h--cccccCCCCEEEEEEEEEecCC--cE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK---SI-H--EIAKGLTGSIISVKVIQANEEM--KK 169 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~---~~-~--~~~~~~vG~~V~vkVl~vd~~~--~r 169 (289)
..|+++.|.|+++++.|+||.+|=.++|+|.++|.+... -++.+ .+ . .......|+.|++||..+..+. .+
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~-fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~ 158 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFV-YDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF 158 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccE-ECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence 589999999999999999999997889999999975432 22211 11 1 1233558999999998776443 35
Q ss_pred EEEEeecc
Q 022938 170 LVFSEKDA 177 (289)
Q Consensus 170 i~lS~k~~ 177 (289)
+.+|++.+
T Consensus 159 ~i~T~~~~ 166 (176)
T PTZ00162 159 AIATINSD 166 (176)
T ss_pred EEEEecCC
Confidence 66677764
No 158
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.61 E-value=4.1e-05 Score=67.15 Aligned_cols=89 Identities=26% Similarity=0.427 Sum_probs=75.8
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~ 261 (289)
.++++|-+ .+.|+||.+...+ ++.|++-.|+||..++.+++...++|-.=.|.|+.+|++++-|.||.+.+.
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCC
Confidence 45566655 7899999996444 599999999999999999999999999999999999999999999999998
Q ss_pred CCchhHHhhhhCCCChH
Q 022938 262 EDPLLETLEKVIPQGLE 278 (289)
Q Consensus 262 ~~p~~~~~~~~~~g~~~ 278 (289)
++--....+++-.--..
T Consensus 92 ~ed~~kC~Er~~ksK~v 108 (304)
T KOG2916|consen 92 PEDKEKCEERFAKSKLV 108 (304)
T ss_pred HHHHHHHHHHHHHhHHH
Confidence 88777777776554333
No 159
>PRK05054 exoribonuclease II; Provisional
Probab=97.53 E-value=0.00079 Score=67.93 Aligned_cols=77 Identities=18% Similarity=0.312 Sum_probs=57.5
Q ss_pred cCC--CEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCc--c--CcCcccch-hcccccCCCCEEEEEEEEEecCCc
Q 022938 98 ESG--FIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSH--S--CKEPQKSI-HEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 98 ~~G--~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~--~--~~~p~~~~-~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
..| +.++|.|++++++|+||++. |++|+||.+.+.+.+ . ..+..... .....+.+||+|+|+|.++|.+.+
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 455 59999999999999999997 799999999996531 1 01111111 001246799999999999999999
Q ss_pred EEEEEe
Q 022938 169 KLVFSE 174 (289)
Q Consensus 169 ri~lS~ 174 (289)
+|.++.
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 988764
No 160
>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=97.47 E-value=0.00033 Score=50.03 Aligned_cols=63 Identities=17% Similarity=0.256 Sum_probs=50.8
Q ss_pred ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccC---cccccCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 022938 189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD---IRDILNEGDEV-RVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~---~~~~~~iGd~V-~vkV~~id~e~~ri~lSlK 258 (289)
|++++| ++.+++|+++ +. ++.|+++..++++ +.++ .-..+++||++ .+.|+ ++..+.|.+|.|
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 GKLVDARVLKKTLNGLEVAIL--PE--EIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec--CC--CcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 567777 8889999997 42 4999999999998 5433 33558999999 99999 877888898875
No 161
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.46 E-value=0.00031 Score=51.24 Aligned_cols=69 Identities=14% Similarity=0.223 Sum_probs=56.9
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEee-cCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLP-FPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip-~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.++|+++. .|+.+.+.|++|.+- |++|.|+ .+|++..+. .... +..+|....|+|+.+|++++-|-||
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~ri-rsi~-------kllVGk~e~v~ViRVDk~KGYIDLs 84 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRA-EKLK-------KKLVGKTINVQVIRTDKLKGYIDVR 84 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHH-Hhhh-------hhhcCCeeEEEEEEECCCCCEEEeE
Confidence 36899998 899999999999975 8999998 999986654 2222 2339999999999999999999887
Q ss_pred e
Q 022938 174 E 174 (289)
Q Consensus 174 ~ 174 (289)
.
T Consensus 85 ~ 85 (86)
T PHA02858 85 H 85 (86)
T ss_pred c
Confidence 4
No 162
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.0024 Score=53.73 Aligned_cols=77 Identities=29% Similarity=0.343 Sum_probs=57.7
Q ss_pred hhcccccccccEEEe-----eeeeEEEEEecCCC-----ceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCC
Q 022938 180 NKYSSRVNVEDIFVG-----RDYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE 249 (289)
Q Consensus 180 ~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G-----~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e 249 (289)
.....-.+.|++|-| ....+.|++-+..+ .+-..|-+|+|+.+..+++++++.|++||.|+|+|++.-
T Consensus 56 ~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~-- 133 (188)
T COG1096 56 KKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG-- 133 (188)
T ss_pred CCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--
Confidence 335566788898888 56666776642111 002567899999999999999999999999999999984
Q ss_pred CCeEEEEEec
Q 022938 250 KSRITLSIKQ 259 (289)
Q Consensus 250 ~~ri~lSlK~ 259 (289)
-.+.||.+.
T Consensus 134 -~~~~Lst~~ 142 (188)
T COG1096 134 -DPIQLSTKG 142 (188)
T ss_pred -CCeEEEecC
Confidence 347777764
No 163
>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=97.20 E-value=0.0022 Score=64.65 Aligned_cols=76 Identities=17% Similarity=0.315 Sum_probs=55.6
Q ss_pred cCC--CEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCC--C-c-cCcCcc-cchhcccccCCCCEEEEEEEEEecCCc
Q 022938 98 ESG--FIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSP--S-H-SCKEPQ-KSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 98 ~~G--~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~--~-~-~~~~p~-~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
+.| +.+.|.|++++++|+||++. |++|+||.+.+.+ . + ...+.. -.+.-...+.+||+|+|+|.++|.+.+
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 59999999999999999995 8999999999965 1 1 111111 011000136699999999999999988
Q ss_pred EEEEE
Q 022938 169 KLVFS 173 (289)
Q Consensus 169 ri~lS 173 (289)
+|.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 88764
No 164
>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=97.17 E-value=0.0011 Score=63.20 Aligned_cols=59 Identities=20% Similarity=0.323 Sum_probs=47.1
Q ss_pred cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCcc-----------CcCcccchhcccccCCCCEEEEEEEE
Q 022938 98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSHS-----------CKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~~-----------~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
..|.++.|+|.++.++ |+||++| +..||+|.+++.+... .+++.+.+ .+||.|.|.|.+
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l------~~G~~IlVQV~K 96 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELL------RPGQSVLVQVVK 96 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhC------cCCCEEEEEEee
Confidence 5899999999999998 9999999 8999999999865311 01222233 389999999986
No 165
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.16 E-value=0.019 Score=50.34 Aligned_cols=86 Identities=17% Similarity=0.197 Sum_probs=65.2
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
+.|+.+-|.|..+...+..|+++ -..|++|.+++.+... ..+....++ +||.|.++|..+|+ .....|+
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~------vGD~v~AkV~~vd~-~~~~~L~ 135 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLN------VGDLVYAKVVDVDR-DGEVELT 135 (239)
T ss_pred CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccc------cCCEEEEEEEEccC-CCceEEE
Confidence 79999999999999999999999 5999999999954432 123334444 99999999999995 5677777
Q ss_pred eecchhhhcccccccccEEEe
Q 022938 174 EKDAVWNKYSSRVNVEDIFVG 194 (289)
Q Consensus 174 ~k~~~~~~~~~~~~~G~iv~G 194 (289)
.|.. -+-.++.|.++..
T Consensus 136 ~k~~----~~GkL~~G~iv~i 152 (239)
T COG1097 136 LKDE----GLGKLKNGQIVKI 152 (239)
T ss_pred eecC----CCccccCCEEEEE
Confidence 7543 3445566666554
No 166
>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=97.13 E-value=0.0027 Score=47.45 Aligned_cols=59 Identities=17% Similarity=0.247 Sum_probs=45.5
Q ss_pred cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccC-----------cccccCCCCEEEEEEEEEeCCCC
Q 022938 188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREKS 251 (289)
Q Consensus 188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~-----------~~~~~~iGd~V~vkV~~id~e~~ 251 (289)
+|+++.| +++|+||.++ + +.+|+|.+.+..+..-+ -...+.+|+.|++||..+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G--p----l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG--P----LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc--C----ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 4788888 8999999996 3 88999998886553222 13458899999999999987655
Q ss_pred e
Q 022938 252 R 252 (289)
Q Consensus 252 r 252 (289)
.
T Consensus 75 ~ 75 (88)
T cd04462 75 D 75 (88)
T ss_pred c
Confidence 4
No 167
>PRK05054 exoribonuclease II; Provisional
Probab=97.04 E-value=0.0024 Score=64.54 Aligned_cols=67 Identities=15% Similarity=0.155 Sum_probs=52.2
Q ss_pred ccc--cEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--c---cC-------cccccCCCCEEEEEEEEEe
Q 022938 187 NVE--DIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I---QD-------IRDILNEGDEVRVKVIKID 247 (289)
Q Consensus 187 ~~G--~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~---~~-------~~~~~~iGd~V~vkV~~id 247 (289)
++| +.+.| +++|+||+|. .. ++.|+||.+.+...+ . .+ -...|++||.|+|+|.++|
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~-~~---~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd 633 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLL-EN---GAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVR 633 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEe-CC---ceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEc
Confidence 455 47777 8999999996 23 499999999996531 1 01 1246999999999999999
Q ss_pred CCCCeEEEEE
Q 022938 248 REKSRITLSI 257 (289)
Q Consensus 248 ~e~~ri~lSl 257 (289)
.++++|.+++
T Consensus 634 ~~~~~i~~~~ 643 (644)
T PRK05054 634 METRSIIARP 643 (644)
T ss_pred cccCeEEEEE
Confidence 9999998874
No 168
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.04 E-value=0.0042 Score=63.48 Aligned_cols=81 Identities=17% Similarity=0.213 Sum_probs=62.3
Q ss_pred HhhcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCccc----chhcccccCCCCEEEEEEEEEecCCc
Q 022938 95 AYKESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQK----SIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 95 ~~~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~----~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
-..+.|+.++|+|+++..+|+||.+. +++|++|.+.+...++.-++.. .-+....++.|+.|++++.+++...+
T Consensus 618 m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~ 697 (706)
T COG0557 618 MKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER 697 (706)
T ss_pred HHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEccccc
Confidence 33589999999999999999999998 5999999999996444222211 00111246699999999999999888
Q ss_pred EEEEEee
Q 022938 169 KLVFSEK 175 (289)
Q Consensus 169 ri~lS~k 175 (289)
++.+++.
T Consensus 698 ~i~~~~v 704 (706)
T COG0557 698 KIDFELV 704 (706)
T ss_pred ceEEEec
Confidence 8887653
No 169
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.95 E-value=0.0012 Score=68.38 Aligned_cols=74 Identities=19% Similarity=0.252 Sum_probs=62.6
Q ss_pred hhcCCCEEEEEEEEEEcC--c-EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938 96 YKESGFIYEGKIQGFNGG--G-LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 96 ~~~~G~iv~g~V~~v~~~--G-~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
.+..|.++.++|++|+.. + +-|.+. |+.||||..++|+..+ .+|...+. +||.|.|+|+++|.++=-+.
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~ 1054 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDV-RRPENRVK------VGQTVYCKVIKIDKERFSVE 1054 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhc-cCHHHhhc------cCceEEEEeeeeeHhhhhhh
Confidence 467899999999999954 2 467788 9999999999999776 88887776 99999999999998776677
Q ss_pred EEeec
Q 022938 172 FSEKD 176 (289)
Q Consensus 172 lS~k~ 176 (289)
||.+.
T Consensus 1055 Ls~r~ 1059 (1299)
T KOG1856|consen 1055 LSCRT 1059 (1299)
T ss_pred hhhhh
Confidence 77664
No 170
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.003 Score=55.31 Aligned_cols=69 Identities=29% Similarity=0.485 Sum_probs=57.4
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
-++||+|-| ...+..|+|+.+ ..+++|.|++.+... .+++..|++||.|.|+|..+|+ .....|+
T Consensus 62 P~~gD~VIG~I~~v~~~~W~VDI~sp-----~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~ 135 (239)
T COG1097 62 PEVGDVVIGKIIEVGPSGWKVDIGSP-----YPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELT 135 (239)
T ss_pred CCCCCEEEEEEEEEcccceEEEcCCc-----cceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEE
Confidence 367888888 788999999743 789999999855542 4678889999999999999997 7889999
Q ss_pred EecC
Q 022938 257 IKQL 260 (289)
Q Consensus 257 lK~~ 260 (289)
+|..
T Consensus 136 ~k~~ 139 (239)
T COG1097 136 LKDE 139 (239)
T ss_pred eecC
Confidence 9765
No 171
>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=96.74 E-value=0.012 Score=43.63 Aligned_cols=70 Identities=19% Similarity=0.203 Sum_probs=55.2
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
+.|+.+-|+|+.+......|+++ -..|++|..++.-.. ++....++ +|+.|-|+|.++++. ....||...
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gat--k~~rp~L~------~GDlV~ArV~~~~~~-~~~eLtc~~ 75 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGAT--KRNRPNLN------VGDLVYARVVKANRD-MEPELSCVD 75 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHccccc--ccccccCC------CCCEEEEEEEecCCC-CCeEEEEeC
Confidence 68999999999999999999999 689999998774332 22233344 999999999999864 456777765
No 172
>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=96.63 E-value=0.009 Score=44.36 Aligned_cols=67 Identities=19% Similarity=0.103 Sum_probs=52.0
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
++||+|-| ...+.+|+|+. ...|++|..++... .+..+..+++||.|-|+|.++|+. ....||+...
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s-----~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~ 76 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGG-----SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS 76 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCC-----CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence 57888888 66788999963 26799998776433 344567799999999999999984 5689998773
No 173
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.58 E-value=0.0099 Score=50.24 Aligned_cols=68 Identities=18% Similarity=0.232 Sum_probs=49.3
Q ss_pred cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-----------c-cCcccccCCCCEEEEEEEEEeC
Q 022938 186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-----------I-QDIRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-----------~-~~~~~~~~iGd~V~vkV~~id~ 248 (289)
-..|++++| +++|+||.++ + .++++|.++|..+. . ++-...+..|+.|++||..+..
T Consensus 79 Pf~gEVv~g~V~~v~~~G~~v~~G--p----~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 152 (176)
T PTZ00162 79 PFKDEVLDAIVTDVNKLGFFAQAG--P----LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRY 152 (176)
T ss_pred cCCCCEEEEEEEEEecceEEEEee--C----eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEe
Confidence 356777777 8999999997 3 77999999997441 1 1224568999999999988865
Q ss_pred CC--CeEEEEEec
Q 022938 249 EK--SRITLSIKQ 259 (289)
Q Consensus 249 e~--~ri~lSlK~ 259 (289)
+. .+...|||+
T Consensus 153 ~~~~~~~i~T~~~ 165 (176)
T PTZ00162 153 DASNLFAIATINS 165 (176)
T ss_pred cCCCcEEEEEecC
Confidence 43 345556665
No 174
>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=96.34 E-value=0.0072 Score=44.47 Aligned_cols=76 Identities=22% Similarity=0.340 Sum_probs=38.1
Q ss_pred CCCCEEEEEEEEEecCCcEEEEEeec--chhhhcccccccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCcccccC
Q 022938 151 LTGSIISVKVIQANEEMKKLVFSEKD--AVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD 228 (289)
Q Consensus 151 ~vG~~V~vkVl~vd~~~~ri~lS~k~--~~~~~~~~~~~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~ 228 (289)
.+|+.|-++|+++.+ +...+..-. ..+. .....+.. .+. . ...|+++.+++.....+.
T Consensus 3 ~vGdiV~~rVtrv~~--~~a~v~Il~v~~~~~---~~~~~~~~----------~l~--~---~f~GiIR~~DVR~te~Dk 62 (82)
T PF10447_consen 3 KVGDIVIARVTRVNP--RQAKVEILCVEGKGN---DSINAGDR----------PLK--E---PFQGIIRKQDVRATEKDK 62 (82)
T ss_dssp -TT-EEEEEEEEE-S--SEEEEEEEES-------------SSS-------------------SS-S-EEEEGGGT-SS--
T ss_pred CCCCEEEEEEEEEec--cEEEEEEEEEEeccc---cccccCCc----------ccc--c---ccEEEEEeeeecccccch
Confidence 489999999999954 333333322 1111 00000110 122 1 277999999887665443
Q ss_pred --cccccCCCCEEEEEEEEE
Q 022938 229 --IRDILNEGDEVRVKVIKI 246 (289)
Q Consensus 229 --~~~~~~iGd~V~vkV~~i 246 (289)
+.+.|++||.|+|+|+++
T Consensus 63 v~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 63 VKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp --GGGT--SSSEEEEEEEEE
T ss_pred hhHHhccCCCCEEEEEEeeC
Confidence 578899999999999975
No 175
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.28 E-value=0.0031 Score=55.63 Aligned_cols=73 Identities=19% Similarity=0.250 Sum_probs=64.0
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEE---CCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRF---FSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l---~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
.++++++-+.|.++...|++|.+ ++++|.+-.+|+|..++ ....+.++ +|..=.|.|+.||.+++-|-||
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRI-RSI~klir------VGr~E~vvVlrVDkekGYIDLS 86 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRI-RSIQKLIR------VGRNEPVVVLRVDKEKGYIDLS 86 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHH-HHHHHHHh------cCCcceEEEEEEcCCCCceech
Confidence 37899999999999999999986 37999999999998776 44555555 9999999999999999999999
Q ss_pred eec
Q 022938 174 EKD 176 (289)
Q Consensus 174 ~k~ 176 (289)
.+.
T Consensus 87 krr 89 (304)
T KOG2916|consen 87 KRR 89 (304)
T ss_pred hcc
Confidence 875
No 176
>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=96.19 E-value=0.012 Score=56.29 Aligned_cols=58 Identities=28% Similarity=0.407 Sum_probs=45.8
Q ss_pred cccccccEEEe-----eee--eEEEEEecCCCceeEEEEEEccCcCcc------------cccCcccccCCCCEEEEEEE
Q 022938 184 SRVNVEDIFVG-----RDY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 244 (289)
Q Consensus 184 ~~~~~G~iv~G-----~~~--G~fV~i~~~~G~~~i~Glv~~sels~~------------~~~~~~~~~~iGd~V~vkV~ 244 (289)
....+|++|.| .+. |+||+|+ .| -.||+|.+++.+. ...++.+.+++||.|.|.|.
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG--~~---k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~ 95 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIG--LE---KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV 95 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcC--CC---ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence 34578999999 555 9999997 54 8999999998653 23345667999999999999
Q ss_pred EE
Q 022938 245 KI 246 (289)
Q Consensus 245 ~i 246 (289)
.=
T Consensus 96 Ke 97 (414)
T TIGR00757 96 KE 97 (414)
T ss_pred eC
Confidence 83
No 177
>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=96.13 E-value=0.016 Score=58.55 Aligned_cols=66 Identities=14% Similarity=0.207 Sum_probs=50.0
Q ss_pred ccc--cEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEe
Q 022938 187 NVE--DIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI-----Q---DI--RDILNEGDEVRVKVIKID 247 (289)
Q Consensus 187 ~~G--~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~--~~~-----~---~~--~~~~~iGd~V~vkV~~id 247 (289)
++| +.+.| +++|+||++. .. ++.|++|.+.+.. +.. . .+ ...|++||.|+|+|.++|
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~-~~---~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd 629 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLL-EN---GAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVR 629 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEe-cC---ceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEec
Confidence 454 36666 8999999996 23 4999999999865 211 1 11 126999999999999999
Q ss_pred CCCCeEEEE
Q 022938 248 REKSRITLS 256 (289)
Q Consensus 248 ~e~~ri~lS 256 (289)
.++++|.+.
T Consensus 630 ~~~~~i~~~ 638 (639)
T TIGR02062 630 METRSIIAR 638 (639)
T ss_pred cccCcEeee
Confidence 999998764
No 178
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.04 E-value=0.074 Score=44.89 Aligned_cols=70 Identities=19% Similarity=0.274 Sum_probs=56.2
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEECC-----------EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFFS-----------LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE 165 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~g-----------v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~ 165 (289)
.+.|+++-|.|+++....+.|++-+ ..|-+|.++.+..+. .+..+.|+ +||.|+++|++.-
T Consensus 62 ~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~-~~~~d~f~------~GDivrA~Vis~~- 133 (188)
T COG1096 62 PKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYV-EKLSDAFR------IGDIVRARVISTG- 133 (188)
T ss_pred CCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccc-cccccccc------cccEEEEEEEecC-
Confidence 5789999999999999999998753 346789999988876 66666665 9999999999863
Q ss_pred CCcEEEEEeec
Q 022938 166 EMKKLVFSEKD 176 (289)
Q Consensus 166 ~~~ri~lS~k~ 176 (289)
..+.||.+.
T Consensus 134 --~~~~Lst~~ 142 (188)
T COG1096 134 --DPIQLSTKG 142 (188)
T ss_pred --CCeEEEecC
Confidence 456676665
No 179
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.96 E-value=0.0056 Score=63.67 Aligned_cols=75 Identities=24% Similarity=0.332 Sum_probs=59.7
Q ss_pred cccccccEEEe------eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 184 SRVNVEDIFVG------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 184 ~~~~~G~iv~G------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
+.+..|.+|.+ ...|.-|.+-..+| +.|+|+.+++|+..+.+|...+++||+|.|+|+++|.++=.+.||+
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G---~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~ 1057 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCG---VTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSC 1057 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCC---CceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhh
Confidence 45778888876 33333333322366 9999999999999999999999999999999999999888888998
Q ss_pred ecCC
Q 022938 258 KQLE 261 (289)
Q Consensus 258 K~~~ 261 (289)
|.++
T Consensus 1058 r~sd 1061 (1299)
T KOG1856|consen 1058 RTSD 1061 (1299)
T ss_pred hhHH
Confidence 8753
No 180
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=95.87 E-value=0.075 Score=43.72 Aligned_cols=70 Identities=19% Similarity=0.200 Sum_probs=45.8
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcc---cchh-cc-cccCCCCEEEEEEEEEecCCc
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQ---KSIH-EI-AKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~---~~~~-~~-~~~~vG~~V~vkVl~vd~~~~ 168 (289)
-.|++++|+|+++++.|+|++.|-++-|+..-.....+. -+|+ ..|. ++ ....+|.+|+++|+.......
T Consensus 80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~-f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~ 154 (170)
T KOG3298|consen 80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYE-FDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET 154 (170)
T ss_pred cCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcc-cCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence 479999999999999999999997777765433332221 1122 1121 11 134589999999987654333
No 181
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.81 E-value=0.0076 Score=58.78 Aligned_cols=74 Identities=30% Similarity=0.482 Sum_probs=59.9
Q ss_pred cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938 182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256 (289)
Q Consensus 182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS 256 (289)
.+.+++.|.++.| ..||+||+++ . ++.|++|.++++.. ..|.+||.+-+.+..+.++++.+.+.
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln--~---~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~ 184 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELN--S---HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFE 184 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecC--h---hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCcccee
Confidence 4678899999999 8999999996 3 59999999998752 34889999999999999988877765
Q ss_pred EecCCCCchhHH
Q 022938 257 IKQLEEDPLLET 268 (289)
Q Consensus 257 lK~~~~~p~~~~ 268 (289)
...+ ++|...
T Consensus 185 ~~~~--~~Y~~~ 194 (715)
T COG1107 185 PVGL--DRYREV 194 (715)
T ss_pred ecCC--ccchhh
Confidence 5544 455543
No 182
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.64 E-value=0.035 Score=52.03 Aligned_cols=61 Identities=20% Similarity=0.334 Sum_probs=49.1
Q ss_pred ccccEEEe-----ee-eeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCC---eEEEEE
Q 022938 187 NVEDIFVG-----RD-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLSI 257 (289)
Q Consensus 187 ~~G~iv~G-----~~-~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~---ri~lSl 257 (289)
++|+++.| .. .++||+++ + +.|++|.++.. +.+.|++||.++|.|.+++...+ .|.||.
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg---~---~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSR 204 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEID---E---IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSR 204 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcC---C---eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEc
Confidence 78999999 22 35899984 3 99999988765 56889999999999999998765 677775
Q ss_pred ec
Q 022938 258 KQ 259 (289)
Q Consensus 258 K~ 259 (289)
..
T Consensus 205 t~ 206 (374)
T PRK12328 205 TS 206 (374)
T ss_pred CC
Confidence 43
No 183
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=95.38 E-value=0.046 Score=55.98 Aligned_cols=71 Identities=31% Similarity=0.507 Sum_probs=56.4
Q ss_pred cccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEEe
Q 022938 184 SRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKID 247 (289)
Q Consensus 184 ~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~id 247 (289)
-+-.+|+.+.| +.+|+||.+.. . +++|++|++.+...+. ......|+.||.|++++.+++
T Consensus 618 m~~~vg~~f~g~V~~v~~~g~~V~l~~-~---~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 618 MKKRVGEEFDGVVTGVTSFGFFVELPE-L---GLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred HHHhcCCEEEEEEEEEEeccEEEEecc-c---ccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 34578888777 89999999952 2 4999999999986422 233446999999999999999
Q ss_pred CCCCeEEEEEe
Q 022938 248 REKSRITLSIK 258 (289)
Q Consensus 248 ~e~~ri~lSlK 258 (289)
...+++.+++-
T Consensus 694 ~~~~~i~~~~v 704 (706)
T COG0557 694 LDERKIDFELV 704 (706)
T ss_pred ccccceEEEec
Confidence 99999988763
No 184
>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=95.29 E-value=0.054 Score=39.83 Aligned_cols=60 Identities=17% Similarity=0.206 Sum_probs=37.3
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-------------------CEEEEeecCCCCCCccCc-CcccchhcccccCCCCEEE
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-------------------SLVGFLPFPQMSPSHSCK-EPQKSIHEIAKGLTGSIIS 157 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-------------------gv~g~ip~sels~~~~~~-~p~~~~~~~~~~~vG~~V~ 157 (289)
++|.++.|+|+++++.-+.+++- ...|.++.+++......+ ...+. |++||.|+
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~------FrpGDIVr 76 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC------FRPGDIVR 76 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--------SSSEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc------cCCCCEEE
Confidence 58999999999999987766541 257888888876543200 12333 45999999
Q ss_pred EEEEEE
Q 022938 158 VKVIQA 163 (289)
Q Consensus 158 vkVl~v 163 (289)
++|+++
T Consensus 77 A~ViSl 82 (82)
T PF10447_consen 77 ARVISL 82 (82)
T ss_dssp EEEEEE
T ss_pred EEEeeC
Confidence 999874
No 185
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.26 E-value=0.049 Score=56.44 Aligned_cols=62 Identities=19% Similarity=0.335 Sum_probs=47.2
Q ss_pred cCCCEEEEEEEEEEc--CcEEEEEC-CEEEEeecCCCCCCccCcCc---------ccchhcccccCCCCEEEEEEEEEec
Q 022938 98 ESGFIYEGKIQGFNG--GGLLVRFF-SLVGFLPFPQMSPSHSCKEP---------QKSIHEIAKGLTGSIISVKVIQANE 165 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~--~G~~V~l~-gv~g~ip~sels~~~~~~~p---------~~~~~~~~~~~vG~~V~vkVl~vd~ 165 (289)
..|.|+.|+|.++.+ .++||++| |..||+|.++...... .++ ...+ ..||.|-|.|.+-..
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f-~~~~~~~~~~~i~~~L------k~GqeILVQV~KEa~ 109 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYF-PANYSAHGRPNIKDVL------REGQEVIVQIDKEER 109 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccc-cccccccccccccccc------CCCCEEEEEEeeccc
Confidence 489999999999997 48999999 9999999999854332 111 1123 389999999986443
Q ss_pred C
Q 022938 166 E 166 (289)
Q Consensus 166 ~ 166 (289)
.
T Consensus 110 g 110 (1068)
T PRK10811 110 G 110 (1068)
T ss_pred C
Confidence 3
No 186
>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=95.25 E-value=0.13 Score=40.85 Aligned_cols=67 Identities=18% Similarity=0.087 Sum_probs=44.9
Q ss_pred CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcc-----cc-hhcccccCCCCEEEEEEEEEec
Q 022938 99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQ-----KS-IHEIAKGLTGSIISVKVIQANE 165 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~-----~~-~~~~~~~~vG~~V~vkVl~vd~ 165 (289)
.|+++.|+|++.+..|+.|.++ =-+.|||.+.|.......... +. -...+.+-.|+.|+|||.++.-
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 6999999999999999999998 578999999997432101000 01 0112334589999999998764
No 187
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.18 E-value=0.017 Score=56.48 Aligned_cols=68 Identities=19% Similarity=0.255 Sum_probs=57.1
Q ss_pred HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
+..+.|..+.|+|.++.++|+||+++ .+.|+++.++++... ++.+|+.+-+.+..+.++.+.+.+.
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~-------------~~~vgdeiiV~v~~vr~~~geidf~ 184 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDP-------------DYAVGDEIIVQVSDVRPEKGEIDFE 184 (715)
T ss_pred hhcccceeeeccccchhhhcceeecChhhhccccccccCCCC-------------CCCCCCeEEEEeeccCCCCCcccee
Confidence 34689999999999999999999999 899999999998521 1239999999999998877776665
Q ss_pred ee
Q 022938 174 EK 175 (289)
Q Consensus 174 ~k 175 (289)
..
T Consensus 185 ~~ 186 (715)
T COG1107 185 PV 186 (715)
T ss_pred ec
Confidence 44
No 188
>PRK11712 ribonuclease G; Provisional
Probab=94.63 E-value=0.095 Score=51.19 Aligned_cols=60 Identities=23% Similarity=0.340 Sum_probs=44.5
Q ss_pred cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCc--cCcC---------cccchhcccccCCCCEEEEEEEEE
Q 022938 98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSH--SCKE---------PQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~--~~~~---------p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
..|.++.|+|.++.++ ++||++| +..||+|.+++.... ...+ ..+.+ ..||.+-|.|.+-
T Consensus 37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l------~~Gq~iLVQV~Ke 110 (489)
T PRK11712 37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELV------RQGQDIMVQVVKD 110 (489)
T ss_pred ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhc------cCCCEEEEEEEeC
Confidence 5899999999999984 8999999 999999999873210 0000 11123 3899999999754
No 189
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=93.79 E-value=0.27 Score=33.90 Aligned_cols=49 Identities=35% Similarity=0.541 Sum_probs=30.1
Q ss_pred eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
+++|+|++-+ .+ -.-++|.+++. ..+++||.|.|-| ..|. .+|+..|+|
T Consensus 13 ~~~g~fL~~~--~~---~~vlLp~~e~~--------~~~~~Gd~v~VFv-Y~D~-~~rl~AT~k 61 (61)
T PF13509_consen 13 NEFGYFLDDG--EG---KEVLLPKSEVP--------EPLKVGDEVEVFV-YLDK-EGRLVATTK 61 (61)
T ss_dssp -SSEEEEEET--T----EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred eCCEEEEECC--CC---CEEEechHHcC--------CCCCCCCEEEEEE-EECC-CCCEEEecC
Confidence 8999999974 32 78999998875 3488999999866 4565 568888775
No 190
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.50 E-value=0.25 Score=47.30 Aligned_cols=66 Identities=8% Similarity=0.044 Sum_probs=48.3
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC---CeEEEEEe
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSIK 258 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~---~ri~lSlK 258 (289)
++|+++.| ...+++|+++..-|-.++.|++|.++.. +.+.|++||.|+|.|.+|+... -.|.||..
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSRt 224 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSRA 224 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEcC
Confidence 78999999 5567899883100100289999987764 5588999999999999998652 35777754
No 191
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=92.77 E-value=0.65 Score=38.74 Aligned_cols=74 Identities=18% Similarity=0.178 Sum_probs=52.2
Q ss_pred cCCCEEEEEEEEEEcCcEEEEE---C------CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRF---F------SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l---~------gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
..|.+++++|..++..-+-|++ + ..+|+||..++.... +|--+.++ .|++||.|.++|++.+ .+.
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tE--kdrv~v~k---sFrPgDiVlAkVis~~-~~~ 140 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATE--KDRVKVYK---SFRPGDIVLAKVISLG-DGS 140 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccc--cchhhhhh---ccCCCcEEEEEEeecC-CCC
Confidence 6899999999999977665554 2 378999999886532 22223332 4569999999999865 345
Q ss_pred EEEEEeecc
Q 022938 169 KLVFSEKDA 177 (289)
Q Consensus 169 ri~lS~k~~ 177 (289)
+..||..++
T Consensus 141 ~y~LTtAen 149 (193)
T KOG3409|consen 141 NYLLTTAEN 149 (193)
T ss_pred cEEEEEecc
Confidence 666665553
No 192
>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=90.93 E-value=1.4 Score=33.58 Aligned_cols=53 Identities=21% Similarity=0.229 Sum_probs=42.9
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
..|.++.|+|..+...-+++++| ...++|+..+.... +|..|.+|.+++.+.+
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~~--------------~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNGE--------------KYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccccc--------------ccccCCEEEEEECCHh
Confidence 48999999999999999999999 68999996654321 2348999999997554
No 193
>PRK10811 rne ribonuclease E; Reviewed
Probab=90.23 E-value=0.71 Score=48.23 Aligned_cols=60 Identities=27% Similarity=0.484 Sum_probs=44.8
Q ss_pred ccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCccccc---------CcccccCCCCEEEEEEEEEeCCC
Q 022938 187 NVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDREK 250 (289)
Q Consensus 187 ~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~---------~~~~~~~iGd~V~vkV~~id~e~ 250 (289)
.+|.||.| .-.++||+|+ .| ..||+|.+++...... .....+++||.|-|-|.+-...+
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG--~g---knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gt 111 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGN 111 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEec--CC---cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCC
Confidence 58999999 6678999997 55 8999999988533211 23456899999999998754333
Q ss_pred C
Q 022938 251 S 251 (289)
Q Consensus 251 ~ 251 (289)
+
T Consensus 112 K 112 (1068)
T PRK10811 112 K 112 (1068)
T ss_pred C
Confidence 3
No 194
>PRK11712 ribonuclease G; Provisional
Probab=88.32 E-value=1.2 Score=43.76 Aligned_cols=59 Identities=24% Similarity=0.455 Sum_probs=43.2
Q ss_pred cccccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCcc------------cccCcccccCCCCEEEEEEE
Q 022938 184 SRVNVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 244 (289)
Q Consensus 184 ~~~~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~------------~~~~~~~~~~iGd~V~vkV~ 244 (289)
....+|.+|.| .=.++||+|+ .| -.||+|.+++... ....+.+.+++||.|-|.|.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG--~~---k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG--LD---KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeC--CC---ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence 34468889988 5677999997 44 8999999987321 01234556999999999998
Q ss_pred EEe
Q 022938 245 KID 247 (289)
Q Consensus 245 ~id 247 (289)
.=.
T Consensus 109 Ke~ 111 (489)
T PRK11712 109 KDP 111 (489)
T ss_pred eCC
Confidence 753
No 195
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=87.69 E-value=0.9 Score=44.53 Aligned_cols=67 Identities=21% Similarity=0.294 Sum_probs=49.1
Q ss_pred cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCccCcCcccc-hhcccccCCCCEEEEEEEEEecCCc
Q 022938 98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSHSCKEPQKS-IHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~~~~~p~~~-~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
..|.++.|.|+++.+. .+||++| +-.||+|.++..+ +. ..+... ++ ...+.||.+-|.|..-...++
T Consensus 36 ~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~-~~~~~~~i~--~~lr~~~~~~Vqv~ke~~G~K 106 (487)
T COG1530 36 IVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YF-RAVLEEKIK--VRLRGGQATLVQVVKEPRGTK 106 (487)
T ss_pred eecCceEEEecccCccchhheeeccCCccceEEecccch-hh-hhcccccce--eeecCCceEEEEEEeecCccc
Confidence 5899999999999985 7999999 8999999999988 32 333220 00 112389998888876654433
No 196
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=85.88 E-value=5.1 Score=33.56 Aligned_cols=78 Identities=24% Similarity=0.334 Sum_probs=49.7
Q ss_pred CCCEEEEEEEEEecCCcEEEEEeecchhhhcccccccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCc
Q 022938 152 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDI 229 (289)
Q Consensus 152 vG~~V~vkVl~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~ 229 (289)
+|+.|.+||..++....+..+ +-+|+.. ++ . ...|++|..++.... .-++
T Consensus 68 ~G~IVtarV~~i~~rfAkv~I-------------~~V~d~~----------lk--~---~FrglirkqdvR~tEkdrv~v 119 (193)
T KOG3409|consen 68 VGAIVTARVSRINLRFAKVDI-------------LSVGDKP----------LK--K---SFRGLIRKQDVRATEKDRVKV 119 (193)
T ss_pred cCcEEEEEEEeeccceeeEEE-------------EEEcCEE----------hh--h---hhcceeehhhccccccchhhh
Confidence 799999999887643222222 2233322 22 2 277889887775432 2235
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIK 258 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK 258 (289)
.+.|++||.|.|+|++.+. +....||..
T Consensus 120 ~ksFrPgDiVlAkVis~~~-~~~y~LTtA 147 (193)
T KOG3409|consen 120 YKSFRPGDIVLAKVISLGD-GSNYLLTTA 147 (193)
T ss_pred hhccCCCcEEEEEEeecCC-CCcEEEEEe
Confidence 5679999999999999764 455666653
No 197
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=85.78 E-value=4.4 Score=33.50 Aligned_cols=61 Identities=20% Similarity=0.249 Sum_probs=40.9
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc----cccC-------cccccCCCCEEEEEEEEEeCCC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVIKIDREK 250 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~----~~~~-------~~~~~~iGd~V~vkV~~id~e~ 250 (289)
-.|++++| ...|+|++++ + ++-++..-....+ .-++ -.+..++|..|+++|+......
T Consensus 80 fKGEVvdgvV~~Vnk~G~F~~~G--P----l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~ 153 (170)
T KOG3298|consen 80 FKGEVVDGVVTKVNKMGVFARSG--P----LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE 153 (170)
T ss_pred cCCcEEEEEEEEEeeeeEEEecc--c----eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence 46889998 8999999997 4 6666654333322 1111 1125888999999999887644
Q ss_pred CeE
Q 022938 251 SRI 253 (289)
Q Consensus 251 ~ri 253 (289)
..+
T Consensus 154 ~~i 156 (170)
T KOG3298|consen 154 TEI 156 (170)
T ss_pred eeE
Confidence 443
No 198
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=84.73 E-value=8 Score=28.65 Aligned_cols=65 Identities=12% Similarity=0.089 Sum_probs=46.4
Q ss_pred CCEEEEEEEEEEcCcEE-EEEC-CEEEEeecCC-CCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938 100 GFIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQ-MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD 176 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~se-ls~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~ 176 (289)
--.++|+|+.+.+++.| |.+. |..-+.+++- |...+ ....+||.|.|.+...|.++++|+.-.+.
T Consensus 6 ~ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r------------IrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 6 LIELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR------------IRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred eEEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee------------EEecCCCEEEEEECcccCCceeEEEEecC
Confidence 44679999999988876 6887 7554444332 11111 22348999999999999999999987764
No 199
>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=82.14 E-value=6 Score=31.29 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=14.6
Q ss_pred CcccccCCCCEEEEEEEEEeC
Q 022938 228 DIRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 228 ~~~~~~~iGd~V~vkV~~id~ 248 (289)
...-.+..|+.|+.||.++.-
T Consensus 56 ~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 56 EQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp SEEEEE-TT-EEEEEEEEEEE
T ss_pred CceeEccCCCEEEEEEeEEEE
Confidence 334457899999999999864
No 200
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=81.91 E-value=38 Score=31.09 Aligned_cols=114 Identities=11% Similarity=0.112 Sum_probs=68.9
Q ss_pred cCCCEEEEEEEEEEc-CcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 98 ESGFIYEGKIQGFNG-GGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~-~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
+.|.++.|+|..-.+ +|+ -+.+++..-.+|.-++ .+|+.++++|-.-| +.+.++
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~~~a-------------------~~g~~~R~~I~a~D-----Vslal~ 285 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKLDA-------------------PVGARLRIRIQARD-----VSLALQ 285 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecCceEEEeeccCC-------------------CCCCcEEEEEEccc-----eEEEec
Confidence 568999999999885 565 3555555555654332 28999999997544 455555
Q ss_pred cchhhhcccccccccEEEe----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEe
Q 022938 176 DAVWNKYSSRVNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 247 (289)
Q Consensus 176 ~~~~~~~~~~~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id 247 (289)
.. -....-++=+|.++.- ..--+++++ +| -.-+..++.++.+. -.+++||.|-|.|.++-
T Consensus 286 ~P-~~~SirNiLp~~v~~i~~~~~~V~v~ld~---~g---~~l~Arit~~srd~-----L~l~~G~~v~AqIKsVs 349 (352)
T COG4148 286 KP-EQTSIRNILPGKVVGIEDDDGQVDVQLDC---GG---KTLWARITPWARDE-----LALKPGQWVYAQIKSVS 349 (352)
T ss_pred Cc-cccchhhccceeEEEEEcCCCcEEEEEEc---CC---cEEEEEccHhhHHh-----hcCCCCCeEEEEEEEEE
Confidence 43 2233345556655544 222344444 33 33444445554332 23899999999998874
No 201
>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=81.51 E-value=13 Score=26.27 Aligned_cols=60 Identities=12% Similarity=0.135 Sum_probs=41.3
Q ss_pred CEEEEEEEEEEcCcEE-EEEC-CEEEEeecCC-CCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938 101 FIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQ-MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF 172 (289)
Q Consensus 101 ~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~se-ls~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l 172 (289)
-.+.|+|+...+++.| |.+. |..-..+++- |...+ ....+||.|.+.+...|.++++|+.
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~r------------I~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHY------------IRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhcc------------EEECCCCEEEEEECcccCCcEeEEe
Confidence 3579999999988876 6877 7555544332 11111 1234899999999999888888763
No 202
>PRK10943 cold shock-like protein CspC; Provisional
Probab=77.34 E-value=12 Score=26.29 Aligned_cols=50 Identities=18% Similarity=0.255 Sum_probs=35.2
Q ss_pred EEEEEEEEEEc-CcE-EEEE-C-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 102 IYEGKIQGFNG-GGL-LVRF-F-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 102 iv~g~V~~v~~-~G~-~V~l-~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.++|+|+..++ .|. |+.- + +-+.|+|++.+..... ..| ..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~-~~l----------~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF-KTL----------AEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCC-CCC----------CCCCEEEEEEEE
Confidence 45899999885 443 5554 4 6899999999875421 112 289999998864
No 203
>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=76.28 E-value=22 Score=24.32 Aligned_cols=49 Identities=16% Similarity=0.221 Sum_probs=34.1
Q ss_pred EEEEEEEEEc---CcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 103 YEGKIQGFNG---GGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 103 v~g~V~~v~~---~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.+|+|+...+ +|.+..-+ +-+.|+|.+++..... ..+ ..|+.|++.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~-----~~l------~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGF-----RSL------KEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSS-----TS--------TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccccc-----ccC------CCCCEEEEEEEE
Confidence 3799999995 34444444 4599999999875431 122 289999999976
No 204
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=75.54 E-value=27 Score=25.00 Aligned_cols=49 Identities=27% Similarity=0.413 Sum_probs=38.2
Q ss_pred hcCCCEEEEEEEEEEcCcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecC
Q 022938 97 KESGFIYEGKIQGFNGGGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEE 166 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~ 166 (289)
.+.|++++..|..+.+.|= +..+.|..-|+|-.+ +|++++++|.++.+.
T Consensus 13 VeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~---------------------~Gd~V~vkI~~v~~~ 62 (73)
T COG3269 13 VEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAE---------------------VGDEVKVKITKVKPN 62 (73)
T ss_pred cccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCC---------------------CCCeeeEEEEEeecc
Confidence 5799999999999998763 444447778888332 899999999988643
No 205
>PRK15464 cold shock-like protein CspH; Provisional
Probab=74.61 E-value=12 Score=26.41 Aligned_cols=49 Identities=10% Similarity=0.173 Sum_probs=35.2
Q ss_pred EEEEEEEEEc-CcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 103 YEGKIQGFNG-GGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 103 v~g~V~~v~~-~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.+|+|+-.++ .|. |+.-+ +-+.|+|.+.+..... ..| ..||+|.+.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~-~~l----------~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDA-EVL----------IPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCC-CCC----------CCCCEEEEEEEE
Confidence 3799999985 454 66554 5899999999954321 122 289999999864
No 206
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=74.21 E-value=24 Score=32.42 Aligned_cols=107 Identities=10% Similarity=0.044 Sum_probs=69.4
Q ss_pred eCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHH
Q 022938 15 DASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAAR 94 (289)
Q Consensus 15 ~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~ 94 (289)
|...+.+.|+- .+.|.+..+-=|.....+|+.++.+|-. .-++++++++- .
T Consensus 239 V~~hd~~y~lt-~l~l~~~~l~v~~~~a~~g~~~R~~I~a-----~DVslal~~P~----~------------------- 289 (352)
T COG4148 239 VLEHDPRYGLT-ALALGDQHLWVPKLDAPVGARLRIRIQA-----RDVSLALQKPE----Q------------------- 289 (352)
T ss_pred ehhcCCCcceE-EEecCceEEEeeccCCCCCCcEEEEEEc-----cceEEEecCcc----c-------------------
Confidence 34444455543 4567788888888888999999999843 44566665331 0
Q ss_pred HhhcCCCEEEEEEEEEEcCcE----EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 95 AYKESGFIYEGKIQGFNGGGL----LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 95 ~~~~~G~iv~g~V~~v~~~G~----~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
...--++.|+|+.+.+.+- .++++|..-.-.++..+. +.+...+|+.|.+.|..+.
T Consensus 290 --~SirNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~sr------------d~L~l~~G~~v~AqIKsVs 349 (352)
T COG4148 290 --TSIRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWAR------------DELALKPGQWVYAQIKSVS 349 (352)
T ss_pred --cchhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhhH------------HhhcCCCCCeEEEEEEEEE
Confidence 1244577999999997543 344456555555555442 3344569999999998764
No 207
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=73.65 E-value=19 Score=25.26 Aligned_cols=51 Identities=18% Similarity=0.303 Sum_probs=35.0
Q ss_pred EEEEEEEEEEc-CcE-EEEE-C-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 102 IYEGKIQGFNG-GGL-LVRF-F-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 102 iv~g~V~~v~~-~G~-~V~l-~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
.++|+|+..++ .|. |+.- + +-+.|+|++.+..... .. + .+|+.|.+.+..-
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~-~~----l------~~G~~V~f~~~~~ 57 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF-KT----L------AEGQRVEFEITNG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCC-CC----C------CCCCEEEEEEEEC
Confidence 35799999884 443 5554 4 5799999999864321 11 2 2899999988643
No 208
>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=73.01 E-value=12 Score=25.38 Aligned_cols=47 Identities=11% Similarity=0.063 Sum_probs=31.4
Q ss_pred CEEEEEEEEEEcCc----EEEEECC---EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 101 FIYEGKIQGFNGGG----LLVRFFS---LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 101 ~iv~g~V~~v~~~G----~~V~l~g---v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
-.+.|+|..+++.| +.+++++ +.+.++.... +.++..+|+.|.+.|.
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~--------------~~L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA--------------EELGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH--------------HHCT-STT-EEEEEE-
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH--------------HHcCCCCCCEEEEEEe
Confidence 36799999999998 5666773 6677765432 2234459999998774
No 209
>PRK15463 cold shock-like protein CspF; Provisional
Probab=72.67 E-value=15 Score=25.94 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=34.9
Q ss_pred EEEEEEEEEc-CcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 103 YEGKIQGFNG-GGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 103 v~g~V~~v~~-~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.+|+|+..+. .|. |+.-+ +-+.|+|++.+..... ..| .+|++|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~-~~l----------~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA-EEL----------TTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCC-CCC----------CCCCEEEEEEEE
Confidence 3799999985 454 55554 5899999999975321 222 289999998764
No 210
>PRK09890 cold shock protein CspG; Provisional
Probab=68.48 E-value=29 Score=24.39 Aligned_cols=49 Identities=16% Similarity=0.258 Sum_probs=34.2
Q ss_pred EEEEEEEEEc-CcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 103 YEGKIQGFNG-GGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 103 v~g~V~~v~~-~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.+|+|+...+ .|. |+.-. +-+.|+|++.+..... .. + .+|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~-~~----l------~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF-RT----L------NENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC-CC----C------CCCCEEEEEEEE
Confidence 3899999884 443 55544 5899999999875422 11 2 289999998754
No 211
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=68.43 E-value=22 Score=25.47 Aligned_cols=49 Identities=16% Similarity=0.213 Sum_probs=34.0
Q ss_pred EEEEEEEEc-CcE-EEEE-C-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 104 EGKIQGFNG-GGL-LVRF-F-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 104 ~g~V~~v~~-~G~-~V~l-~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
+|+|+-.+. .|. |+.- + +-+.|+|++.+...-. ..| ..|+.|.+.+..-
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~-~~l----------~~G~~V~f~~~~~ 55 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY-RTL----------KAGQSVQFDVHQG 55 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCC-CCC----------CCCCEEEEEEEEC
Confidence 588888885 443 5544 4 6999999999864321 112 2899999998653
No 212
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=67.56 E-value=14 Score=24.87 Aligned_cols=42 Identities=17% Similarity=0.161 Sum_probs=25.4
Q ss_pred EEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 105 GKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 105 g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
|++....++-.||... +-+-|||..+|... .-||+|.|+++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A----------------~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGA----------------MDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS-----------------TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCC----------------CCCCEEEEEEec
Confidence 3344443333466655 68899998777543 279999999997
No 213
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=67.43 E-value=8.1 Score=37.94 Aligned_cols=75 Identities=23% Similarity=0.277 Sum_probs=54.0
Q ss_pred hcccccccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCcccccC-----cccccCCCCEEEEEEEEEeC
Q 022938 181 KYSSRVNVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----IRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 181 ~~~~~~~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~-----~~~~~~iGd~V~vkV~~id~ 248 (289)
.......+|.+|.| .=..+||+++ .+ -.||+|.+++.+ +... +...++.||.+-+.|..-..
T Consensus 30 ~~~~~~~~gniy~grv~~i~p~~~aafvdig--~~---r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~ 103 (487)
T COG1530 30 RGAKEQIVGNIYKGRVTRVLPSLEAAFVDIG--LE---RNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR 103 (487)
T ss_pred cCCcEeeecCceEEEecccCccchhheeecc--CC---ccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence 34555678999999 4567899997 33 789999999988 4332 34589999999999988766
Q ss_pred CCCeEEEEEecCC
Q 022938 249 EKSRITLSIKQLE 261 (289)
Q Consensus 249 e~~ri~lSlK~~~ 261 (289)
.++--.||..-+.
T Consensus 104 G~Kga~lT~~Is~ 116 (487)
T COG1530 104 GTKGARLTTDISL 116 (487)
T ss_pred ccccccceeEEee
Confidence 5554455554443
No 214
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=66.06 E-value=32 Score=24.14 Aligned_cols=48 Identities=21% Similarity=0.287 Sum_probs=33.7
Q ss_pred EEEEEEEEc-CcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 104 EGKIQGFNG-GGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 104 ~g~V~~v~~-~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
+|+|+...+ .|. |+.-. +-+.|+|++.+..... .. + .+|+.|.+.+..
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~-~~----l------~~G~~V~f~~~~ 57 (70)
T PRK10354 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGY-KS----L------DEGQKVSFTIES 57 (70)
T ss_pred eEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCC-CC----C------CCCCEEEEEEEE
Confidence 899999884 343 55544 5899999999864321 11 2 289999998764
No 215
>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=65.69 E-value=8.3 Score=26.46 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=22.8
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSI 257 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSl 257 (289)
...+-+||++++.|+.+|.-+-.+.+|+
T Consensus 38 g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 38 GVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred ceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 3457899999999999998777777764
No 216
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=64.04 E-value=36 Score=25.23 Aligned_cols=51 Identities=24% Similarity=0.264 Sum_probs=34.9
Q ss_pred EEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938 200 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259 (289)
Q Consensus 200 fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~ 259 (289)
-|.++ +| ..-+.|++- ++..-.-...+||.|.|-+.-.|.++++|..-.|.
T Consensus 23 rV~Le--nG---~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 23 RVTLE--NG---VEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEeC--CC---CEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 34664 55 566666541 12221223668999999999999999999988874
No 217
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=63.87 E-value=21 Score=30.27 Aligned_cols=66 Identities=21% Similarity=0.172 Sum_probs=45.3
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccch------h-----cccccCCCCEEEEEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSI------H-----EIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~------~-----~~~~~~vG~~V~vkVl~vd 164 (289)
-.|+++.|+|++-...|+-|.++ =-+.|+|.+-|..... .+|.+.. . ..+=+-+|..|++||.+..
T Consensus 80 F~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~-f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~ 157 (202)
T KOG3297|consen 80 FVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCV-FEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDES 157 (202)
T ss_pred ccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcc-cccccEEEEEEecccCCCCceeEecCCCeEEEEEeeec
Confidence 48999999999999999999998 5678899887764432 2221110 0 0011237888999997653
No 218
>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=62.72 E-value=29 Score=23.50 Aligned_cols=31 Identities=19% Similarity=0.243 Sum_probs=24.9
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCC
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMS 132 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels 132 (289)
-+.|+|..+.+..++++.+ |.+-++|.+.+.
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~ 36 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLS 36 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHH
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHH
Confidence 3689999999999999999 578888866543
No 219
>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=62.00 E-value=34 Score=24.17 Aligned_cols=46 Identities=30% Similarity=0.370 Sum_probs=30.6
Q ss_pred EEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 022938 200 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 254 (289)
Q Consensus 200 fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~ 254 (289)
-|.+. +| ..-++|++- +...-.-...+||.|.+.+...|.++++|.
T Consensus 21 ~V~l~--ng---~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 21 RVELE--NG---HEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEC--CC---CEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 34664 55 666777642 122112336789999999999999888875
No 220
>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=60.73 E-value=11 Score=32.71 Aligned_cols=84 Identities=11% Similarity=0.148 Sum_probs=55.7
Q ss_pred hHHHHHHHhhcC--CCEEEEEEEEEEcCcEEEEECCEEEEeecCCC-CCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 88 ADWKAARAYKES--GFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQM-SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 88 ~~~~~l~~~~~~--G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sel-s~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
..|-++...++. |+++.|++.+..+.|+.++++|+..-+|.+++ ...+ ..|.+.. ..+-.-.-..|+++|..++
T Consensus 61 eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~G~~~~ip~d~L~~Lg~--g~~~Qi~-~rFG~V~hlPvev~~v~~~ 137 (225)
T PF09883_consen 61 EEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVDGIFVPIPKDELKPLGP--GSPRQIR-RRFGLVQHLPVEVEFVKVE 137 (225)
T ss_pred HHhCCCCchhcccCCceEEEEEEeecccceEEEeecccccCcHHHhcccCC--CCHHHHH-HHhCcccCCceEEEEEEcc
Confidence 345555444566 99999999999999999999899899999998 4333 3344332 1222234566788888876
Q ss_pred cCCcEEEEEee
Q 022938 165 EEMKKLVFSEK 175 (289)
Q Consensus 165 ~~~~ri~lS~k 175 (289)
.. ....+|-+
T Consensus 138 ~~-~~~rltd~ 147 (225)
T PF09883_consen 138 DG-IEARLTDE 147 (225)
T ss_pred cC-cccccCHH
Confidence 43 33444433
No 221
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=60.52 E-value=20 Score=30.63 Aligned_cols=60 Identities=17% Similarity=0.201 Sum_probs=40.6
Q ss_pred EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC-cEEEEEeecchhhhcccccccccEEEe
Q 022938 122 LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM-KKLVFSEKDAVWNKYSSRVNVEDIFVG 194 (289)
Q Consensus 122 v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~-~ri~lS~k~~~~~~~~~~~~~G~iv~G 194 (289)
++|++|..++. |.+.+. +|+++++.+.++.... +++.+|+........+..+++-++.+|
T Consensus 2 ~~~~l~~~~~~-------~~e~~~------~g~ri~~~~~~v~~~~~g~~~~srt~~~~~~~L~~~evpEi~~g 62 (190)
T COG0195 2 VEAILPKREQI-------PGENFK------VGDRIRALLYEVQKEAKGQIELSRTIPELLEKLFEIEVPEIGDG 62 (190)
T ss_pred ceeEcchhhcC-------CCcccc------cCcEEEEEEeeeeecCcccEEEEeccHHHHHHHHHhhcccccCC
Confidence 57899988865 344444 9999999999998643 368889887655544444444444444
No 222
>PRK14998 cold shock-like protein CspD; Provisional
Probab=59.17 E-value=62 Score=22.99 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=33.9
Q ss_pred EEEEEEEEc-CcE-EEEE-C-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 104 EGKIQGFNG-GGL-LVRF-F-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 104 ~g~V~~v~~-~G~-~V~l-~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
+|+|+-.+. .|. |+.- + +-+.|+|++.+..... .. + ..|++|.+.+..-
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~-~~----l------~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY-RT----L------KAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCC-CC----C------CCCCEEEEEEEEC
Confidence 588888884 443 5554 4 6899999999864321 11 2 2899999998754
No 223
>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=58.18 E-value=30 Score=24.17 Aligned_cols=49 Identities=16% Similarity=0.235 Sum_probs=33.5
Q ss_pred EEEEEEEEc-CcE-EEEE-C-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 104 EGKIQGFNG-GGL-LVRF-F-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 104 ~g~V~~v~~-~G~-~V~l-~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
+|+|+-.+. .|. |+.- + +-+.|+|.+.+..... .. + ..|++|.+.+..-
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~-~~----l------~~G~~V~f~~~~~ 55 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGY-RT----L------KAGQKVQFEVVQG 55 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCC-CC----C------CCCCEEEEEEEEC
Confidence 588998884 444 5554 4 6899999999864321 11 2 2899999987643
No 224
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=57.98 E-value=58 Score=24.65 Aligned_cols=50 Identities=6% Similarity=-0.031 Sum_probs=37.9
Q ss_pred hhhhhhHHHHHHHhhcCCCEE------EEEEEEEEcCcEEEEEC-CEEEEeecCCCC
Q 022938 83 QSRSSADWKAARAYKESGFIY------EGKIQGFNGGGLLVRFF-SLVGFLPFPQMS 132 (289)
Q Consensus 83 ~~~~~~~~~~l~~~~~~G~iv------~g~V~~v~~~G~~V~l~-gv~g~ip~sels 132 (289)
|..+.+...++.+.++.|+.+ .|+|+++.+..+.|+++ ++..-+-.+.+.
T Consensus 30 QrKr~K~~~~ml~sL~kGD~VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~~~k~aI~ 86 (97)
T COG1862 30 QRKRMKEHQELLNSLKKGDEVVTIGGIVGTVTKVGDDTVEIELGDGTKIKFEKEAIA 86 (97)
T ss_pred HHHHHHHHHHHHHhccCCCEEEEcCCeEEEEEEEecCcEEEEECCCeEEEEEHHHHH
Confidence 445566777888889999975 79999999988888888 776666555443
No 225
>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=57.49 E-value=40 Score=23.19 Aligned_cols=63 Identities=14% Similarity=0.077 Sum_probs=36.6
Q ss_pred CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS 173 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS 173 (289)
|+.++-+|..++..|-.+--+ .+.|.-- . .+.++. ...+..+||++++.|+.+|--+-.+.+|
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv-~-AtryH~---------~g~nl~pGqK~kaviLhvD~l~~~VhVS 64 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTV-L-ASRYHK---------EGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEE-E-EEEEEe---------cceecCCCceeEEEEEEEeeEEeEEEEe
Confidence 566777888877665444433 3555411 1 111111 1112238999999999999766566555
No 226
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=56.58 E-value=45 Score=28.99 Aligned_cols=60 Identities=20% Similarity=0.220 Sum_probs=44.9
Q ss_pred cCCCEEEEEEEEEEcCcEEEEECC-EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFFS-LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE 165 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~g-v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~ 165 (289)
.+|+.|-|.|++-...+.-|+++| -.+.+|.-.+.-.-....| .+ .+|+.|.++|...++
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl------~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NL------QVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--cc------ccccEEEEEEEecCC
Confidence 689999999999999999999996 6777776655433221223 23 399999999986653
No 227
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=56.21 E-value=76 Score=24.57 Aligned_cols=48 Identities=8% Similarity=-0.014 Sum_probs=36.6
Q ss_pred hhhhHHHHHHHhhcCCCEE------EEEEEEEEcCcEEEEEC-CEEEEeecCCCC
Q 022938 85 RSSADWKAARAYKESGFIY------EGKIQGFNGGGLLVRFF-SLVGFLPFPQMS 132 (289)
Q Consensus 85 ~~~~~~~~l~~~~~~G~iv------~g~V~~v~~~G~~V~l~-gv~g~ip~sels 132 (289)
.+.+...++.+.+++|+.+ .|+|.++.+.-+.++++ |+.--+..+.++
T Consensus 27 Kr~K~~~~m~~~Lk~GD~VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~r~AI~ 81 (109)
T PRK05886 27 KAMQATIDLHESLQPGDRVHTTSGLQATIVGITDDTVDLEIAPGVVTTWMKLAVR 81 (109)
T ss_pred HHHHHHHHHHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhhhee
Confidence 3444566788889999976 79999999888888887 776666655554
No 228
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=52.36 E-value=1.1e+02 Score=32.43 Aligned_cols=52 Identities=19% Similarity=0.220 Sum_probs=31.1
Q ss_pred cccccEEEe------eeeeEEEEEecCCCceeEEEEEEccCcCccc----ccCcccccCCCCEEEEE
Q 022938 186 VNVEDIFVG------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVK 242 (289)
Q Consensus 186 ~~~G~iv~G------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~----~~~~~~~~~iGd~V~vk 242 (289)
+.+|+.|.- .-.|....+ +| .+.-+++..+.-..+ ...+..+|++||.|+|.
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~v---dg--~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi 469 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESV---DG--TIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVI 469 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEec---cC--ceEEEeeccccCCCccccchHhhhhhccCCCeEEEE
Confidence 677876543 344555555 44 355555553333332 34577889999999873
No 229
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=52.14 E-value=82 Score=23.04 Aligned_cols=44 Identities=7% Similarity=-0.036 Sum_probs=32.2
Q ss_pred hhhHHHHHHHhhcCCCEE------EEEEEEEEcCcEEEEEC-CEEEEeecC
Q 022938 86 SSADWKAARAYKESGFIY------EGKIQGFNGGGLLVRFF-SLVGFLPFP 129 (289)
Q Consensus 86 ~~~~~~~l~~~~~~G~iv------~g~V~~v~~~G~~V~l~-gv~g~ip~s 129 (289)
+.+..++..+.+++|+.+ .|+|.++.+.-+.+++. |+.--+.++
T Consensus 27 ~~k~~~~m~~~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~i~~~r~ 77 (84)
T TIGR00739 27 RRKAHKKLIESLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTEITFSKN 77 (84)
T ss_pred HHHHHHHHHHhCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhH
Confidence 334556778889999975 79999999888888887 655544433
No 230
>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=51.93 E-value=72 Score=21.56 Aligned_cols=49 Identities=10% Similarity=0.132 Sum_probs=34.6
Q ss_pred EEEEEEEEc---CcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 104 EGKIQGFNG---GGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 104 ~g~V~~v~~---~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
+|+|+...+ +|.+..-+ |-+.|+|.+++...-. ..| .+|+.|.+.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~-~~~----------~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGF-RSL----------EEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCC-CcC----------CCCCEEEEEEEEC
Confidence 588888885 45555555 7999999999875421 112 2899999988754
No 231
>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=50.65 E-value=20 Score=24.45 Aligned_cols=47 Identities=11% Similarity=0.125 Sum_probs=29.6
Q ss_pred CEEEEEEEEEEcCcEEEE----EC-C--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938 101 FIYEGKIQGFNGGGLLVR----FF-S--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI 161 (289)
Q Consensus 101 ~iv~g~V~~v~~~G~~V~----l~-g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl 161 (289)
-.+.|+|.++...|..++ ++ + +.+.++...+ ..+...+|+.|.+.+.
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~--------------~~l~l~~G~~v~~~ik 60 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV--------------AELGLKPGKEVYAVIK 60 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH--------------hhCCCCCCCEEEEEEE
Confidence 468999999998775443 43 2 3444553322 1223459999998885
No 232
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=48.69 E-value=52 Score=26.65 Aligned_cols=53 Identities=17% Similarity=0.215 Sum_probs=41.6
Q ss_pred cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
..|..+.|+|-.+...-++++|| ...++|.+-++.-. +|..|.+|..+++..+
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~e--------------~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNGE--------------AYQKGARVRLRLIDLE 134 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCHH--------------HhhcCceEEEEEcChh
Confidence 57899999999999999999999 57788876665321 2348999998887553
No 233
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=45.82 E-value=6.2 Score=38.15 Aligned_cols=76 Identities=18% Similarity=0.378 Sum_probs=52.4
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCcc--CcCcc--cc-hhcccccCCCCEEEEEEEEEecCCcE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHS--CKEPQ--KS-IHEIAKGLTGSIISVKVIQANEEMKK 169 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~--~~~p~--~~-~~~~~~~~vG~~V~vkVl~vd~~~~r 169 (289)
......+.+.|..+.+.|+-|++= |..+|||..-+-..+- .-+++ .. ++-...|.+|+.++|.+.+|..+++.
T Consensus 559 ~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRs 638 (645)
T COG4776 559 AGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRS 638 (645)
T ss_pred cccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhhh
Confidence 345668899999999999999973 9999999877644321 01111 11 12224567899999999988877665
Q ss_pred EEE
Q 022938 170 LVF 172 (289)
Q Consensus 170 i~l 172 (289)
|+.
T Consensus 639 ii~ 641 (645)
T COG4776 639 IIA 641 (645)
T ss_pred hhc
Confidence 543
No 234
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=45.73 E-value=1.1e+02 Score=21.99 Aligned_cols=65 Identities=15% Similarity=0.196 Sum_probs=43.6
Q ss_pred CCCEEEEEEEEEEcCcEE-EEEC-CEEEEeecCC-CCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 99 SGFIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQ-MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~se-ls~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
..-.+.|+|.....++.| |.+. |..-.-+++- |... .....+||.|.+.....|.++++|....+
T Consensus 5 d~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~------------~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 5 DEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKN------------RIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred cccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchhe------------eEEeCCCCEEEEEecccccccccEEEEec
Confidence 345679999999988765 8887 7544444322 1110 11234899999999999888888876544
No 235
>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=44.81 E-value=89 Score=23.93 Aligned_cols=50 Identities=18% Similarity=0.337 Sum_probs=37.4
Q ss_pred ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeC
Q 022938 187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDR 248 (289)
Q Consensus 187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~ 248 (289)
..|.+|.| ...-+||+++ | +..+.|....... +.|..|..|.+++...+-
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG---~--KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlEL 76 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFG---G--KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLEL 76 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeC---C--ceeEEEecccccc-------cccccCCEEEEEECCHhh
Confidence 46667777 5668999995 4 6889998765432 458889999999987754
No 236
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.95 E-value=21 Score=30.94 Aligned_cols=85 Identities=14% Similarity=0.196 Sum_probs=53.4
Q ss_pred HHHHHH--HhhcCCCEEEEEEEEEEcCc--EEEEEC--C---EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEE
Q 022938 89 DWKAAR--AYKESGFIYEGKIQGFNGGG--LLVRFF--S---LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVK 159 (289)
Q Consensus 89 ~~~~l~--~~~~~G~iv~g~V~~v~~~G--~~V~l~--g---v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vk 159 (289)
.|.++. ...+.|+++-|+.....+-| ++|+++ | .++++|.-++....- ..|-..+...+-.-.-..++|.
T Consensus 63 efgei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~g-ekpvrqi~r~FG~V~~lPveV~ 141 (247)
T COG4044 63 EFGEIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFG-EKPVRQIIRRFGWVDHLPVEVE 141 (247)
T ss_pred HhCCCCccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccC-CCcHHHHHHHcCCcccCceEEE
Confidence 444444 45689999999999999755 555554 2 578999888866553 4451111112222346678888
Q ss_pred EEEEecCCcEEEEEe
Q 022938 160 VIQANEEMKKLVFSE 174 (289)
Q Consensus 160 Vl~vd~~~~ri~lS~ 174 (289)
|.+++...+.|-+-+
T Consensus 142 V~evnk~~~EIea~l 156 (247)
T COG4044 142 VNEVNKLAQEIEARL 156 (247)
T ss_pred EEeccchhhhhhhhh
Confidence 988886555444433
No 237
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=43.11 E-value=79 Score=28.39 Aligned_cols=103 Identities=12% Similarity=0.046 Sum_probs=66.0
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF 172 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l 172 (289)
-+.|+++-|+|..|..+-.-|+++ ...+.++.+-+...-. .+...+.++...-+..|+.+.+.|-++- ..+.+.|
T Consensus 83 pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~-~dGs~sL 161 (301)
T KOG3013|consen 83 PEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF-HDGSLSL 161 (301)
T ss_pred CccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhc-cCCeEEE
Confidence 389999999999999999999999 7999998887653211 0111111110112338999988887775 3455555
Q ss_pred EeecchhhhcccccccccEEEe--------------eeeeEEEEEe
Q 022938 173 SEKDAVWNKYSSRVNVEDIFVG--------------RDYGAFIHLR 204 (289)
Q Consensus 173 S~k~~~~~~~~~~~~~G~iv~G--------------~~~G~fV~i~ 204 (289)
-.+.. .+-++..|..+.- .+.|+=|-++
T Consensus 162 hTRS~----KYGKL~~G~lvkVpp~Lvkr~K~hfh~lp~g~~vIlG 203 (301)
T KOG3013|consen 162 HTRSL----KYGKLGQGILVKVPPALVKRSKTHFHNLPGGVDVILG 203 (301)
T ss_pred Eecch----hcccccCceEEEeCHHHhhhhhhhhccCCCCeEEEEe
Confidence 44432 3344566665554 4577777775
No 238
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=41.94 E-value=4.7e+02 Score=28.08 Aligned_cols=80 Identities=19% Similarity=0.052 Sum_probs=43.9
Q ss_pred ccCCCeEEEEEEEEeCCCCeEe------eeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEE-cCc
Q 022938 42 ERICQRNLCPVGKFSTNAAKIT------PTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFN-GGG 114 (289)
Q Consensus 42 ~~vG~~v~~~Vl~~d~~~~~i~------ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~-~~G 114 (289)
|..||.|++.+-+..-.++.+. +++.....+.+.+. +-...+|.+.+++|+.+...--..+ +.|
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl---------~~~~~eLrKyF~~GDhVKVi~G~~eG~tG 478 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPL---------EVPASELRKYFEPGDHVKVIAGRYEGDTG 478 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCcc---------ccchHhhhhhccCCCeEEEEeccccCCcc
Confidence 9999999988765544333221 11111111112211 1223456777999997664222222 569
Q ss_pred EEEEEC-CEEEEeecCC
Q 022938 115 LLVRFF-SLVGFLPFPQ 130 (289)
Q Consensus 115 ~~V~l~-gv~g~ip~se 130 (289)
++|++. +.-.|+.-..
T Consensus 479 lVvrVe~~~vi~~Sd~t 495 (1024)
T KOG1999|consen 479 LVVRVEQGDVILLSDLT 495 (1024)
T ss_pred eEEEEeCCeEEEEecCc
Confidence 999998 6666655443
No 239
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.26 E-value=71 Score=27.29 Aligned_cols=52 Identities=10% Similarity=0.021 Sum_probs=37.8
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
.+.|+|..+.+..++++++ |.+-++|.+.+..- | ..|+.+.+.+.-+-++..
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~~l-----~----------~~g~~~~l~t~~~vrEd~ 57 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPALI-----G----------GLGQRVRVFTHLHVREDA 57 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHHhc-----c----------cCCCeEEEEEEEEEecCC
Confidence 4689999999999999998 57777775554311 1 168999888876654443
No 240
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=40.68 E-value=75 Score=27.07 Aligned_cols=51 Identities=10% Similarity=-0.059 Sum_probs=37.4
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
.+.|+|..+.+..++++++ |.+-++|.+.+.. ...|+.+.+.+...-++..
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~~----------------l~~g~~v~l~t~~~vred~ 56 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYE----------------LNLEQKAQVFTHLVVREDA 56 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh----------------cCCCCeEEEEEEEEEecCC
Confidence 4689999999999999998 5677777555421 1258989888876654443
No 241
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=39.65 E-value=58 Score=20.93 Aligned_cols=32 Identities=16% Similarity=0.089 Sum_probs=24.0
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecC
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFP 129 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~s 129 (289)
++.|+++... ....+.-..++.+|..|++|.+
T Consensus 15 ~~~Gd~i~v~-~~~~~~W~~g~~~g~~G~~P~~ 46 (49)
T PF14604_consen 15 FKKGDVITVL-EKSDDGWWYGRNTGRTGLFPAN 46 (49)
T ss_dssp B-TTEEEEEE-EESSTSEEEEEETTEEEEEEGG
T ss_pred EcCCCEEEEE-EeCCCCEEEEEECCEEEEECHH
Confidence 5789998876 4445666778878999999965
No 242
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=38.46 E-value=1.5e+02 Score=22.67 Aligned_cols=48 Identities=8% Similarity=0.026 Sum_probs=35.7
Q ss_pred hhhhHHHHHHHhhcCCCEE------EEEEEEEEcCcEEEEEC-CEEEEeecCCCC
Q 022938 85 RSSADWKAARAYKESGFIY------EGKIQGFNGGGLLVRFF-SLVGFLPFPQMS 132 (289)
Q Consensus 85 ~~~~~~~~l~~~~~~G~iv------~g~V~~v~~~G~~V~l~-gv~g~ip~sels 132 (289)
.+.+..+++.+.+++|+.+ .|+|.++.+.-+.++++ |+.--+..+.+.
T Consensus 41 K~~k~~~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r~aI~ 95 (106)
T PRK05585 41 KRQKEHKKMLSSLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQKSAIA 95 (106)
T ss_pred HHHHHHHHHHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhHHhh
Confidence 3344557788889999987 79999999888888887 766555555443
No 243
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.01 E-value=84 Score=26.91 Aligned_cols=52 Identities=17% Similarity=0.126 Sum_probs=37.4
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
.++|+|..+.+..++++.+ |.+-++|.+.+..- | .+|+.+.+.+.-+-++..
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~~l-----~----------~~g~~v~l~t~~~vrEd~ 57 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLAAI-----G----------AIGDEVFLYTHLIVREDA 57 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHHh-----c----------cCCCeEEEEEEEEEecCC
Confidence 4689999999999999998 56777775543211 1 179999888876654443
No 244
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=36.91 E-value=51 Score=22.10 Aligned_cols=34 Identities=24% Similarity=0.524 Sum_probs=26.2
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCc
Q 022938 229 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264 (289)
Q Consensus 229 ~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p 264 (289)
+.+.+.+|+.+.++|++++ .+.+.|.+.....-|
T Consensus 8 ~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~~v~ 41 (54)
T PF02599_consen 8 VGESIVIGDDIEITVLEIS--GGQVKLGIDAPKEVP 41 (54)
T ss_dssp TT-EEEETTTEEEEEEEEE--TTEEEEEEEECTTSE
T ss_pred CCCEEEECCCEEEEEEEEc--CCEEEEEEECCCCCE
Confidence 4466778999999999998 688999988765433
No 245
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=36.46 E-value=38 Score=32.80 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=25.8
Q ss_pred CCCEEEEEEEEEecCCcEEEEEeecchhh
Q 022938 152 TGSIISVKVIQANEEMKKLVFSEKDAVWN 180 (289)
Q Consensus 152 vG~~V~vkVl~vd~~~~ri~lS~k~~~~~ 180 (289)
=|++|+..|.++|.++++..+|++.....
T Consensus 47 WGDEiEy~vV~fDd~~kk~rv~l~~e~iL 75 (640)
T KOG3754|consen 47 WGDEIEYMVVKFDDKNKKARVSLRAEKIL 75 (640)
T ss_pred ccceeEEEEEecccccceeeeeeeHHHHH
Confidence 69999999999999999999999986443
No 246
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=36.31 E-value=52 Score=24.18 Aligned_cols=32 Identities=28% Similarity=0.423 Sum_probs=20.8
Q ss_pred cccCCCCEEEEEEEEEeCC-------CCeEEEEEecCCC
Q 022938 231 DILNEGDEVRVKVIKIDRE-------KSRITLSIKQLEE 262 (289)
Q Consensus 231 ~~~~iGd~V~vkV~~id~e-------~~ri~lSlK~~~~ 262 (289)
..|++||+|.++++-.+.+ +..+.+.++....
T Consensus 9 ~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~g 47 (99)
T PF01835_consen 9 PIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPSG 47 (99)
T ss_dssp SEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETTS
T ss_pred cCcCCCCEEEEEEEEeccccccccccCCceEEEEECCCC
Confidence 5689999999998844443 2466677666543
No 247
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=32.82 E-value=1.3e+02 Score=19.51 Aligned_cols=38 Identities=26% Similarity=0.247 Sum_probs=27.8
Q ss_pred hcccccccccEEEe-eeeeEEEEEecCCCceeEEEEEEccCcC
Q 022938 181 KYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVS 222 (289)
Q Consensus 181 ~~~~~~~~G~iv~G-~~~G~fV~i~~~~G~~~i~Glv~~sels 222 (289)
.....++.|..+.- ...|-++++. .+| ..|.|+.+.|+
T Consensus 16 ~vv~~l~~g~~v~v~~~~~~W~~V~-~~g---~~GWv~~~~lw 54 (55)
T PF06347_consen 16 PVVARLEPGVPVRVIECRGGWCKVR-ADG---RTGWVHKSLLW 54 (55)
T ss_pred CEEEEECCCCEEEEEEccCCeEEEE-ECC---eEEeEEeeecc
Confidence 34566777877777 6677777776 466 89999988774
No 248
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=32.29 E-value=89 Score=22.72 Aligned_cols=46 Identities=20% Similarity=0.261 Sum_probs=33.1
Q ss_pred ccCCCCEEEEEEE----------E---EeCCCCeEEEEEecCCCCchhHHhhhhCCCCh
Q 022938 232 ILNEGDEVRVKVI----------K---IDREKSRITLSIKQLEEDPLLETLEKVIPQGL 277 (289)
Q Consensus 232 ~~~iGd~V~vkV~----------~---id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~ 277 (289)
.|.+||-|.+++- + .+.+++.+.+.+|.....+....+.+..+|+.
T Consensus 29 ~~~pGQ~v~v~~~~~~~~~~R~yS~~s~~~~~~~~~~~ik~~~~G~~S~~L~~l~~Gd~ 87 (99)
T PF00970_consen 29 DFKPGQFVSVRVPINGKQVSRPYSPASSPDDKGYLEFAIKRYPNGRVSRYLHQLKPGDE 87 (99)
T ss_dssp SSTTT-EEEEEEEETTEEEEEEEEBCSSTTSSSEEEEEEEECTTSHHHHHHHTSCTTSE
T ss_pred ccCcceEEEEEEccCCcceecceeEeeecCCCCcEEEEEEeccCCHHHHHHHhCCCCCE
Confidence 4777888887777 1 12345688999999877778888888888875
No 249
>PRK01712 carbon storage regulator; Provisional
Probab=32.16 E-value=94 Score=21.67 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=26.2
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCC
Q 022938 229 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 263 (289)
Q Consensus 229 ~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~ 263 (289)
+.+.+.+||.++++|+.+. .+.+.|++..-..-
T Consensus 8 ~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~~v 40 (64)
T PRK01712 8 VGESLMIGDDIEVTVLGVK--GNQVRIGINAPKEV 40 (64)
T ss_pred CCCEEEeCCCEEEEEEEEe--CCEEEEEEECCCCc
Confidence 4466778999999999997 67899988775443
No 250
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=31.79 E-value=1.1e+02 Score=21.02 Aligned_cols=36 Identities=17% Similarity=0.166 Sum_probs=28.7
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCC
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMS 132 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels 132 (289)
+..|..++|.|.+..++-++++.+|..-++-...+|
T Consensus 18 L~NG~~l~G~I~~fD~ftVll~~~g~qqLIYKhAIS 53 (61)
T cd01716 18 LVNGVQLKGQIESFDNFTVLLESDGKQQLVYKHAIS 53 (61)
T ss_pred EeCCcEEEEEEEEEcceEEEEEECCcEEEEEeeeeE
Confidence 468999999999999999999988755555544443
No 251
>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=31.70 E-value=1.4e+02 Score=19.38 Aligned_cols=47 Identities=23% Similarity=0.179 Sum_probs=26.3
Q ss_pred EEEEEEEcCcEEEEEC-C-EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 105 GKIQGFNGGGLLVRFF-S-LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 105 g~V~~v~~~G~~V~l~-g-v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
|+|....+.-.|+... + -+.|+|.+.+.. .. . ....|+.|.|++..-
T Consensus 2 G~i~~~~~g~gfv~~~~~~~~i~v~~~~~~~-~~-~----------~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQG-GL-K----------SLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCeeEEecCCCCccEEEEhHHhhc-CC-C----------cCCCCCEEEEEEEEc
Confidence 5555555432344444 3 578888665422 10 0 123799999999753
No 252
>PF09628 YvfG: YvfG protein; InterPro: IPR018590 Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. ; PDB: 2GSV_A 2JS1_B.
Probab=31.37 E-value=30 Score=23.69 Aligned_cols=14 Identities=7% Similarity=0.375 Sum_probs=10.9
Q ss_pred CChHHHHHHHhhhh
Q 022938 275 QGLEPYLKSFYKKM 288 (289)
Q Consensus 275 g~~~~~~~~~~~~~ 288 (289)
-+-.||||+||+..
T Consensus 23 ~~ki~AmNaYYr~V 36 (68)
T PF09628_consen 23 EDKIHAMNAYYRSV 36 (68)
T ss_dssp S-CCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 56789999999854
No 253
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.16 E-value=1.3e+02 Score=25.73 Aligned_cols=51 Identities=14% Similarity=0.066 Sum_probs=36.9
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
.+.|+|..+.+..++++.+ |.+-++|.+.+.. ...|+.+.+.+.-+-++..
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~~----------------l~~g~~v~l~t~~~vrEd~ 56 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLAR----------------LVEGQEAELHTRLVVREDA 56 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHHHHH----------------cCCCCeEEEEEEEEEccCC
Confidence 4689999999999999998 5667777443321 1279999888876655543
No 254
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=31.12 E-value=85 Score=26.82 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=30.7
Q ss_pred EEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC-CeEEEEEe
Q 022938 212 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK-SRITLSIK 258 (289)
Q Consensus 212 i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~-~ri~lSlK 258 (289)
+.|+++..+.. +.+.|++|+.+++.+.++..+. +.+.+|.-
T Consensus 2 ~~~~l~~~~~~------~~e~~~~g~ri~~~~~~v~~~~~g~~~~srt 43 (190)
T COG0195 2 VEAILPKREQI------PGENFKVGDRIRALLYEVQKEAKGQIELSRT 43 (190)
T ss_pred ceeEcchhhcC------CCcccccCcEEEEEEeeeeecCcccEEEEec
Confidence 56888877664 4578999999999999998643 44666643
No 255
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.63 E-value=1.4e+02 Score=25.34 Aligned_cols=46 Identities=11% Similarity=0.142 Sum_probs=34.1
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
.++|+|..+.+..++++.+ |.+-++|.+.+.. + ..|+.+.+.+..+
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~~----------l------~~g~~v~l~t~~~ 51 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLST----------C------KIGDNIKLYIETY 51 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh----------h------CCCCeEEEEEEEE
Confidence 4789999999999999998 4666777544321 1 2799998888643
No 256
>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=29.59 E-value=1.5e+02 Score=20.32 Aligned_cols=56 Identities=13% Similarity=0.132 Sum_probs=33.2
Q ss_pred EEEEEEEEEEcCcEE-EEEC-CE--EEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938 102 IYEGKIQGFNGGGLL-VRFF-SL--VGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV 171 (289)
Q Consensus 102 iv~g~V~~v~~~G~~-V~l~-gv--~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~ 171 (289)
.+.|.|++...++.| |.+. |. .+.+|-. +. .......|+.|.|-+...|..+++|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK-~r-------------~~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPGK-FR-------------KRIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-HH-HH-------------TCC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccc-ee-------------eeEecCCCCEEEEEecccCCCeEEEE
Confidence 457899999988765 7777 64 4555533 21 11223489999887765554444443
No 257
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=28.69 E-value=1.8e+02 Score=20.85 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=19.9
Q ss_pred EEEEEEEEEcCcEEEEECCEEEEeec
Q 022938 103 YEGKIQGFNGGGLLVRFFSLVGFLPF 128 (289)
Q Consensus 103 v~g~V~~v~~~G~~V~l~gv~g~ip~ 128 (289)
+.|+|.++.+..+.|+++|++--+..
T Consensus 5 iP~~V~~i~~~~A~v~~~G~~~~v~l 30 (76)
T TIGR00074 5 IPGQVVEIDENIALVEFCGIKRDVSL 30 (76)
T ss_pred cceEEEEEcCCEEEEEcCCeEEEEEE
Confidence 57889999988899999975544443
No 258
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=28.55 E-value=90 Score=24.34 Aligned_cols=23 Identities=35% Similarity=0.562 Sum_probs=18.4
Q ss_pred ccCCCCEEEEEEEEEeCCCCeEE
Q 022938 232 ILNEGDEVRVKVIKIDREKSRIT 254 (289)
Q Consensus 232 ~~~iGd~V~vkV~~id~e~~ri~ 254 (289)
.|.+||+|++.|.=++.++.|+.
T Consensus 20 ~f~~GDtvrv~vki~Eg~keR~Q 42 (115)
T COG0335 20 SFRPGDTVRVHVKIVEGSKERVQ 42 (115)
T ss_pred CCCCCCEEEEEEEEEeCCeEEEe
Confidence 48999999998887777676664
No 259
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.53 E-value=1.6e+02 Score=25.29 Aligned_cols=50 Identities=8% Similarity=-0.090 Sum_probs=34.9
Q ss_pred EEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938 102 IYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~ 167 (289)
-++|+|..+.+..++++.+| .+-++|.+.+.. ...|+.+.+.+.-.-++.
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~~~----------------l~~g~~v~l~t~~~vrED 55 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCLAE----------------LRLLEDVEILTYLHTRED 55 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHHHh----------------cCCCCcEEEEEEEEEecC
Confidence 46899999999999999984 666676543321 126888888875443333
No 260
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=28.21 E-value=1.8e+02 Score=19.25 Aligned_cols=49 Identities=24% Similarity=0.281 Sum_probs=32.9
Q ss_pred cCCCEEEEEEEEEEcCcEE-EEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938 98 ESGFIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE 165 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~ 165 (289)
..|++++..|.+..+.|.. -... +..-++|... | .+|+.++|+|.+..+
T Consensus 3 ~~G~~~~VlVe~~~~~g~~~gr~~~~~~V~v~~~~---------~----------~iG~~v~v~I~~~~~ 53 (61)
T PF01938_consen 3 YVGKTLEVLVEELGDEGQGIGRTDNGKVVFVPGGL---------P----------LIGEFVKVRITKAKK 53 (61)
T ss_dssp -TTEEEEEEEEEE-TTSEEEEEET-TEEEEETT-----------T------------TEEEEEEEEEE-S
T ss_pred cCCcEEEEEEEEecCCCEEEEEeCCCeEEEECCCC---------C----------CCCCEEEEEEEEeeC
Confidence 5899999999999976654 4455 6777777441 1 169999999998853
No 261
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=28.04 E-value=3.9e+02 Score=22.91 Aligned_cols=47 Identities=26% Similarity=0.331 Sum_probs=35.0
Q ss_pred hcCCCEEEEEEEEEEcCcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938 97 KESGFIYEGKIQGFNGGGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd 164 (289)
++.|+.++++|.++...|- +..++|...|+|.. .+|+.|.+++....
T Consensus 145 ~~~~e~~~v~Ie~l~~~G~GVak~~g~~vfV~ga---------------------lpGE~V~vri~k~k 192 (201)
T PRK12336 145 IEEGKTYEVEITGTGRKGDGVAKKGKYTIFVPGA---------------------KKGEVVKVKIKKIS 192 (201)
T ss_pred CccCCEEEEEEEEccCCCceEEEECCEEEEeCCC---------------------CCCCEEEEEEEEec
Confidence 4678889999999997664 34456777777722 28999999998774
No 262
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=27.69 E-value=3.2e+02 Score=21.90 Aligned_cols=58 Identities=10% Similarity=0.042 Sum_probs=39.5
Q ss_pred cCCCEEEEEEEEEEcCc---------EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938 98 ESGFIYEGKIQGFNGGG---------LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G---------~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~ 167 (289)
..|.+.+-+|..+...| ++|+++ +-..+.++.. .+|++. .+|++|++.+......+
T Consensus 62 ~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~-------~~p~~v-------~iGm~V~~v~~~~~~~~ 127 (140)
T COG1545 62 GEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD-------VDPDDV-------EIGMKVEAVFRKREEDG 127 (140)
T ss_pred CCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe-------cCcccc-------cCCCEEEEEEEEccccC
Confidence 57888888888888765 567787 4556666554 122221 39999999998776555
Q ss_pred cE
Q 022938 168 KK 169 (289)
Q Consensus 168 ~r 169 (289)
..
T Consensus 128 ~~ 129 (140)
T COG1545 128 GR 129 (140)
T ss_pred Cc
Confidence 43
No 263
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=27.51 E-value=1.5e+02 Score=19.94 Aligned_cols=28 Identities=14% Similarity=0.000 Sum_probs=19.0
Q ss_pred CcccccCCCeE-----------EEEEEEEeCCCCeEeee
Q 022938 38 PLIIERICQRN-----------LCPVGKFSTNAAKITPT 65 (289)
Q Consensus 38 p~~~~~vG~~v-----------~~~Vl~~d~~~~~i~ls 65 (289)
|+.+|..|+.| +++|+++|..+++..+-
T Consensus 2 p~~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~ 40 (55)
T PF09465_consen 2 PSRKFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVL 40 (55)
T ss_dssp SSSSS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEE
T ss_pred CcccccCCCEEEEECCCCCcEEEEEEEEecccCceEEEE
Confidence 56677888776 56788888877766655
No 264
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=27.33 E-value=1.3e+02 Score=17.35 Aligned_cols=16 Identities=44% Similarity=0.684 Sum_probs=12.0
Q ss_pred EEEEEEEeCCCCeEEE
Q 022938 240 RVKVIKIDREKSRITL 255 (289)
Q Consensus 240 ~vkV~~id~e~~ri~l 255 (289)
.++|.++|+++.++.+
T Consensus 16 ~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 16 IGKIVEIDRSKVRVTV 31 (32)
T ss_dssp EEEEEEEETTTTEEEE
T ss_pred eEEEEEEECCCCEEEE
Confidence 4689999987767654
No 265
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=27.29 E-value=1.5e+02 Score=25.16 Aligned_cols=50 Identities=10% Similarity=0.060 Sum_probs=36.1
Q ss_pred EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecC
Q 022938 102 IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEE 166 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~ 166 (289)
.+.|+|..+.+..++++.+ |.+-++|...+..-. ..|+.+.+.+...-++
T Consensus 4 ~i~G~i~~~~~~~~ii~~~gvGY~v~~~~~~~~~l~---------------~~~~~~~l~~~~~~rd 55 (192)
T PRK00116 4 YLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLYELP---------------EVGEEVKLYTHLVVRE 55 (192)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHhcc---------------CCCCeEEEEEEEEEec
Confidence 4689999999999999998 577777755543210 1688888888755433
No 266
>COG1278 CspC Cold shock proteins [Transcription]
Probab=26.62 E-value=1.4e+02 Score=21.02 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=31.3
Q ss_pred EEEEEEEEc-CcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 104 EGKIQGFNG-GGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 104 ~g~V~~v~~-~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
+|+|+-.++ .|. |+.-. +-+.|+|+|.+...-. +.+ ..||+|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~-----~~L------~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGF-----RTL------REGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCC-----ccc------CCCCEEEEEEec
Confidence 577777773 333 44444 4899999999854332 112 389999998863
No 267
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=26.61 E-value=1.1e+02 Score=19.79 Aligned_cols=35 Identities=23% Similarity=0.293 Sum_probs=26.8
Q ss_pred cCCCEEEEEEEEEEc-CcEEEEEC--CEEEEeecCCCC
Q 022938 98 ESGFIYEGKIQGFNG-GGLLVRFF--SLVGFLPFPQMS 132 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~-~G~~V~l~--gv~g~ip~sels 132 (289)
..|..+.|+|.++.+ ..+.|.+- |-..-++.+++.
T Consensus 14 ~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~ 51 (57)
T smart00333 14 EDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLR 51 (57)
T ss_pred CCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHee
Confidence 379999999999998 66666653 677778777654
No 268
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.37 E-value=2.6e+02 Score=20.41 Aligned_cols=43 Identities=14% Similarity=0.164 Sum_probs=29.7
Q ss_pred EEEEEEEEEcCc--EEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEE
Q 022938 103 YEGKIQGFNGGG--LLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKV 160 (289)
Q Consensus 103 v~g~V~~v~~~G--~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkV 160 (289)
+.|+|..+.+.. +.|+++|+.-=+..+-+.... .+||.|-+-+
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~~v---------------~~GdyVLVHv 49 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGGVKREVNLDLVGEEV---------------KVGDYVLVHV 49 (82)
T ss_pred cccEEEEEeCCCceEEEEeccEeEEEEeeeecCcc---------------ccCCEEEEEe
Confidence 578999999753 799999977666555443211 2899886655
No 269
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=26.02 E-value=1.6e+02 Score=20.33 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=26.2
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEECCEEEEeec
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPF 128 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~ 128 (289)
+..|..++|.|.+..++-++++.+|-.-++-.
T Consensus 22 L~nG~~l~G~I~~fD~ftVll~~~g~qqLIYK 53 (61)
T TIGR02383 22 LVNGVQLKGVIESFDNFTVLLESQGKQQLIYK 53 (61)
T ss_pred EeCCcEEEEEEEEEeeeEEEEEECCcEEEEEE
Confidence 46899999999999999999998875445443
No 270
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=25.98 E-value=1.4e+02 Score=19.39 Aligned_cols=34 Identities=18% Similarity=0.083 Sum_probs=22.8
Q ss_pred hcCCCEEEEEEEEEE-cCcEEEEECCEEEEeecCCC
Q 022938 97 KESGFIYEGKIQGFN-GGGLLVRFFSLVGFLPFPQM 131 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~-~~G~~V~l~gv~g~ip~sel 131 (289)
++.|+++... ..-. +.......+|..|++|.+-+
T Consensus 18 ~~~Gd~i~v~-~~~~~~~ww~~~~~g~~G~~P~~~v 52 (55)
T PF07653_consen 18 FKKGDVIEVL-GEKDDDGWWLGENNGRRGWFPSSYV 52 (55)
T ss_dssp B-TTEEEEEE-EEECSTSEEEEEETTEEEEEEGGGE
T ss_pred EecCCEEEEE-EeecCCCEEEEEECCcEEEEcHHHE
Confidence 5789988754 1333 34467777899999997654
No 271
>PRK00568 carbon storage regulator; Provisional
Probab=24.90 E-value=1.3e+02 Score=21.66 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=25.4
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEecCCC
Q 022938 229 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 262 (289)
Q Consensus 229 ~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~ 262 (289)
..+.+.+||.++++|++++ ++.+.+.+..-..
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISID--RGSVRLGFEAPES 39 (76)
T ss_pred CCCeEEeCCCeEEEEEEEc--CCEEEEEEECCCC
Confidence 3466778999999999997 6789888876543
No 272
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=24.67 E-value=1.6e+02 Score=22.18 Aligned_cols=40 Identities=13% Similarity=0.259 Sum_probs=30.9
Q ss_pred CCCEEEEEEEEEecCCcEEEEEeecchhhhcccccccccEEE
Q 022938 152 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFV 193 (289)
Q Consensus 152 vG~~V~vkVl~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~ 193 (289)
.|....+.+ .|.+++.|.++.-....+.+...+++|+++.
T Consensus 33 ~g~~~~~~l--~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~ 72 (104)
T cd04474 33 EGKLFSFDL--LDEDGGEIRATFFNDAVDKFYDLLEVGKVYY 72 (104)
T ss_pred CcEEEEEEE--EECCCCEEEEEEehHHHHHhhcccccccEEE
Confidence 355555555 5766889999988877788888999999884
No 273
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.62 E-value=61 Score=28.12 Aligned_cols=73 Identities=22% Similarity=0.312 Sum_probs=45.9
Q ss_pred cccccccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc----ccccC--CCCEEEEEEEEEeC
Q 022938 182 YSSRVNVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----RDILN--EGDEVRVKVIKIDR 248 (289)
Q Consensus 182 ~~~~~~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~----~~~~~--iGd~V~vkV~~id~ 248 (289)
.+.+++.|+++.| .-||++|.++.. |---..+++|.-+|....-..| ...|- .--.|+|-|..+|.
T Consensus 69 sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~-~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk 147 (247)
T COG4044 69 SLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVL-GPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNK 147 (247)
T ss_pred ccccCCCCcEEEEEEeeeccceeEEEcccccc-CCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccc
Confidence 3588999999999 678889988521 1002567888776654433222 33332 34567777888887
Q ss_pred CCCeEEE
Q 022938 249 EKSRITL 255 (289)
Q Consensus 249 e~~ri~l 255 (289)
..+.|..
T Consensus 148 ~~~EIea 154 (247)
T COG4044 148 LAQEIEA 154 (247)
T ss_pred hhhhhhh
Confidence 5555543
No 274
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.36 E-value=1.8e+02 Score=24.63 Aligned_cols=50 Identities=16% Similarity=0.011 Sum_probs=35.3
Q ss_pred EEEEEEEEEEcCcEEEE-EC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938 102 IYEGKIQGFNGGGLLVR-FF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~-l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~ 167 (289)
-++|+|..+.+..++++ .+ |.+-++|.+.+.. ...|+.+...+.-.-++.
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~~~~~~~----------------l~~g~~v~l~t~~~vrEd 56 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFISLFCSAK----------------IQKGEKHELFITQIIKED 56 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEecHHHHHH----------------cCCCCeEEEEEEEEEecC
Confidence 46899999999999999 57 5677777544321 127998888886554443
No 275
>PTZ00320 ribosomal protein L14; Provisional
Probab=24.21 E-value=4.5e+02 Score=22.33 Aligned_cols=77 Identities=17% Similarity=0.237 Sum_probs=47.1
Q ss_pred eeEeCCCCCCccceeEeecccccccCCcccccCCCe----EEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhh
Q 022938 12 TCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQR----NLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSS 87 (289)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~----v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~ 87 (289)
.|-|-++|++--....+ .....-.+||. |.|-|.+..+..+.- -.
T Consensus 67 ~VaDNSGAK~V~CIkVl--------~~rr~A~IGDi~~~~IvVsVKka~P~~~~~-~~---------------------- 115 (188)
T PTZ00320 67 HCVDNTNCKHVRLISKA--------TAERFAHCRVFPAVAHRVSVQRFKSGRGEV-SR---------------------- 115 (188)
T ss_pred EEEeCCCCcEEEEEEEe--------cCCCceeeccccCceEEEEEeecccCcccc-cc----------------------
Confidence 35555555543333333 22245689999 888887766643300 00
Q ss_pred hHHHHHHHhhcCCCEEEEEEEEEEc-----CcEEEEEC-CEEEEe
Q 022938 88 ADWKAARAYKESGFIYEGKIQGFNG-----GGLLVRFF-SLVGFL 126 (289)
Q Consensus 88 ~~~~~l~~~~~~G~iv~g~V~~v~~-----~G~~V~l~-gv~g~i 126 (289)
...+.|+++.|.|++... .|.++.++ +.-.+|
T Consensus 116 -------~kVKKG~V~kAVIVRTKK~irR~DGs~IrFDdNAaVLI 153 (188)
T PTZ00320 116 -------HRVKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILM 153 (188)
T ss_pred -------CceecCCEEEEEEEEECcccCCCCCCEEEeCCcEEEEE
Confidence 014689999999999873 69999998 443333
No 276
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=24.12 E-value=1.5e+02 Score=23.69 Aligned_cols=47 Identities=17% Similarity=0.046 Sum_probs=32.8
Q ss_pred CCCEEEEEEEEEEcCc--EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEE
Q 022938 99 SGFIYEGKIQGFNGGG--LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKV 160 (289)
Q Consensus 99 ~G~iv~g~V~~v~~~G--~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkV 160 (289)
.-..+.|++.+..... +.|+|. |. .-+...++ ..++.++||.|++.=
T Consensus 21 ~~~yYPa~~~~~~~~~~~~~V~Fedg~-~~i~~~dv--------------~~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 21 NLKYYPATCVGSGVDRDRSLVRFEDGT-YEIKNEDV--------------KYLDLRIGDTVKVDG 70 (131)
T ss_pred CCeEeeEEEEeecCCCCeEEEEEecCc-eEeCcccE--------------eeeeeecCCEEEECC
Confidence 5567799999987555 899998 66 55665554 224556999987644
No 277
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=24.07 E-value=1.4e+02 Score=25.20 Aligned_cols=30 Identities=30% Similarity=0.531 Sum_probs=23.8
Q ss_pred cccCCCCEEEE----------EEEEEeCCCCeEEEEEecC
Q 022938 231 DILNEGDEVRV----------KVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 231 ~~~~iGd~V~v----------kV~~id~e~~ri~lSlK~~ 260 (289)
..|.+||.|++ +|.++|.+++++.+.+-..
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~if 161 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIF 161 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEe
Confidence 45778888764 8999999999998877553
No 278
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=24.03 E-value=1.1e+02 Score=21.88 Aligned_cols=29 Identities=17% Similarity=0.453 Sum_probs=23.3
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQL 260 (289)
Q Consensus 230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~ 260 (289)
.+.+.+||-|.++|++++ ++.+.+.+...
T Consensus 9 ~Esi~IgddI~itVl~i~--gnqVkiGi~AP 37 (73)
T COG1551 9 GESIMIGDDIEITVLSIK--GNQVKIGINAP 37 (73)
T ss_pred CceEEecCCeEEEEEEEc--CCeEEEeecCC
Confidence 456779999999999997 56777777654
No 279
>PF14444 S1-like: S1-like
Probab=23.31 E-value=2.5e+02 Score=19.15 Aligned_cols=15 Identities=13% Similarity=0.505 Sum_probs=11.2
Q ss_pred EEEEEEEEEEc-CcEE
Q 022938 102 IYEGKIQGFNG-GGLL 116 (289)
Q Consensus 102 iv~g~V~~v~~-~G~~ 116 (289)
+++|.|++..+ +|++
T Consensus 3 ~~~GvVTkl~~~yG~I 18 (58)
T PF14444_consen 3 VFTGVVTKLCDDYGFI 18 (58)
T ss_pred eEEEEEEEEeCCcceE
Confidence 57999999985 5543
No 280
>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=23.21 E-value=2.9e+02 Score=19.79 Aligned_cols=61 Identities=18% Similarity=0.201 Sum_probs=39.6
Q ss_pred EEEEEEEEEcCcEE-EEEC-CEE--EEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc
Q 022938 103 YEGKIQGFNGGGLL-VRFF-SLV--GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA 177 (289)
Q Consensus 103 v~g~V~~v~~~G~~-V~l~-gv~--g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~ 177 (289)
+.|+|+....++.| |.+. |.. +.+|-. +. ...-...|+.|.|.....|..+++|+--....
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK-~r-------------k~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGK-MR-------------KRVWINEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchh-hc-------------ccEEEcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 46899999988875 6776 644 444422 11 11223489999999888877777776655443
No 281
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=22.65 E-value=2e+02 Score=26.06 Aligned_cols=47 Identities=23% Similarity=0.265 Sum_probs=37.3
Q ss_pred hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938 97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163 (289)
Q Consensus 97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v 163 (289)
-.+|++-+|.|.+..+.|.+|++| +--+.++-. + .+|.+|.++|.+.
T Consensus 103 ~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~~--------------~------~~~~RvTvri~~~ 150 (272)
T COG2106 103 PKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSSP--------------A------PPGARVTVRIISR 150 (272)
T ss_pred ccceeecceEEEEecCCceEEEecCCcceeccCC--------------C------CCCceEEEEEEec
Confidence 368999999999999999999998 555555421 1 2899999999866
No 282
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=22.24 E-value=2.4e+02 Score=24.29 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=37.5
Q ss_pred EEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938 102 IYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~ 167 (289)
-+.|+|+.+.+.-++|+.+| -...+|.+.+..- | .+|+.+...+..+-++.
T Consensus 4 ~l~G~v~~~~~~~ivie~~GVGY~i~~~~~~~~~l-----~----------~~g~~~~l~t~~~vREd 56 (201)
T COG0632 4 YLRGKVTEKNPDYIVIEVNGVGYEINVPMRTLAEL-----P----------EVGEEVKLFTHLVVRED 56 (201)
T ss_pred eeEEEEEEecCCEEEEEeCCEEEEEEcChHHHhhc-----c----------cCCCeEEEEEEEeehhh
Confidence 36899999999999999984 6666775543211 1 27999999988776554
No 283
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.15 E-value=2e+02 Score=24.38 Aligned_cols=51 Identities=12% Similarity=0.020 Sum_probs=36.3
Q ss_pred EEEEEEEEEEcCcEEEEE-C--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938 102 IYEGKIQGFNGGGLLVRF-F--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK 168 (289)
Q Consensus 102 iv~g~V~~v~~~G~~V~l-~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ 168 (289)
-+.|+|..+.+..++++. + |.+-++|.+.+.. + ..|+.+.+.+.-+-++..
T Consensus 4 ~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~~~----------l------~~g~~v~l~t~~~vrEd~ 57 (188)
T PRK14606 4 GISGRVLKKSGNVLLVETKSGVVFEIVCDVQTSEE----------V------EEGGECFLHTFLSVSQDG 57 (188)
T ss_pred eEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHHHH----------c------CCCCeEEEEEEEEEecCC
Confidence 468999999999999994 4 6777777444321 1 279999998876654443
No 284
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=22.15 E-value=1.7e+02 Score=18.64 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=18.9
Q ss_pred cCCCEEEEEEEEEEcCcE-EEEEC
Q 022938 98 ESGFIYEGKIQGFNGGGL-LVRFF 120 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G~-~V~l~ 120 (289)
..++.++|++..+.+.|. +|+..
T Consensus 10 ~~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 10 TGDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp ETSCEEEEEEEEEETTSEEEEEET
T ss_pred ECCeEEEEEEEEECCCCEEEEEEC
Confidence 468889999999998886 56666
No 285
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.88 E-value=2.9e+02 Score=19.31 Aligned_cols=61 Identities=10% Similarity=0.103 Sum_probs=34.0
Q ss_pred CEEEEEEEEEEcCc-EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938 101 FIYEGKIQGFNGGG-LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF 172 (289)
Q Consensus 101 ~iv~g~V~~v~~~G-~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l 172 (289)
-...|.|++...++ ..|... |..-.++..--- ... ...-.+||.|.+.+...+...++|+.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gkl-----r~~------~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELENGHEVLAHISGKM-----RKN------YIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccce-----eeC------CcccCCCCEEEEEEcccCCCeEEEEE
Confidence 35679999988774 456554 533333321100 000 00123899999998766655666654
No 286
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.35 E-value=2.1e+02 Score=24.54 Aligned_cols=51 Identities=20% Similarity=0.184 Sum_probs=34.6
Q ss_pred EEEEEEEEEEcCcE-EEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938 102 IYEGKIQGFNGGGL-LVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167 (289)
Q Consensus 102 iv~g~V~~v~~~G~-~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~ 167 (289)
.+.|+|..+.+..+ +++++ |.+-++|.+.+..- | ..|+.+...+.-+-++.
T Consensus 4 ~l~G~v~~~~~~~~vviev~GvGY~v~i~~~~~~~l-----~----------~~g~~v~l~t~~~vrEd 57 (203)
T PRK14602 4 YLEGRVAERRENSCVVLTPGGVGYEVFLPAHTLARL-----P----------EKGGQVSFFVHTVVRED 57 (203)
T ss_pred eEEEEEEEEcCCcEEEEEeCCEEEEEEcCHHHHHHh-----c----------cCCCeEEEEEEEEEecC
Confidence 46899999988755 68998 56677775443211 1 16999988887665444
No 287
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=21.12 E-value=1.9e+02 Score=20.67 Aligned_cols=40 Identities=8% Similarity=0.192 Sum_probs=31.4
Q ss_pred CCCEEEEEEEEEecCCcEEEEEeecchhhhcccccccccEEE
Q 022938 152 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFV 193 (289)
Q Consensus 152 vG~~V~vkVl~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~ 193 (289)
.|..+.+.+ +|.++.+|.++......+.....+++|.++.
T Consensus 17 ~~~~~~miL--~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~ 56 (86)
T cd04480 17 SGESLEMVL--VDEKGNRIHATIPKRLAAKFRPLLKEGKWYT 56 (86)
T ss_pred CCcEEEEEE--EcCCCCEEEEEECHHHHHhhhhhceeCCEEE
Confidence 466666655 6777779999999887788888899998874
No 288
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=20.89 E-value=1.9e+02 Score=20.49 Aligned_cols=32 Identities=25% Similarity=0.575 Sum_probs=25.5
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEecCCC
Q 022938 229 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 262 (289)
Q Consensus 229 ~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~ 262 (289)
+.+.+.+||.++++|+.+. .+.+.|.+..-..
T Consensus 8 ~gE~I~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (69)
T TIGR00202 8 VNESIQIGDDIEVKVLSVK--GDQVKLGIEAPKE 39 (69)
T ss_pred CCCEEEeCCCEEEEEEEEc--CCeEEEEEECCCC
Confidence 4566788999999999997 6788888876543
No 289
>CHL00084 rpl19 ribosomal protein L19
Probab=20.78 E-value=1.2e+02 Score=23.91 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=16.7
Q ss_pred ccCCCCEEEEEEEEEeCCCCeEE
Q 022938 232 ILNEGDEVRVKVIKIDREKSRIT 254 (289)
Q Consensus 232 ~~~iGd~V~vkV~~id~e~~ri~ 254 (289)
.|++||+|++.+.-.+-++.|+.
T Consensus 22 ~f~~GDtV~V~~~i~eg~k~R~q 44 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNKERVQ 44 (117)
T ss_pred ccCCCCEEEEEEEEecCCeeEec
Confidence 48999999998866655555553
No 290
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=20.70 E-value=1.3e+02 Score=20.43 Aligned_cols=18 Identities=11% Similarity=0.342 Sum_probs=16.4
Q ss_pred EEEEEEEEEcCcEEEEEC
Q 022938 103 YEGKIQGFNGGGLLVRFF 120 (289)
Q Consensus 103 v~g~V~~v~~~G~~V~l~ 120 (289)
++|+|.++..+.++|++.
T Consensus 16 ~~G~V~kv~eNSVIVdIT 33 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDIT 33 (57)
T ss_pred cEEEEEEEecCcEEEEEE
Confidence 699999999999999984
No 291
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=20.34 E-value=3.2e+02 Score=21.42 Aligned_cols=92 Identities=22% Similarity=0.344 Sum_probs=53.5
Q ss_pred cCCCEEEEEEEEEEcCc-EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938 98 ESGFIYEGKIQGFNGGG-LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK 175 (289)
Q Consensus 98 ~~G~iv~g~V~~v~~~G-~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k 175 (289)
+.|--+.|+|.+..+.| ++|++. +-.--+|.+++-...... .. ...+||.|-+.
T Consensus 10 ~DG~YY~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~--~~------~L~~GD~VLA~---------------- 65 (124)
T PF15057_consen 10 EDGFYYPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAM--RH------SLQVGDKVLAP---------------- 65 (124)
T ss_pred CCCcEEeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcc--cC------cCCCCCEEEEe----------------
Confidence 57889999999987655 578995 666666666653221101 11 23489988665
Q ss_pred cchhhhcccccccccEEEe------eeeeEEEEEecCCCceeEEEEEEccCc
Q 022938 176 DAVWNKYSSRVNVEDIFVG------RDYGAFIHLRFPDGLYHLTGLVHVSEV 221 (289)
Q Consensus 176 ~~~~~~~~~~~~~G~iv~G------~~~G~fV~i~~~~G~~~i~Glv~~sel 221 (289)
|+..-..+-+|.++.| .+.-+-|.+ .+| ....++..++
T Consensus 66 ---~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f--~ng---~~~~vp~~~~ 109 (124)
T PF15057_consen 66 ---WEPDDCRYGPGTVIAGPERRASEDKEYTVRF--YNG---KTAKVPRGEV 109 (124)
T ss_pred ---cCcCCCEEeCEEEEECccccccCCceEEEEE--ECC---CCCccchhhE
Confidence 2222223778888776 333334444 355 5555555544
No 292
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=20.21 E-value=3.9e+02 Score=20.23 Aligned_cols=66 Identities=14% Similarity=0.130 Sum_probs=42.3
Q ss_pred CCEEEEEEEEEEcCcEE-EEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc
Q 022938 100 GFIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA 177 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~ 177 (289)
...+.|+|+....++.| |.+. |..-+++++- .. . ...-...|+.|.|.....|..+++|+.-...+
T Consensus 20 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G---K~--R-------k~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 87 (100)
T PRK04012 20 EGEVFGVVEQMLGANRVRVRCMDGVERMGRIPG---KM--K-------KRMWIREGDVVIVAPWDFQDEKADIIWRYTKP 87 (100)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch---hh--c-------ccEEecCCCEEEEEecccCCCEEEEEEEcCHH
Confidence 34468999999988876 6766 6544444221 00 0 11123489999999988887777777655543
No 293
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=20.13 E-value=4.5e+02 Score=23.43 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=30.2
Q ss_pred CCEEEEEEEEEEcCcEE----EEEC-C--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938 100 GFIYEGKIQGFNGGGLL----VRFF-S--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ 162 (289)
Q Consensus 100 G~iv~g~V~~v~~~G~~----V~l~-g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~ 162 (289)
.-.+.|+|.++...|.. ++++ | +.+.++.... +.+...+|+.|.+.+..
T Consensus 199 rN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~--------------~~L~L~~G~~V~a~iKa 254 (263)
T PRK10676 199 DNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEA--------------ARLSLQQGDAVTAYFNA 254 (263)
T ss_pred hheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHH--------------HhcCCCCCCEEEEEEEc
Confidence 45789999999876543 3443 3 4444443221 12334599999998863
Done!