Query 005707
Match_columns 681
No_of_seqs 284 out of 2114
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 12:32:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005707.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005707hhsearch_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 3.8E-47 8.2E-52 420.9 23.0 274 44-379 118-401 (541)
2 PRK13806 rpsA 30S ribosomal pr 100.0 2.3E-40 5E-45 367.8 26.6 274 44-377 128-415 (491)
3 PRK12269 bifunctional cytidyla 100.0 6E-39 1.3E-43 374.3 26.0 270 44-377 506-788 (863)
4 PRK12269 bifunctional cytidyla 100.0 1.4E-38 3.1E-43 371.1 26.4 274 45-377 414-701 (863)
5 COG0539 RpsA Ribosomal protein 100.0 8.9E-39 1.9E-43 354.5 22.6 268 44-377 205-485 (541)
6 PRK06299 rpsA 30S ribosomal pr 100.0 2.3E-37 5E-42 347.9 24.8 273 44-377 127-409 (565)
7 TIGR00717 rpsA ribosomal prote 100.0 5.8E-36 1.3E-40 332.5 25.5 272 45-377 114-395 (516)
8 TIGR00717 rpsA ribosomal prote 100.0 3.8E-35 8.2E-40 326.0 25.8 272 44-378 200-483 (516)
9 PRK06299 rpsA 30S ribosomal pr 100.0 2.7E-34 5.8E-39 323.1 25.1 269 44-377 214-496 (565)
10 PRK07899 rpsA 30S ribosomal pr 100.0 1.8E-34 3.9E-39 319.8 22.8 269 44-377 48-329 (486)
11 PRK07899 rpsA 30S ribosomal pr 100.0 1.2E-33 2.6E-38 313.3 23.8 232 45-338 136-369 (486)
12 PRK06676 rpsA 30S ribosomal pr 100.0 4.1E-32 8.8E-37 292.7 24.1 271 44-377 30-313 (390)
13 PRK06676 rpsA 30S ribosomal pr 100.0 1.1E-31 2.4E-36 289.3 23.4 237 44-341 118-356 (390)
14 PRK13806 rpsA 30S ribosomal pr 100.0 7.3E-32 1.6E-36 299.9 21.9 236 44-341 215-463 (491)
15 PRK00087 4-hydroxy-3-methylbut 100.0 7.6E-30 1.7E-34 292.0 26.0 270 45-377 316-598 (647)
16 PRK07400 30S ribosomal protein 100.0 2.6E-29 5.7E-34 266.1 23.4 224 44-340 44-273 (318)
17 PRK00087 4-hydroxy-3-methylbut 100.0 2.5E-29 5.5E-34 287.8 23.9 234 44-338 402-638 (647)
18 PRK07400 30S ribosomal protein 100.0 1E-27 2.2E-32 254.0 21.7 197 144-378 28-232 (318)
19 PTZ00248 eukaryotic translatio 99.7 1.3E-18 2.8E-23 184.3 -1.7 149 143-322 12-173 (319)
20 KOG1070 rRNA processing protei 99.7 1.8E-15 4E-20 178.9 23.1 293 52-408 1009-1332(1710)
21 KOG1070 rRNA processing protei 99.6 2.7E-15 5.8E-20 177.6 14.9 169 140-336 502-673 (1710)
22 COG1098 VacB Predicted RNA bin 99.6 3.2E-15 7E-20 138.4 5.8 80 144-224 2-81 (129)
23 PTZ00248 eukaryotic translatio 99.5 8.3E-15 1.8E-19 155.5 6.0 120 256-377 10-148 (319)
24 COG1098 VacB Predicted RNA bin 99.5 1.3E-14 2.9E-19 134.4 4.9 79 259-339 2-81 (129)
25 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 2.2E-13 4.8E-18 116.1 8.5 71 145-215 1-74 (74)
26 PF00575 S1: S1 RNA binding do 99.4 6E-13 1.3E-17 111.2 10.2 73 145-217 2-74 (74)
27 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 4E-13 8.6E-18 115.7 8.4 75 142-216 9-83 (83)
28 cd05705 S1_Rrp5_repeat_hs14 S1 99.4 6.5E-13 1.4E-17 113.2 7.5 71 260-330 1-74 (74)
29 PRK08582 hypothetical protein; 99.4 1.9E-12 4.1E-17 123.2 10.7 81 144-225 2-82 (139)
30 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 1.6E-12 3.4E-17 107.7 8.6 70 148-217 1-70 (70)
31 PRK08582 hypothetical protein; 99.4 3.2E-12 7E-17 121.6 10.7 81 259-341 2-83 (139)
32 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 4E-12 8.6E-17 108.6 10.0 71 144-220 1-72 (74)
33 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 3.1E-12 6.7E-17 108.6 8.9 70 148-217 1-72 (73)
34 cd05706 S1_Rrp5_repeat_sc10 S1 99.3 5.6E-12 1.2E-16 105.4 10.1 73 145-217 1-73 (73)
35 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.3 3.8E-12 8.2E-17 105.7 8.6 69 148-216 1-69 (69)
36 PF00575 S1: S1 RNA binding do 99.3 4.4E-12 9.6E-17 106.0 9.0 72 259-332 1-74 (74)
37 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 3.5E-12 7.6E-17 107.8 8.4 71 145-217 1-72 (72)
38 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 5.6E-12 1.2E-16 107.6 9.7 70 259-336 1-73 (74)
39 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 4.1E-12 8.8E-17 107.4 7.8 71 260-332 1-72 (72)
40 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 8.9E-12 1.9E-16 105.2 9.5 70 146-216 2-72 (73)
41 COG2996 Predicted RNA-bindinin 99.3 1.3E-10 2.9E-15 120.3 19.9 178 144-377 2-191 (287)
42 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 5.4E-12 1.2E-16 108.6 7.9 75 255-331 7-83 (83)
43 cd05707 S1_Rrp5_repeat_sc11 S1 99.3 7.7E-12 1.7E-16 103.6 7.9 68 148-215 1-68 (68)
44 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.3 9.9E-12 2.1E-16 104.8 8.6 69 148-216 1-71 (71)
45 cd05703 S1_Rrp5_repeat_hs12_sc 99.3 7.7E-12 1.7E-16 106.2 7.9 70 263-332 1-72 (73)
46 cd04452 S1_IF2_alpha S1_IF2_al 99.3 1.8E-11 3.9E-16 102.7 9.7 74 145-218 1-76 (76)
47 cd05691 S1_RPS1_repeat_ec6 S1_ 99.3 1.7E-11 3.6E-16 101.7 9.3 72 148-219 1-72 (73)
48 PRK07252 hypothetical protein; 99.3 2E-11 4.3E-16 113.7 10.1 78 146-223 2-79 (120)
49 cd05708 S1_Rrp5_repeat_sc12 S1 99.3 3.1E-11 6.7E-16 100.9 9.6 74 146-219 1-75 (77)
50 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 2.9E-11 6.2E-16 100.4 9.0 70 148-217 1-70 (70)
51 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 2.4E-11 5.2E-16 100.1 7.7 68 148-215 1-69 (69)
52 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 2.4E-11 5.2E-16 100.7 7.7 68 263-332 1-70 (70)
53 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 5.7E-11 1.2E-15 99.4 10.0 71 260-332 1-73 (73)
54 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 4.1E-11 8.9E-16 99.5 7.9 67 263-331 1-69 (69)
55 cd05684 S1_DHX8_helicase S1_DH 99.2 8.1E-11 1.8E-15 100.3 9.7 73 263-337 1-77 (79)
56 cd05692 S1_RPS1_repeat_hs4 S1_ 99.2 7.5E-11 1.6E-15 95.7 8.9 69 148-217 1-69 (69)
57 cd05684 S1_DHX8_helicase S1_DH 99.2 7.8E-11 1.7E-15 100.4 9.3 72 148-221 1-76 (79)
58 PRK05807 hypothetical protein; 99.2 9.3E-11 2E-15 111.3 10.6 75 144-220 2-76 (136)
59 PRK08059 general stress protei 99.2 8.1E-11 1.8E-15 109.5 10.0 82 142-223 2-83 (123)
60 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 6E-11 1.3E-15 100.0 8.2 67 263-331 1-71 (71)
61 cd05686 S1_pNO40 S1_pNO40: pNO 99.2 1.1E-10 2.3E-15 98.7 9.1 69 261-331 2-72 (73)
62 cd05689 S1_RPS1_repeat_ec4 S1_ 99.2 1.1E-10 2.3E-15 97.4 8.6 71 145-215 1-72 (72)
63 PLN00207 polyribonucleotide nu 99.2 4.1E-11 8.8E-16 141.1 8.3 84 256-341 747-832 (891)
64 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 5.1E-11 1.1E-15 107.4 7.0 76 145-220 1-98 (100)
65 PRK07252 hypothetical protein; 99.2 1.6E-10 3.5E-15 107.6 10.2 76 261-338 2-79 (120)
66 cd04452 S1_IF2_alpha S1_IF2_al 99.2 1.7E-10 3.7E-15 96.7 9.1 71 261-333 2-76 (76)
67 TIGR02063 RNase_R ribonuclease 99.2 1.6E-11 3.5E-16 143.1 3.9 158 26-216 539-708 (709)
68 COG2996 Predicted RNA-bindinin 99.2 3.3E-09 7.3E-14 110.1 20.3 145 144-335 70-219 (287)
69 cd05685 S1_Tex S1_Tex: The C-t 99.1 1.1E-10 2.4E-15 94.6 7.6 68 148-215 1-68 (68)
70 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.1 1.6E-10 3.5E-15 96.2 8.2 66 148-215 1-66 (66)
71 PLN00207 polyribonucleotide nu 99.1 1E-10 2.2E-15 137.8 9.0 83 143-226 749-832 (891)
72 PRK05807 hypothetical protein; 99.1 3E-10 6.4E-15 107.8 10.5 74 259-335 2-76 (136)
73 cd05691 S1_RPS1_repeat_ec6 S1_ 99.1 2.8E-10 6.1E-15 94.4 8.7 70 263-334 1-72 (73)
74 cd05689 S1_RPS1_repeat_ec4 S1_ 99.1 2.7E-10 5.8E-15 95.0 8.6 69 260-329 1-71 (72)
75 cd04465 S1_RPS1_repeat_ec2_hs2 99.1 3.1E-10 6.6E-15 93.9 8.8 67 148-217 1-67 (67)
76 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 1.6E-10 3.5E-15 95.6 7.2 66 263-330 1-68 (68)
77 smart00316 S1 Ribosomal protei 99.1 3.6E-10 7.9E-15 91.1 9.1 72 146-217 1-72 (72)
78 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 3.1E-10 6.7E-15 94.9 8.9 72 261-334 1-75 (77)
79 PRK11642 exoribonuclease R; Pr 99.1 5.7E-11 1.2E-15 140.2 6.0 164 26-218 551-726 (813)
80 cd04472 S1_PNPase S1_PNPase: P 99.1 3E-10 6.6E-15 92.6 8.4 68 148-216 1-68 (68)
81 cd05692 S1_RPS1_repeat_hs4 S1_ 99.1 2.9E-10 6.2E-15 92.2 8.0 68 263-332 1-69 (69)
82 PRK08059 general stress protei 99.1 3.8E-10 8.2E-15 105.0 9.7 80 257-338 2-83 (123)
83 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 7.9E-11 1.7E-15 106.2 5.0 77 260-336 1-99 (100)
84 cd05688 S1_RPS1_repeat_ec3 S1_ 99.1 3.4E-10 7.4E-15 92.1 8.1 68 147-215 1-68 (68)
85 cd05690 S1_RPS1_repeat_ec5 S1_ 99.1 2.5E-10 5.5E-15 94.0 7.4 67 263-330 1-69 (69)
86 PHA02945 interferon resistance 99.1 6.2E-10 1.4E-14 98.1 9.3 77 142-221 6-86 (88)
87 TIGR00358 3_prime_RNase VacB a 99.1 6.1E-11 1.3E-15 137.3 3.7 155 26-216 487-653 (654)
88 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.1 5.9E-10 1.3E-14 96.3 8.8 74 145-219 4-81 (86)
89 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 8.9E-10 1.9E-14 91.4 8.2 68 263-332 1-70 (70)
90 COG1093 SUI2 Translation initi 99.0 4.5E-10 9.7E-15 115.9 7.3 81 144-224 8-90 (269)
91 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 1.3E-09 2.9E-14 90.7 7.6 64 263-330 1-66 (66)
92 cd04453 S1_RNase_E S1_RNase_E: 99.0 2.3E-09 5E-14 94.6 9.2 74 144-217 4-82 (88)
93 cd04471 S1_RNase_R S1_RNase_R: 99.0 3E-09 6.5E-14 90.3 9.4 70 147-216 1-82 (83)
94 cd05685 S1_Tex S1_Tex: The C-t 99.0 1.4E-09 2.9E-14 88.2 6.8 66 263-330 1-68 (68)
95 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.0 2E-09 4.3E-14 93.0 8.1 75 260-334 4-81 (86)
96 cd04454 S1_Rrp4_like S1_Rrp4_l 98.9 3.6E-09 7.8E-14 90.9 9.1 73 145-218 4-76 (82)
97 PRK03987 translation initiatio 98.9 2.7E-09 5.8E-14 111.4 9.9 80 144-223 5-86 (262)
98 cd04472 S1_PNPase S1_PNPase: P 98.9 3.4E-09 7.4E-14 86.4 8.0 67 263-331 1-68 (68)
99 smart00316 S1 Ribosomal protei 98.9 3.5E-09 7.7E-14 85.4 7.9 70 261-332 1-72 (72)
100 cd04465 S1_RPS1_repeat_ec2_hs2 98.9 4.9E-09 1.1E-13 86.7 8.2 65 263-332 1-67 (67)
101 COG2183 Tex Transcriptional ac 98.9 1.7E-09 3.8E-14 125.0 7.0 82 140-221 651-732 (780)
102 cd05702 S1_Rrp5_repeat_hs11_sc 98.9 6.4E-09 1.4E-13 86.9 8.0 63 148-210 1-65 (70)
103 cd04453 S1_RNase_E S1_RNase_E: 98.9 6E-09 1.3E-13 91.9 8.1 74 259-332 4-82 (88)
104 PRK11824 polynucleotide phosph 98.9 6E-09 1.3E-13 121.6 10.5 76 143-219 617-692 (693)
105 cd04471 S1_RNase_R S1_RNase_R: 98.9 1.2E-08 2.6E-13 86.6 9.5 70 262-331 1-82 (83)
106 cd00164 S1_like S1_like: Ribos 98.9 5.6E-09 1.2E-13 82.8 6.7 65 151-215 1-65 (65)
107 TIGR02696 pppGpp_PNP guanosine 98.8 6.1E-09 1.3E-13 120.9 9.0 71 144-215 644-718 (719)
108 PHA02945 interferon resistance 98.8 1.3E-08 2.8E-13 89.9 8.9 73 260-337 9-87 (88)
109 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 1.1E-08 2.3E-13 83.3 7.7 66 262-330 1-68 (68)
110 cd04473 S1_RecJ_like S1_RecJ_l 98.8 2.4E-08 5.2E-13 85.4 10.1 68 140-216 9-76 (77)
111 PRK03987 translation initiatio 98.8 1E-08 2.2E-13 107.1 8.8 76 260-337 6-85 (262)
112 cd04473 S1_RecJ_like S1_RecJ_l 98.8 2.8E-08 6E-13 85.0 9.6 66 256-331 10-76 (77)
113 cd05702 S1_Rrp5_repeat_hs11_sc 98.8 1.4E-08 3E-13 84.9 7.5 64 263-326 1-64 (70)
114 PRK11824 polynucleotide phosph 98.8 1.5E-08 3.3E-13 118.3 10.1 76 257-334 616-692 (693)
115 TIGR02696 pppGpp_PNP guanosine 98.8 9.9E-09 2.1E-13 119.2 8.2 70 259-330 644-718 (719)
116 PRK09521 exosome complex RNA-b 98.8 5.3E-08 1.2E-12 96.8 11.5 75 257-334 59-143 (189)
117 COG1093 SUI2 Translation initi 98.8 5.2E-09 1.1E-13 108.2 4.2 76 261-338 10-89 (269)
118 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 3.4E-08 7.4E-13 84.9 8.5 72 261-334 5-77 (82)
119 COG1185 Pnp Polyribonucleotide 98.7 4.1E-08 8.8E-13 112.4 8.0 79 255-335 612-691 (692)
120 cd04455 S1_NusA S1_NusA: N-uti 98.7 1.1E-07 2.3E-12 79.4 8.5 64 146-216 2-67 (67)
121 PRK09202 nusA transcription el 98.6 4.7E-08 1E-12 109.5 7.3 71 142-219 127-201 (470)
122 PRK05054 exoribonuclease II; P 98.6 1.7E-08 3.8E-13 116.9 3.9 148 26-216 481-643 (644)
123 COG2183 Tex Transcriptional ac 98.6 4.3E-08 9.3E-13 113.7 6.8 79 255-335 651-731 (780)
124 cd00164 S1_like S1_like: Ribos 98.6 8.7E-08 1.9E-12 75.9 6.4 63 266-330 1-65 (65)
125 COG0557 VacB Exoribonuclease R 98.6 1.8E-08 3.8E-13 118.0 3.4 160 18-217 533-704 (706)
126 TIGR03591 polynuc_phos polyrib 98.6 6.9E-08 1.5E-12 112.7 8.1 70 144-214 615-684 (684)
127 cd04460 S1_RpoE S1_RpoE: RpoE, 98.6 1.8E-07 3.9E-12 83.5 8.6 75 149-224 1-91 (99)
128 cd04460 S1_RpoE S1_RpoE: RpoE, 98.6 2.7E-07 5.8E-12 82.4 9.1 76 264-340 1-92 (99)
129 PRK09202 nusA transcription el 98.5 5.2E-08 1.1E-12 109.2 4.4 123 172-334 72-201 (470)
130 COG1185 Pnp Polyribonucleotide 98.5 1.2E-07 2.7E-12 108.6 7.2 77 142-219 614-690 (692)
131 PRK09521 exosome complex RNA-b 98.5 2.4E-07 5.1E-12 92.2 8.0 73 143-218 60-142 (189)
132 TIGR03591 polynuc_phos polyrib 98.5 1.7E-07 3.6E-12 109.6 7.4 72 256-329 612-684 (684)
133 PRK04163 exosome complex RNA-b 98.5 4.7E-07 1E-11 93.2 9.1 73 144-217 60-136 (235)
134 TIGR02062 RNase_B exoribonucle 98.4 8.4E-08 1.8E-12 111.2 3.1 147 26-215 477-638 (639)
135 cd04455 S1_NusA S1_NusA: N-uti 98.4 9E-07 1.9E-11 73.8 8.1 61 261-330 2-66 (67)
136 PRK04163 exosome complex RNA-b 98.4 2.3E-06 5E-11 88.2 11.9 75 260-334 61-138 (235)
137 KOG1067 Predicted RNA-binding 98.4 4.3E-07 9.3E-12 101.8 6.5 83 141-224 662-744 (760)
138 TIGR00448 rpoE DNA-directed RN 98.3 2.5E-06 5.4E-11 84.2 9.4 79 144-223 78-172 (179)
139 PRK12327 nusA transcription el 98.2 2.2E-06 4.8E-11 93.5 6.9 70 142-218 127-200 (362)
140 TIGR01953 NusA transcription t 98.2 2.4E-06 5.2E-11 92.6 7.2 72 142-220 124-200 (341)
141 TIGR00448 rpoE DNA-directed RN 98.2 9.2E-06 2E-10 80.2 9.6 78 260-338 79-172 (179)
142 TIGR02063 RNase_R ribonuclease 98.1 7E-06 1.5E-10 96.4 9.8 74 258-331 623-708 (709)
143 KOG1067 Predicted RNA-binding 98.1 2.8E-06 6.1E-11 95.5 5.0 83 256-340 662-745 (760)
144 COG1095 RPB7 DNA-directed RNA 98.1 1E-05 2.2E-10 80.6 7.7 77 144-221 78-170 (183)
145 PRK11642 exoribonuclease R; Pr 98.1 1.2E-05 2.5E-10 95.9 9.5 72 261-332 642-725 (813)
146 TIGR01953 NusA transcription t 98.1 3E-06 6.5E-11 91.9 4.1 114 186-334 78-199 (341)
147 PRK08563 DNA-directed RNA poly 98.0 2E-05 4.2E-10 78.2 9.5 75 144-219 78-168 (187)
148 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.0 1.7E-05 3.6E-10 70.8 8.0 73 145-218 4-86 (92)
149 PRK12327 nusA transcription el 98.0 3.3E-06 7.3E-11 92.1 3.4 71 254-333 124-200 (362)
150 TIGR00358 3_prime_RNase VacB a 98.0 2E-05 4.3E-10 92.0 9.5 71 261-331 571-653 (654)
151 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.9 2.4E-05 5.2E-10 69.8 6.5 75 260-334 4-87 (92)
152 PHA02858 EIF2a-like PKR inhibi 97.9 3.5E-05 7.5E-10 68.0 6.6 73 142-216 11-85 (86)
153 PRK08563 DNA-directed RNA poly 97.8 8.1E-05 1.8E-09 73.8 9.4 76 259-335 78-169 (187)
154 COG1095 RPB7 DNA-directed RNA 97.8 6.7E-05 1.4E-09 74.8 7.9 80 257-337 76-171 (183)
155 PF13509 S1_2: S1 domain; PDB: 97.7 0.00013 2.8E-09 60.4 7.7 61 147-217 1-61 (61)
156 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.6 0.00028 6E-09 62.6 9.0 64 147-211 1-75 (88)
157 KOG2916 Translation initiation 97.5 7.2E-05 1.6E-09 78.0 3.9 81 144-224 13-95 (304)
158 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.5 0.00025 5.4E-09 61.2 6.1 70 263-332 1-72 (72)
159 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00053 1.1E-08 59.2 6.6 68 148-217 1-72 (72)
160 PHA02858 EIF2a-like PKR inhibi 97.3 0.00045 9.7E-09 61.1 5.9 72 256-331 10-85 (86)
161 TIGR00757 RNaseEG ribonuclease 97.3 0.00062 1.3E-08 75.9 8.5 74 144-217 22-109 (414)
162 PF13509 S1_2: S1 domain; PDB: 97.3 0.00072 1.6E-08 56.0 6.8 61 262-332 1-61 (61)
163 PRK12328 nusA transcription el 97.2 0.00088 1.9E-08 73.6 8.3 68 145-219 136-207 (374)
164 PTZ00162 DNA-directed RNA poly 97.2 0.0019 4.1E-08 64.3 9.3 74 144-218 78-165 (176)
165 COG1107 Archaea-specific RecJ- 97.2 0.001 2.2E-08 75.9 8.2 163 139-331 114-282 (715)
166 COG1097 RRP4 RNA-binding prote 97.2 0.0022 4.8E-08 66.5 9.8 73 144-217 61-137 (239)
167 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.1 0.0027 5.9E-08 56.5 8.6 72 145-218 4-75 (86)
168 TIGR00757 RNaseEG ribonuclease 97.1 0.00086 1.9E-08 74.8 6.7 65 258-322 21-97 (414)
169 PRK05054 exoribonuclease II; P 97.0 0.0018 3.9E-08 75.8 9.0 69 263-331 562-643 (644)
170 COG1097 RRP4 RNA-binding prote 97.0 0.012 2.7E-07 61.1 13.4 80 261-340 63-145 (239)
171 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.9 0.0036 7.7E-08 55.6 7.9 61 262-323 1-70 (88)
172 PTZ00162 DNA-directed RNA poly 96.8 0.004 8.7E-08 62.0 8.3 75 259-334 78-166 (176)
173 PRK12329 nusA transcription el 96.5 0.0085 1.8E-07 67.2 8.6 68 145-218 150-225 (449)
174 COG1096 Predicted RNA-binding 96.5 0.012 2.6E-07 59.2 8.6 73 142-217 59-141 (188)
175 COG1107 Archaea-specific RecJ- 96.4 0.0063 1.4E-07 69.7 7.1 76 255-338 115-190 (715)
176 PF10447 EXOSC1: Exosome compo 96.4 0.0068 1.5E-07 53.6 5.9 60 146-205 3-82 (82)
177 TIGR02062 RNase_B exoribonucle 96.3 0.009 2E-07 70.1 7.8 67 263-329 558-637 (639)
178 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.3 0.021 4.5E-07 51.0 8.3 72 260-334 4-76 (86)
179 KOG1856 Transcription elongati 96.2 0.0052 1.1E-07 74.5 5.2 80 143-222 981-1063(1299)
180 PRK12328 nusA transcription el 96.1 0.018 3.8E-07 63.6 8.5 69 256-333 130-206 (374)
181 PF10447 EXOSC1: Exosome compo 96.0 0.012 2.6E-07 52.1 5.2 62 261-322 3-82 (82)
182 KOG2916 Translation initiation 96.0 0.0037 8E-08 65.6 2.1 75 261-337 15-93 (304)
183 PRK10811 rne ribonuclease E; R 95.8 0.017 3.7E-07 69.8 6.9 63 261-323 37-108 (1068)
184 PRK12329 nusA transcription el 95.7 0.033 7.2E-07 62.6 8.4 70 256-333 144-225 (449)
185 PRK10811 rne ribonuclease E; R 95.7 0.025 5.3E-07 68.4 7.8 60 146-205 37-107 (1068)
186 COG0557 VacB Exoribonuclease R 95.6 0.033 7.1E-07 66.1 8.2 75 257-331 617-703 (706)
187 PRK11712 ribonuclease G; Provi 95.2 0.05 1.1E-06 62.2 7.7 73 145-217 36-122 (489)
188 PRK11712 ribonuclease G; Provi 94.9 0.041 9E-07 62.8 6.2 64 259-322 35-110 (489)
189 KOG1856 Transcription elongati 94.9 0.03 6.4E-07 68.3 5.0 77 256-334 979-1060(1299)
190 COG1096 Predicted RNA-binding 94.7 0.2 4.3E-06 50.7 9.4 106 257-375 59-174 (188)
191 KOG3298 DNA-directed RNA polym 93.6 0.32 7E-06 48.2 8.2 65 145-210 79-154 (170)
192 PF08292 RNA_pol_Rbc25: RNA po 93.4 0.42 9.2E-06 45.3 8.5 61 147-207 3-76 (122)
193 COG1530 CafA Ribonucleases G a 91.4 0.31 6.7E-06 55.8 5.8 75 144-219 34-115 (487)
194 KOG3298 DNA-directed RNA polym 91.1 0.98 2.1E-05 44.9 8.1 63 260-323 79-150 (170)
195 COG1530 CafA Ribonucleases G a 90.6 0.32 6.9E-06 55.8 4.9 67 257-324 32-103 (487)
196 PF10246 MRP-S35: Mitochondria 89.2 1.6 3.4E-05 40.5 7.3 58 141-206 18-75 (104)
197 PRK12442 translation initiatio 88.9 1.9 4.1E-05 38.9 7.4 65 150-218 8-73 (87)
198 TIGR00008 infA translation ini 88.5 2 4.3E-05 37.1 7.0 61 150-214 6-67 (68)
199 PF10246 MRP-S35: Mitochondria 87.0 2.2 4.8E-05 39.5 6.8 54 261-323 22-75 (104)
200 KOG3409 Exosomal 3'-5' exoribo 86.9 2.1 4.6E-05 43.1 7.1 74 143-217 64-147 (193)
201 PF08292 RNA_pol_Rbc25: RNA po 84.4 3.4 7.4E-05 39.2 7.0 62 262-323 3-75 (122)
202 PF00313 CSD: 'Cold-shock' DNA 83.9 9.3 0.0002 31.5 8.7 50 151-204 1-53 (66)
203 KOG3409 Exosomal 3'-5' exoribo 83.3 4 8.6E-05 41.2 7.2 71 261-331 67-146 (193)
204 cd05700 S1_Rrp5_repeat_hs9 S1_ 81.9 4 8.6E-05 34.7 5.5 63 263-331 1-65 (65)
205 cd04458 CSP_CDS Cold-Shock Pro 81.2 6.9 0.00015 32.2 6.9 57 267-330 2-62 (65)
206 PF00313 CSD: 'Cold-shock' DNA 79.1 15 0.00033 30.3 8.3 53 266-326 1-57 (66)
207 PRK12442 translation initiatio 78.6 8.8 0.00019 34.7 7.1 64 265-334 8-74 (87)
208 PRK09890 cold shock protein Cs 77.2 13 0.00029 31.7 7.6 55 266-326 5-62 (70)
209 PRK15464 cold shock-like prote 72.8 18 0.0004 31.1 7.3 56 266-327 5-63 (70)
210 KOG1004 Exosomal 3'-5' exoribo 72.7 12 0.00026 39.0 7.2 62 145-207 63-124 (230)
211 PRK09937 stationary phase/star 72.4 19 0.00042 31.3 7.4 62 267-334 3-67 (74)
212 PRK04012 translation initiatio 72.0 13 0.00028 34.3 6.6 68 144-217 17-85 (100)
213 COG0361 InfA Translation initi 71.9 23 0.0005 31.3 7.7 66 148-217 6-72 (75)
214 PRK10943 cold shock-like prote 71.8 23 0.00049 30.3 7.6 55 265-325 3-60 (69)
215 TIGR00008 infA translation ini 71.2 18 0.0004 31.3 6.9 58 265-328 6-66 (68)
216 cd05700 S1_Rrp5_repeat_hs9 S1_ 70.9 11 0.00025 32.0 5.4 65 148-216 1-65 (65)
217 PRK10943 cold shock-like prote 69.9 16 0.00034 31.2 6.3 51 150-204 3-56 (69)
218 PRK09507 cspE cold shock prote 69.6 25 0.00055 30.0 7.5 55 265-325 3-60 (69)
219 PRK15464 cold shock-like prote 69.4 26 0.00057 30.2 7.5 50 151-204 5-57 (70)
220 PRK15463 cold shock-like prote 68.8 26 0.00056 30.1 7.3 54 266-325 5-61 (70)
221 PRK09937 stationary phase/star 67.9 29 0.00064 30.2 7.6 60 152-217 3-65 (74)
222 PRK09890 cold shock protein Cs 67.8 38 0.00082 29.0 8.2 50 151-204 5-57 (70)
223 PRK14998 cold shock-like prote 66.3 32 0.00069 29.8 7.5 60 267-332 3-65 (73)
224 PRK09507 cspE cold shock prote 65.1 24 0.00051 30.1 6.4 51 150-204 3-56 (69)
225 PRK15463 cold shock-like prote 64.0 21 0.00045 30.7 5.9 50 151-204 5-57 (70)
226 PRK10354 RNA chaperone/anti-te 62.5 45 0.00098 28.4 7.6 54 266-325 5-61 (70)
227 PRK10354 RNA chaperone/anti-te 62.0 52 0.0011 28.1 7.9 50 151-204 5-57 (70)
228 cd05793 S1_IF1A S1_IF1A: Trans 61.7 25 0.00053 30.9 6.0 62 151-217 2-64 (77)
229 COG4148 ModC ABC-type molybdat 61.2 1.5E+02 0.0032 32.9 12.8 122 136-322 221-348 (352)
230 PRK14998 cold shock-like prote 60.3 48 0.001 28.8 7.5 59 152-216 3-64 (73)
231 KOG1999 RNA polymerase II tran 58.1 1.5E+02 0.0032 37.3 13.4 69 308-376 407-498 (1024)
232 KOG3297 DNA-directed RNA polym 57.7 20 0.00044 36.6 5.4 62 144-205 78-156 (202)
233 TIGR02381 cspD cold shock doma 56.9 41 0.00088 28.6 6.4 55 267-327 3-60 (68)
234 TIGR02381 cspD cold shock doma 56.5 50 0.0011 28.0 6.9 49 152-204 3-54 (68)
235 KOG4078 Putative mitochondrial 55.5 19 0.0004 35.5 4.5 56 145-207 80-135 (173)
236 COG4044 Uncharacterized protei 54.4 14 0.00029 38.6 3.6 83 141-223 69-163 (247)
237 smart00652 eIF1a eukaryotic tr 54.2 60 0.0013 28.9 7.2 65 150-219 6-71 (83)
238 PF03459 TOBE: TOBE domain; I 53.9 32 0.00069 27.9 5.1 47 150-203 6-58 (64)
239 KOG2102 Exosomal 3'-5' exoribo 53.5 7.2 0.00016 48.4 1.8 34 24-57 766-799 (941)
240 KOG4078 Putative mitochondrial 52.8 31 0.00067 34.0 5.6 54 261-323 81-134 (173)
241 cd04458 CSP_CDS Cold-Shock Pro 52.0 62 0.0013 26.5 6.6 50 152-205 2-54 (65)
242 KOG3013 Exosomal 3'-5' exoribo 51.7 20 0.00044 38.4 4.5 73 144-217 82-164 (301)
243 PRK06763 F0F1 ATP synthase sub 51.1 1.1E+02 0.0023 32.0 9.3 44 149-201 40-84 (213)
244 COG0361 InfA Translation initi 50.3 86 0.0019 27.8 7.4 63 263-331 6-71 (75)
245 COG1278 CspC Cold shock protei 48.3 49 0.0011 28.7 5.5 54 267-326 3-59 (67)
246 PRK10676 DNA-binding transcrip 45.4 2.2E+02 0.0047 30.3 11.1 115 150-321 129-254 (263)
247 KOG1004 Exosomal 3'-5' exoribo 43.7 83 0.0018 33.0 7.3 60 261-323 64-123 (230)
248 PF07076 DUF1344: Protein of u 43.7 1E+02 0.0023 26.3 6.6 57 265-331 4-60 (61)
249 cd04456 S1_IF1A_like S1_IF1A_l 40.2 1E+02 0.0022 27.2 6.4 64 151-219 2-67 (78)
250 PRK04012 translation initiatio 40.0 1.7E+02 0.0037 27.1 8.1 63 262-331 19-82 (100)
251 PF15057 DUF4537: Domain of un 39.8 1.5E+02 0.0032 28.2 7.9 97 261-377 10-112 (124)
252 PF03459 TOBE: TOBE domain; I 39.4 56 0.0012 26.4 4.5 47 264-319 5-57 (64)
253 PRK15136 multidrug efflux syst 38.8 1.9E+02 0.0042 32.2 9.9 15 307-321 333-347 (390)
254 TIGR00523 eIF-1A eukaryotic/ar 38.6 1.3E+02 0.0028 27.8 7.1 64 149-217 19-84 (99)
255 TIGR00638 Mop molybdenum-pteri 38.2 40 0.00087 27.5 3.4 48 150-204 8-61 (69)
256 cd04322 LysRS_N LysRS_N: N-ter 37.5 1.9E+02 0.0041 26.1 8.0 68 150-217 3-75 (108)
257 PRK00276 infA translation init 34.0 2.3E+02 0.0051 24.2 7.6 61 150-214 8-69 (72)
258 COG1278 CspC Cold shock protei 33.1 1.4E+02 0.0029 26.0 5.9 49 152-204 3-54 (67)
259 PF02599 CsrA: Global regulato 32.3 51 0.0011 27.3 3.1 31 305-335 8-38 (54)
260 CHL00010 infA translation init 31.8 2.7E+02 0.0058 24.4 7.7 64 151-218 9-73 (78)
261 cd05793 S1_IF1A S1_IF1A: Trans 31.1 2.5E+02 0.0053 24.7 7.3 59 266-331 2-61 (77)
262 PF01176 eIF-1a: Translation i 30.4 56 0.0012 27.5 3.1 59 150-213 4-63 (65)
263 TIGR00638 Mop molybdenum-pteri 30.4 42 0.0009 27.4 2.3 48 264-320 7-60 (69)
264 CHL00010 infA translation init 29.7 2.8E+02 0.0061 24.3 7.5 63 266-334 9-74 (78)
265 PF14985 TM140: TM140 protein 28.9 15 0.00034 36.5 -0.5 8 662-669 45-52 (181)
266 KOG4134 DNA-dependent RNA poly 27.9 39 0.00084 35.7 2.1 66 255-329 100-167 (253)
267 PRK01712 carbon storage regula 27.1 95 0.0021 26.8 3.9 30 305-334 8-37 (64)
268 PRK00568 carbon storage regula 25.2 97 0.0021 27.5 3.7 30 305-334 8-37 (76)
269 PF00773 RNB: RNB domain CAUTI 24.6 16 0.00034 39.1 -1.5 37 15-54 280-316 (325)
270 COG4776 Rnb Exoribonuclease II 24.6 27 0.00059 40.3 0.3 70 144-213 558-640 (645)
271 COG2106 Uncharacterized conser 24.5 1.6E+02 0.0034 32.0 5.9 49 144-205 102-150 (272)
272 COG1551 CsrA RNA-binding globa 24.2 93 0.002 27.4 3.4 29 306-334 9-37 (73)
273 PLN00208 translation initiatio 24.1 2.2E+02 0.0048 28.2 6.3 65 145-214 28-93 (145)
274 PF12337 DUF3637: Protein of u 22.6 1.3E+02 0.0029 25.4 3.8 39 26-64 2-40 (67)
275 PF02083 Urotensin_II: Urotens 22.5 36 0.00079 20.3 0.4 10 658-667 3-12 (12)
276 PF08206 OB_RNB: Ribonuclease 22.1 1.6E+02 0.0035 24.1 4.3 43 268-321 1-44 (58)
277 TIGR00202 csrA carbon storage 21.8 1.3E+02 0.0028 26.3 3.8 30 305-334 8-37 (69)
278 smart00652 eIF1a eukaryotic tr 21.3 5.5E+02 0.012 22.9 7.8 53 265-324 6-59 (83)
279 PF14654 Epiglycanin_C: Mucin, 21.0 33 0.00073 31.8 0.1 13 664-677 39-51 (106)
280 PF08206 OB_RNB: Ribonuclease 20.8 2.2E+02 0.0048 23.3 4.8 42 154-204 2-44 (58)
281 TIGR00523 eIF-1A eukaryotic/ar 20.7 4.1E+02 0.0089 24.6 7.1 54 263-323 18-72 (99)
282 TIGR00739 yajC preprotein tran 20.6 1.9E+02 0.0041 25.8 4.8 37 142-178 35-77 (84)
283 smart00357 CSP Cold shock prot 20.4 2.8E+02 0.006 21.6 5.3 47 268-322 2-50 (64)
284 COG1545 Predicted nucleic-acid 20.3 3.8E+02 0.0083 25.9 7.2 59 262-329 63-132 (140)
285 COG3269 Predicted RNA-binding 20.2 3.3E+02 0.0071 24.2 5.9 50 142-206 10-60 (73)
286 COG2106 Uncharacterized conser 20.1 1.9E+02 0.004 31.5 5.3 52 257-323 100-151 (272)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-47 Score=420.91 Aligned_cols=274 Identities=26% Similarity=0.359 Sum_probs=244.7
Q ss_pred ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL 123 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da 123 (681)
..|+++|++|+|||+|+|+++.. +-.++..|+|+++.++|+++|++++ ++++|+| +.-++
T Consensus 118 KGG~~Vdi~gvr~FlP~S~v~~r--~v~d~~~~~Gk~~~~kiie~d~~~n---~vv~SrR---------------~~~e~ 177 (541)
T COG0539 118 KGGLTVDIEGVRAFLPGSLVDVR--PVRDLDPLIGKELEFKILELDKKRN---NVVLSRR---------------AVLEE 177 (541)
T ss_pred cCcEEEEECCEEEeccHHHhccc--ccccccccCCceEEEEEEEEccccC---cEEEEhH---------------HHhhH
Confidence 47899999999999999999976 2234667899999999999999999 9999998 11111
Q ss_pred HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707 124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203 (681)
Q Consensus 124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl 203 (681)
++ .+.+.. .+..|++|+++.|+|+++++||+||+|+| ++||||+++|+|.++.+|.+.|++||.|+|+|+
T Consensus 178 ~~----~~~r~e-----~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi 247 (541)
T COG0539 178 ER----SEQREE-----LLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVI 247 (541)
T ss_pred HH----HHHHHH-----HHhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEE
Confidence 11 111112 26789999999999999999999999999 999999999999999999999999999999999
Q ss_pred EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707 204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP 283 (681)
Q Consensus 204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg 283 (681)
++|.+++||.||+|++.++||. ....+|++|+.+.|+|+++++|||||++.
T Consensus 248 ~~D~e~~RVsLSlK~l~~dPw~-----------------------------~i~~~~~~g~~v~G~Vt~i~~~GafVei~ 298 (541)
T COG0539 248 SLDEERGRVSLSLKQLEEDPWE-----------------------------GIEKKYPVGDKVEGKVTNLTDYGAFVEIE 298 (541)
T ss_pred EEccCCCeEEEEehhcccCcHH-----------------------------HHhhhcCCCCEEEEEEEEeecCcEEEEec
Confidence 9999999999999999999994 56788999999999999999999999999
Q ss_pred CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEEeec
Q 005707 284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHAATN 353 (681)
Q Consensus 284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~~i~ 353 (681)
+|++||+|.||++|.+... |.+.+++||.|.|+||.|| ++||.|+||+...|||.. ..+.|.|. +++
T Consensus 299 ~GvEGlvhvSEisw~~~~~--P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~-~~t 375 (541)
T COG0539 299 EGVEGLVHVSEISWTKKNV--PSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVK-SIT 375 (541)
T ss_pred CCccceeechhhcccccCC--HHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEe-eec
Confidence 9999999999999998643 8999999999999999997 699999999999999882 34688888 899
Q ss_pred ccEEEEEEcCCeEEEeeCCccccccc
Q 005707 354 PFVLAFRSNKDISSFLDERDKSATAA 379 (681)
Q Consensus 354 ~fGlfV~l~~gI~GfIp~~els~~~~ 379 (681)
+||+|+.+.+|+.||+|.++++|...
T Consensus 376 ~~g~fv~le~gidG~vh~~d~sw~~~ 401 (541)
T COG0539 376 DFGAFVELEGGIDGLVHLSDLSWDRP 401 (541)
T ss_pred ccceEEccCCCccceEEHHhcCcccc
Confidence 99999999999999999999998644
No 2
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2.3e-40 Score=367.78 Aligned_cols=274 Identities=20% Similarity=0.254 Sum_probs=234.9
Q ss_pred ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL 123 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da 123 (681)
..++++++.|++||+|.+++++... ..+..++|+.+.|+|+++|++++ +++||+| ......
T Consensus 128 ~~G~~V~i~g~~~flP~s~~~~~~~--~~~~~~vG~~i~~~V~~id~~~~---~v~lSrk--------------~~~~~~ 188 (491)
T PRK13806 128 KGGFNVEVLGRRAFCPVSQIDLRYV--EDPESYVGQTFQFLITRVEENGR---NIVVSRR--------------ALLERE 188 (491)
T ss_pred cCCEEEEECCEEEEEEHHHhccccC--CChHHcCCCeEEEEEEEEECCCC---eEEEEee--------------hhhhhh
Confidence 4678899999999999999997622 23445799999999999999888 8999987 110000
Q ss_pred HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707 124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203 (681)
Q Consensus 124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl 203 (681)
.. . .... -+..+++|+++.|+|+++.++|+||+|++++.||||+++++|.++.++.+.|++||.|+|+|+
T Consensus 189 ~~----~-~~~~-----~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl 258 (491)
T PRK13806 189 QK----E-ALEA-----FMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVL 258 (491)
T ss_pred hH----H-HHHH-----HHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEE
Confidence 00 0 0000 034689999999999999999999999877999999999999999999999999999999999
Q ss_pred EEeccC----CceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707 204 EANAET----GRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF 279 (681)
Q Consensus 204 ~VD~ek----grI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF 279 (681)
++|.++ +||.||+|++..+||. ....+|++|+++.|+|+++.++|+|
T Consensus 259 ~id~~~~~~~~ri~lS~K~~~~~p~~-----------------------------~~~~~~~~G~~v~G~V~~v~~~G~f 309 (491)
T PRK13806 259 GIERAKKGKGLRISLSIKQAGGDPWD-----------------------------TVGDRLKAGDKVTGKVVRLAPFGAF 309 (491)
T ss_pred EEecccCCcceEEEEEehhhhcccch-----------------------------hhhccCCCCCEEEEEEEEEeCceEE
Confidence 999876 4799999999988882 4577899999999999999999999
Q ss_pred EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEE
Q 005707 280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIH 349 (681)
Q Consensus 280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~ 349 (681)
|++++|++||+|.++++|... ..++...|++||.|+|+|+++| ++|+.||+|++..|||. ++.+.|+|+
T Consensus 310 V~l~~gv~Glvh~sels~~~~-~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~ 388 (491)
T PRK13806 310 VEILPGIEGLVHVSEMSWTRR-VNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVE 388 (491)
T ss_pred EEeCCCcEEEEEHHHcCcccc-cCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEE
Confidence 999999999999999998431 2356788999999999999997 58999999999999987 356799999
Q ss_pred EeecccEEEEEEcCCeEEEeeCCccccc
Q 005707 350 AATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 350 ~~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.+||+||++.+|+.||||.+++++.
T Consensus 389 -~i~~~G~FV~l~~gv~Gli~~se~s~~ 415 (491)
T PRK13806 389 -KRAQFGLFVNLAPGVTGLLPASVISRA 415 (491)
T ss_pred -EEecCceEEEcCCCcEEEEEHHHcCcc
Confidence 899999999999999999999999986
No 3
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=6e-39 Score=374.25 Aligned_cols=270 Identities=19% Similarity=0.268 Sum_probs=234.2
Q ss_pred ceeEEeccCCceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
..++.++++|++||+|.++++|.. .+...+. .+|+.+.|+|+++|++++ +++||.| ....
T Consensus 506 ~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~---rI~LSlK--------------~l~~- 566 (863)
T PRK12269 506 SFGAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEK---RINLSLK--------------HFQP- 566 (863)
T ss_pred CCcEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCC---eEEEEEe--------------cccc-
Confidence 578999999999999999999862 2222223 379999999999999988 9999987 0000
Q ss_pred hHHhhhchhhhhcCCCCCC-cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCEEEE
Q 005707 123 LAESRRSRTARKSEMPPVK-NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQEVKV 200 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt-~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~VkV 200 (681)
.+... .+.+++|+++.|+|+++.+||+||+|+.+++||+|+++++| .++.+|.+.|++||.|+|
T Consensus 567 --------------~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~v 632 (863)
T PRK12269 567 --------------DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVEC 632 (863)
T ss_pred --------------chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEE
Confidence 01111 34689999999999999999999999877999999999999 578899999999999999
Q ss_pred EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707 201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI 280 (681)
Q Consensus 201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV 280 (681)
+|+++|+++++|.||+|++..+||. ....+|++|+++.|+|+++++||+||
T Consensus 633 kVl~iD~e~~rIsLS~K~l~~~Pw~-----------------------------~~~~~~~vG~~v~G~V~~i~~~G~fV 683 (863)
T PRK12269 633 MILGYDIQAGRVSLGLKQVTANPWE-----------------------------EIEARYPVGARFTRRIVKVTNAGAFI 683 (863)
T ss_pred EEEEEecccCceEEEehhcccCchH-----------------------------HHHHhCCCCCEEEEEEEEEecceEEE
Confidence 9999999999999999999999993 34678999999999999999999999
Q ss_pred EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEE
Q 005707 281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHA 350 (681)
Q Consensus 281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~ 350 (681)
+|++|++||||.++++|.+.. .++...|++||.|+|+|+++| ++||.||+|++..|||+ ++.+.|+|.
T Consensus 684 ~l~~gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~- 761 (863)
T PRK12269 684 EMEEGIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVS- 761 (863)
T ss_pred EeCCCcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEE-
Confidence 999999999999999997631 234568999999999999997 59999999999999988 245788998
Q ss_pred eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 351 ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 351 ~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.+||+||++.+|+.||+|.+++++.
T Consensus 762 ~v~~~GvFVeL~~gVeGlI~~s~lsdd 788 (863)
T PRK12269 762 SVTDFGIFVRVPGGVEGLVRKQHLVEN 788 (863)
T ss_pred EEecCeEEEEcCCCeEEEEEHHHcCCc
Confidence 799999999999999999999999986
No 4
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=1.4e-38 Score=371.09 Aligned_cols=274 Identities=24% Similarity=0.268 Sum_probs=233.6
Q ss_pred eeEEeccC-CceeEEeCcccCcccccccchhhcccceeEEEEEecCCCC--CCCCcceecCCCCCcccccccccccCCCh
Q 005707 45 QRFLLPLP-SSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPA--ADDDSAGASDIPSDVETSESSSIKSEASP 121 (681)
Q Consensus 45 ~~l~~dl~-glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~--~~~~~lvlSer~s~v~~ae~ss~~sea~~ 121 (681)
.++++|++ |++||||.+|++.. ....+..++|+.+.|+|+++|... .+..++++|+| .+..
T Consensus 414 gG~~Vdig~~~~gfiP~se~~~~--~~~~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr--------------~~l~ 477 (863)
T PRK12269 414 SGFEVDLGAGMMAFLPISQSDCQ--KVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRR--------------RYLE 477 (863)
T ss_pred CEEEEEECCCcEEEEEHHHhccc--cccchHHhCCCeEEEEEEEEecccccCCCCeEEEEHH--------------HHHH
Confidence 47889995 89999999999865 333466789999999999998632 22337999987 1111
Q ss_pred hhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEE
Q 005707 122 TLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR 201 (681)
Q Consensus 122 daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVk 201 (681)
+..+ ..+.. .+..+++|++|.|+|+++.++|+||+++| ++||||+++++|.++.++.+.|++||.|+|+
T Consensus 478 e~~~-----~~~ee-----~~~~l~~G~~V~G~Vk~i~~~G~fVdl~G-v~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vk 546 (863)
T PRK12269 478 ERAR-----QAREE-----FFNSVHIEDSVSGVVKSFTSFGAFIDLGG-FDGLLHVNDMSWGHVARPREFVKKGQTIELK 546 (863)
T ss_pred HHHH-----HHHHH-----HHhcCCCCCEEEEEEEEEeCCcEEEEECC-EEEEEEchhccccccCCHHHhccCCCEEEEE
Confidence 1111 11111 15679999999999999999999999965 9999999999999999999999999999999
Q ss_pred EEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707 202 LIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS 281 (681)
Q Consensus 202 Vl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe 281 (681)
|+++|+++++|.||+|.+..+||. ....+|++|+++.|+|+++.+||+||+
T Consensus 547 Vi~iD~e~~rI~LSlK~l~~~p~~-----------------------------~~~~~~~vG~iV~G~V~~I~~fG~fVe 597 (863)
T PRK12269 547 VIRLDQAEKRINLSLKHFQPDPWL-----------------------------EFENKFGVNDVVKGRVTKIADFGAFIE 597 (863)
T ss_pred EEEEecCCCeEEEEEeccccchhh-----------------------------hhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence 999999999999999999888883 346679999999999999999999999
Q ss_pred eCCCeEEEEeCCCCCcc-cccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707 282 LPEGEEGFLPTSEESDD-GFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA 350 (681)
Q Consensus 282 Ig~GIeGLLpiSELSd~-~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~ 350 (681)
|++|++||+|+++++|. +. .+|...|++||+|+|+|+++| ++|+.||+|++..|||+. +.+.|+|.
T Consensus 598 L~~gveGLvhiSEls~~~~~--~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~- 674 (863)
T PRK12269 598 LAEGIEGLAHISEFSWVKKT--SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIV- 674 (863)
T ss_pred ecCCceeeeEHHHhcCcccc--CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEE-
Confidence 99999999999999994 42 356788999999999999998 589999999999999972 45788998
Q ss_pred eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 351 ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 351 ~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.+||+||.+.+|+.||||.+++++.
T Consensus 675 ~i~~~G~fV~l~~gV~GlIh~sels~~ 701 (863)
T PRK12269 675 KVTNAGAFIEMEEGIDGFLHVDDLSWV 701 (863)
T ss_pred EEecceEEEEeCCCcEEEEEhHHhhcc
Confidence 899999999999999999999999875
No 5
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-39 Score=354.46 Aligned_cols=268 Identities=22% Similarity=0.294 Sum_probs=240.0
Q ss_pred ceeEEeccCCceeEEeCcccCcc-cccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSA-LQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~-~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
+.++.+|++|+.||+|.++++|. ..+...... +|+.|.|+|+.+|++++ |+.||=+
T Consensus 205 ~~GafVdigGvdGLlHiseiS~~rv~~P~~vvk-vGd~VkvkVi~~D~e~~---RVsLSlK------------------- 261 (541)
T COG0539 205 DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVK-VGDEVKVKVISLDEERG---RVSLSLK------------------- 261 (541)
T ss_pred cCcEEEEecCeeeEEehhhccccccCCHHHhcc-cCCEEEEEEEEEccCCC---eEEEEeh-------------------
Confidence 68899999999999999999998 444455566 89999999999999999 8888765
Q ss_pred hHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707 123 LAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV 200 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV 200 (681)
+....||. ...+.+|+.+.|+|+++++||+||++..+++||+|+|||+|.+...|.+++++||.|.|
T Consensus 262 -----------~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V 330 (541)
T COG0539 262 -----------QLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEV 330 (541)
T ss_pred -----------hcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEE
Confidence 22334554 46899999999999999999999999999999999999999999889999999999999
Q ss_pred EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707 201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI 280 (681)
Q Consensus 201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV 280 (681)
+|+++|++++||.|++|++..+||+ .....|++|.++.|+|++++++|+||
T Consensus 331 ~Vl~id~e~rRIsL~iKq~~~~pw~-----------------------------~~~~~~~~g~~v~g~v~~~t~~g~fv 381 (541)
T COG0539 331 KVLDIDPERRRISLGLKQLKENPWE-----------------------------EFADKHPVGDVVEGKVKSITDFGAFV 381 (541)
T ss_pred EEEeeCchhceEEeeehhhhcChhh-----------------------------hhhhhcCCCCeEEEEEeeecccceEE
Confidence 9999999999999999999999993 34566999999999999999999999
Q ss_pred EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707 281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA 350 (681)
Q Consensus 281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~ 350 (681)
.+++|++||+|.++++|.... .+...|+.|+.++++||.+| ++|+.|++|++..+||.. ..++|.|.
T Consensus 382 ~le~gidG~vh~~d~sw~~~~--~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~- 458 (541)
T COG0539 382 ELEGGIDGLVHLSDLSWDRPG--EEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVK- 458 (541)
T ss_pred ccCCCccceEEHHhcCccccC--cHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEEEEEE-
Confidence 999999999999999998743 23449999999999999998 479999999999999983 45688888
Q ss_pred eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 351 ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 351 ~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.++|+|+++.+++.||++.++++..
T Consensus 459 ~i~~~G~~v~l~~~v~G~i~~~~~~~~ 485 (541)
T COG0539 459 SVKDKGAFVELGGGVEGLIRLSELSRD 485 (541)
T ss_pred EEccCceEEEecCceeeeeecchhhhh
Confidence 899999999999999999999999985
No 6
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.3e-37 Score=347.87 Aligned_cols=273 Identities=26% Similarity=0.336 Sum_probs=234.6
Q ss_pred ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL 123 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da 123 (681)
..+++++++|++||+|.+++++.. ...+..++|+.+.|+|+++|.+++ +++||+| .+....
T Consensus 127 ~~G~~V~~~g~~gfip~s~~~~~~--~~~~~~~vG~~i~~~V~~~d~~~~---~i~lS~k--------------~~~~~~ 187 (565)
T PRK06299 127 KGGFTVDLNGVEAFLPGSQVDVRP--VRDTDPLEGKELEFKVIKLDKKRN---NIVVSRR--------------AVLEEE 187 (565)
T ss_pred CCEEEEEECCEEEEEEHHHccCcC--CCChHHhCCCEEEEEEEEEECCCC---EEEEEhH--------------Hhhhhh
Confidence 468899999999999999999863 223456799999999999999998 9999998 111010
Q ss_pred HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707 124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203 (681)
Q Consensus 124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl 203 (681)
+... +.. .+.++++|+++.|+|+.+.++|+||+++ ++.||||+++++|.++.++.+.|++||.|+|+|+
T Consensus 188 ~~~~-----~~~-----~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~ 256 (565)
T PRK06299 188 RAEE-----REE-----LLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVL 256 (565)
T ss_pred hhhH-----HHH-----HHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEE
Confidence 0000 001 1567999999999999999999999998 5999999999999999999999999999999999
Q ss_pred EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707 204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP 283 (681)
Q Consensus 204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg 283 (681)
.+|+++++|.||+|.+..+||. ....+|++|+++.|+|+++.++|+||+|+
T Consensus 257 ~~d~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l~ 307 (565)
T PRK06299 257 KFDKEKKRVSLGLKQLGEDPWE-----------------------------AIEKKYPVGSKVKGKVTNITDYGAFVELE 307 (565)
T ss_pred EEeCCCCeEEEEEEecccChhH-----------------------------HHHhhCCCCCEEEEEEEEEeCCeEEEEeC
Confidence 9999999999999999989983 34567999999999999999999999999
Q ss_pred CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEeec
Q 005707 284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAATN 353 (681)
Q Consensus 284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~i~ 353 (681)
+|++||+|.++++|.+. ..+|...|++||.|.|+|+.+| ++++.||+|+...+||. ++.+.|.|. .++
T Consensus 308 ~~v~Glv~~sel~~~~~-~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~-~v~ 385 (565)
T PRK06299 308 EGIEGLVHVSEMSWTKK-NKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVK-NIT 385 (565)
T ss_pred CCCEEEEEHHHcCcccc-ccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEE-EEe
Confidence 99999999999998642 2345567999999999999997 48999999999999986 356789998 799
Q ss_pred ccEEEEEEcCCeEEEeeCCccccc
Q 005707 354 PFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 354 ~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
++|+||++.+++.||+|.+++++.
T Consensus 386 ~~G~fV~l~~~v~g~i~~s~l~~~ 409 (565)
T PRK06299 386 DFGAFVGLEGGIDGLVHLSDISWD 409 (565)
T ss_pred cceEEEECCCCCEEEEEHHHcCcc
Confidence 999999998899999999999864
No 7
>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=5.8e-36 Score=332.54 Aligned_cols=272 Identities=28% Similarity=0.356 Sum_probs=231.7
Q ss_pred eeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhH
Q 005707 45 QRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLA 124 (681)
Q Consensus 45 ~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~dae 124 (681)
.+++++++|++||+|.++++....+ ....++|+.+.|+|+++|...+ ++++|+| ......+
T Consensus 114 ~g~~V~i~g~~~flP~s~~~~~~~~--~~~~~vG~~i~~~v~~~~~~~~---~iv~Srk--------------~~l~~~~ 174 (516)
T TIGR00717 114 GGFIVDLNGVEAFLPGSQVDVKPIK--DLDSLIGKTLKFKIIKLDQKRN---NIVVSRR--------------AYLEEER 174 (516)
T ss_pred CEEEEEECCEEEEEeHHHhcCcccC--chhhhCCCEEEEEEEEEECCCC---cEEEEHH--------------HHHHHHH
Confidence 6788999999999999998764211 2345799999999999999877 8999987 1111111
Q ss_pred HhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 125 ESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 125 k~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+ . .+.. .+..+++|++++|+|+++.++|+||+++| ++||||.++++|.+..++.+.|++|+.|+|+|+.
T Consensus 175 ~----~-~~~~-----~~~~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~ 243 (516)
T TIGR00717 175 S----Q-AREE-----LLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIK 243 (516)
T ss_pred H----H-HHHH-----HHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEE
Confidence 0 0 0111 14579999999999999999999999976 9999999999999999999999999999999999
Q ss_pred EeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCC
Q 005707 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPE 284 (681)
Q Consensus 205 VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~ 284 (681)
+|++++++.||+|.+..+||. ....++++|+++.|+|+++.++|+||++++
T Consensus 244 ~d~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~ 294 (516)
T TIGR00717 244 FDKEKGRISLSLKQLGEDPWE-----------------------------AIEKKFPVGDKITGRVTNLTDYGVFVEIEE 294 (516)
T ss_pred EECCCCcEEEEEEecchhHHH-----------------------------HHHhhccCCCEEEEEEEEeeCCcEEEEeCC
Confidence 999999999999999888883 345679999999999999999999999999
Q ss_pred CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEeecc
Q 005707 285 GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAATNP 354 (681)
Q Consensus 285 GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~i~~ 354 (681)
|+.||||.++++|.+. ..++...|++||.|.|+|+.+| ++++.||+|+...+||. ++.+.|+|. .+.+
T Consensus 295 ~v~g~v~~sels~~~~-~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~-~v~~ 372 (516)
T TIGR00717 295 GIEGLVHVSEMSWVKK-NSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIK-KITD 372 (516)
T ss_pred CCEEEEEHHHcCCccc-cCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEE-EEec
Confidence 9999999999998632 2234567999999999999997 58999999999999984 467789999 7999
Q ss_pred cEEEEEEcCCeEEEeeCCccccc
Q 005707 355 FVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 355 fGlfV~l~~gI~GfIp~~els~~ 377 (681)
+|+||.+.+|+.||+|.+++++.
T Consensus 373 ~G~fV~l~~~v~glv~~s~ls~~ 395 (516)
T TIGR00717 373 FGAFVELEGGIDGLIHLSDISWD 395 (516)
T ss_pred ceEEEECCCCCEEEEEHHHCcCc
Confidence 99999999999999999999975
No 8
>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=3.8e-35 Score=326.02 Aligned_cols=272 Identities=19% Similarity=0.239 Sum_probs=230.1
Q ss_pred ceeEEeccCCceeEEeCcccCcccccc-cchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHK-SALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~-~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
+.++.++++|+.||+|.+++++...+. ..+.. +|+.+.|+|+.+|.+++ ++.+|.+ .+...
T Consensus 200 ~~G~~V~l~g~~g~lp~~e~s~~~~~~~~~~~~-vG~~v~v~Vl~~d~~~~---~i~lS~k--------------~~~~~ 261 (516)
T TIGR00717 200 DFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVK-VGQEVKVKVIKFDKEKG---RISLSLK--------------QLGED 261 (516)
T ss_pred CCeEEEEECCEEEEEEHHHcCCCCCCCHHHhcc-CCCEEEEEEEEEECCCC---cEEEEEE--------------ecchh
Confidence 467888999999999999998763222 22233 89999999999999888 8899877 11000
Q ss_pred hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEE
Q 005707 123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVR 201 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVk 201 (681)
+. . . ....+++|+++.|+|+++.++|+||+++.++.||||+++++|+ ...++...|++||.|+|+
T Consensus 262 p~---~------~-----~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~ 327 (516)
T TIGR00717 262 PW---E------A-----IEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVM 327 (516)
T ss_pred HH---H------H-----HHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEE
Confidence 00 0 0 0246889999999999999999999998889999999999986 456677789999999999
Q ss_pred EEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707 202 LIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS 281 (681)
Q Consensus 202 Vl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe 281 (681)
|+.+|++++++.||+|.+..+||. ....++++|+++.|+|++++++|+||+
T Consensus 328 V~~id~~~~~i~lS~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~v~~~G~fV~ 378 (516)
T TIGR00717 328 ILDIDPERRRLSLGLKQCKANPWE-----------------------------QFEEKHPVGDRVTGKIKKITDFGAFVE 378 (516)
T ss_pred EEEEcCCCCEEEEEehhcccCcHH-----------------------------HHHHhCCCCCEEEEEEEEEecceEEEE
Confidence 999999999999999998888883 345678999999999999999999999
Q ss_pred eCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEEEe
Q 005707 282 LPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIHAA 351 (681)
Q Consensus 282 Ig~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~~~ 351 (681)
+++|++||+|.++++|.+. ..++...|++||.|.|+|+.+| ++||.||+|++..|||. ++.+.|.|. .
T Consensus 379 l~~~v~glv~~s~ls~~~~-~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~-~ 456 (516)
T TIGR00717 379 LEGGIDGLIHLSDISWDKD-GREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVT-E 456 (516)
T ss_pred CCCCCEEEEEHHHCcCccc-CCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEE-E
Confidence 9999999999999999753 1234678999999999999997 58999999999999985 245788888 7
Q ss_pred ecccEEEEEEcCCeEEEeeCCcccccc
Q 005707 352 TNPFVLAFRSNKDISSFLDERDKSATA 378 (681)
Q Consensus 352 i~~fGlfV~l~~gI~GfIp~~els~~~ 378 (681)
+.++|+||++.+++.||+|.+++++..
T Consensus 457 v~~~G~fV~l~~~~~Glv~~s~l~~~~ 483 (516)
T TIGR00717 457 IKDFGAFVELPGGVEGLIRNSELSENR 483 (516)
T ss_pred EecceEEEEcCCCeEEEEEHHHcCccc
Confidence 999999999999999999999999863
No 9
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.7e-34 Score=323.09 Aligned_cols=269 Identities=23% Similarity=0.296 Sum_probs=231.0
Q ss_pred ceeEEeccCCceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
+.++.++++|+.||+|.++++|.. .+...+.. +|+.+.|+|+.+|.+++ ++.||.+ ...
T Consensus 214 ~~G~~V~i~g~~glv~~se~s~~~~~~~~~~~k-vG~~v~v~V~~~d~~~~---~i~lS~k--------------~~~-- 273 (565)
T PRK06299 214 DYGAFVDLGGVDGLLHITDISWKRVNHPSEVVN-VGDEVKVKVLKFDKEKK---RVSLGLK--------------QLG-- 273 (565)
T ss_pred CCeEEEEECCEEEEEEHHHhcccccCCHhhcCC-CCCEEEEEEEEEeCCCC---eEEEEEE--------------ecc--
Confidence 467888999999999999998862 22222333 79999999999999888 8899876 000
Q ss_pred hHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEE
Q 005707 123 LAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVK 199 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~Vk 199 (681)
..+|. ...+++|+++.|+|+++.++|+||+|+.++.||+|+++++|. +..++...|++||.|+
T Consensus 274 --------------~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~ 339 (565)
T PRK06299 274 --------------EDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVE 339 (565)
T ss_pred --------------cChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEE
Confidence 01111 246889999999999999999999998789999999999986 4577778899999999
Q ss_pred EEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707 200 VRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF 279 (681)
Q Consensus 200 VkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF 279 (681)
|+|+++|+++++|.||+|.+..+||. ....+|++|+++.|+|+++.++|+|
T Consensus 340 v~V~~id~~~~~i~ls~k~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~v~~~G~f 390 (565)
T PRK06299 340 VMVLEIDEEKRRISLGLKQCKENPWE-----------------------------EFAEKYPVGDVVEGKVKNITDFGAF 390 (565)
T ss_pred EEEEEEcCCCCEEEEehHHhccchhh-----------------------------hHHHhCCCCCEEEEEEEEEecceEE
Confidence 99999999999999999999888882 3456789999999999999999999
Q ss_pred EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC--------cceeeeEEE
Q 005707 280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN--------LQLTQGVIH 349 (681)
Q Consensus 280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e--------~~lv~G~V~ 349 (681)
|+|+++++||+|.++++|.+. ...+...|++||.|+|+|+++| +++|.||+|+...|||. ++.+.|+|.
T Consensus 391 V~l~~~v~g~i~~s~l~~~~~-~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~ 469 (565)
T PRK06299 391 VGLEGGIDGLVHLSDISWDKK-GEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVT 469 (565)
T ss_pred EECCCCCEEEEEHHHcCcccc-ccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEE
Confidence 999999999999999998763 1345789999999999999997 58999999999999985 357899998
Q ss_pred EeecccEEEEEEcCCeEEEeeCCccccc
Q 005707 350 AATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 350 ~~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.++|+||.+.+|+.||||.+++++.
T Consensus 470 -~v~~~G~fV~l~~gi~g~i~~se~s~~ 496 (565)
T PRK06299 470 -EVKDKGAFVELEDGVEGLIRASELSRD 496 (565)
T ss_pred -EEecCceEEecCCCcEEEEEHHHhcch
Confidence 899999999999999999999999876
No 10
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.8e-34 Score=319.83 Aligned_cols=269 Identities=21% Similarity=0.255 Sum_probs=220.8
Q ss_pred ceeEEeccC-CceeEEeCcccCcccc-cccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCCh
Q 005707 44 SQRFLLPLP-SSVRFFSQFQSGSALQ-HKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASP 121 (681)
Q Consensus 44 ~~~l~~dl~-glrGfIP~sq~~~~~~-~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~ 121 (681)
..++++|+. +++||||.+++++... +...... +|+.|.++|+.+|.... +++||.| .+
T Consensus 48 ~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~-vGd~Ie~~V~~~~~~~g---~liLS~k--------------~~-- 107 (486)
T PRK07899 48 RDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVE-VGDEVEALVLQKEDKEG---RLILSKK--------------RA-- 107 (486)
T ss_pred CCcEEEEECCCcEEEEEHHHhcccccCChhhcCC-CCCEEEEEEEEEECCCC---eEEEEeh--------------hh--
Confidence 467889987 7899999999987521 1122233 89999999999988777 7999987 00
Q ss_pred hhHHhhhchhhhhcCCCCCCcC-CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707 122 TLAESRRSRTARKSEMPPVKNE-DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV 200 (681)
Q Consensus 122 daek~~~kr~~rk~e~~~lt~~-~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV 200 (681)
. . ....-.+. .++.|++++|+|+++.++|+||+| | ++||||.+++++.++.++.. .+|+.|+|
T Consensus 108 --~---~-------~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-G-i~gflP~Sel~~~~~~~~~~--~vGq~V~v 171 (486)
T PRK07899 108 --Q---Y-------ERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-G-LRGFLPASLVEMRRVRDLQP--YIGQEIEA 171 (486)
T ss_pred --c---c-------cchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-C-CEEEEEhhHhcccccCChhh--cCCCEEEE
Confidence 0 0 00000122 245799999999999999999999 4 89999999999988887765 39999999
Q ss_pred EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707 201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI 280 (681)
Q Consensus 201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV 280 (681)
+|+.+|+++++|.||+|.+....+. ..| ...+.++++|+++.|+|++++++|+||
T Consensus 172 kVleid~~~~~ivLSrr~~l~~~~~---------------~~~----------~~~~~~lk~G~iv~G~V~~i~~~G~FV 226 (486)
T PRK07899 172 KIIELDKNRNNVVLSRRAWLEQTQS---------------EVR----------SEFLNQLQKGQVRKGVVSSIVNFGAFV 226 (486)
T ss_pred EEEEEECCCCEEEEEhHHHHHhhhH---------------HHH----------HHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 9999999999999999976443221 001 245788999999999999999999999
Q ss_pred EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707 281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA 350 (681)
Q Consensus 281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~ 350 (681)
+|+ |++||||.++++|.++. ++...|++||.|+|+|+++| ++||.||+|++..|||.. +.+.|+|.
T Consensus 227 dlg-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~- 302 (486)
T PRK07899 227 DLG-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVT- 302 (486)
T ss_pred EEC-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEE-
Confidence 996 89999999999998854 45788999999999999997 589999999999999872 45789999
Q ss_pred eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 351 ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 351 ~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.+||+||++.+|+.||+|.+++++.
T Consensus 303 ~I~~fGvFVeL~~gieGLvh~SeLs~~ 329 (486)
T PRK07899 303 KLVPFGAFVRVEEGIEGLVHISELAER 329 (486)
T ss_pred EEeccEEEEEeCCCcEEEEEHHHcCcc
Confidence 899999999999999999999999875
No 11
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.2e-33 Score=313.28 Aligned_cols=232 Identities=28% Similarity=0.383 Sum_probs=198.6
Q ss_pred eeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhH
Q 005707 45 QRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLA 124 (681)
Q Consensus 45 ~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~dae 124 (681)
.++++++ |++||+|.+++++.. ...+..++|+.+.|+|+++|.+++ +++||+| + ......
T Consensus 136 ~G~~Vdl-Gi~gflP~Sel~~~~--~~~~~~~vGq~V~vkVleid~~~~---~ivLSrr------~--------~l~~~~ 195 (486)
T PRK07899 136 GGLILDI-GLRGFLPASLVEMRR--VRDLQPYIGQEIEAKIIELDKNRN---NVVLSRR------A--------WLEQTQ 195 (486)
T ss_pred CeEEEEE-CCEEEEEhhHhcccc--cCChhhcCCCEEEEEEEEEECCCC---EEEEEhH------H--------HHHhhh
Confidence 5788899 899999999999863 223456799999999999999988 8999987 0 000000
Q ss_pred HhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 125 ESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 125 k~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
. ..+.. .+..+++|+++.|+|+++.++|+||+|+| ++||||+++|+|.++.++.+.|++||.|+|+|+.
T Consensus 196 ----~-~~~~~-----~~~~lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~ 264 (486)
T PRK07899 196 ----S-EVRSE-----FLNQLQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLD 264 (486)
T ss_pred ----H-HHHHH-----HHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEE
Confidence 0 00111 14578999999999999999999999976 9999999999999999999999999999999999
Q ss_pred EeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCC
Q 005707 205 ANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPE 284 (681)
Q Consensus 205 VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~ 284 (681)
+|+++++|.||+|++..+||. ....++++|+++.|+|+++.++|+||+|.+
T Consensus 265 iD~e~~rI~LSlK~~~~dPw~-----------------------------~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~ 315 (486)
T PRK07899 265 VDMDRERVSLSLKATQEDPWQ-----------------------------QFARTHAIGQIVPGKVTKLVPFGAFVRVEE 315 (486)
T ss_pred EECCCCEEEEEEeeccccchh-----------------------------hhHHhcCCCCEEEEEEEEEeccEEEEEeCC
Confidence 999999999999999999982 345668899999999999999999999999
Q ss_pred CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707 285 GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG 338 (681)
Q Consensus 285 GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP 338 (681)
|++||||++++++.++. .+...|++||.|+|+|+++| ++||.||+|+...+-
T Consensus 316 gieGLvh~SeLs~~~v~--~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 316 GIEGLVHISELAERHVE--VPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred CcEEEEEHHHcCccccc--CccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence 99999999999998764 35788999999999999997 699999999986553
No 12
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.1e-32 Score=292.66 Aligned_cols=271 Identities=20% Similarity=0.272 Sum_probs=221.0
Q ss_pred ceeEEecc-C-CceeEEeCcccCccc-ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCC
Q 005707 44 SQRFLLPL-P-SSVRFFSQFQSGSAL-QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEAS 120 (681)
Q Consensus 44 ~~~l~~dl-~-glrGfIP~sq~~~~~-~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~ 120 (681)
+.++++++ . ++.||+|.+++.+.. ........ +|+.+.|.|+.+|.+.+ +++||.++. .
T Consensus 30 ~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~-vGd~v~~~V~~v~~~~~---~i~lS~k~~--------------~ 91 (390)
T PRK06676 30 DKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVK-VGDELEVYVLKVEDGEG---NLLLSKRRL--------------E 91 (390)
T ss_pred CCeEEEEEecCCcEEEEEHHHhccccccCcccccC-CCCEEEEEEEEEECCCC---CEEEEHHHh--------------h
Confidence 36789998 4 899999999987641 11111233 89999999999999888 899988610 0
Q ss_pred hhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEE
Q 005707 121 PTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKV 200 (681)
Q Consensus 121 ~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkV 200 (681)
.. +..... ...++.|+++.|+|+++.++|+||+++| +.||||++++++.+..++... +|+.++|
T Consensus 92 --~~-----~~~~~~------~~~~~~G~~v~g~V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~~--vG~~v~~ 155 (390)
T PRK06676 92 --AE-----KAWDKL------EEKFEEGEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTLEV 155 (390)
T ss_pred --hh-----hhHHHH------HHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHHc--CCCEEEE
Confidence 00 000000 2356899999999999999999999976 799999999999888887653 9999999
Q ss_pred EEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE
Q 005707 201 RLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI 280 (681)
Q Consensus 201 kVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV 280 (681)
+|+.+|++++++.||+|.+....+. ..+...+.++++|+++.|+|+++.++|+||
T Consensus 156 ~Vl~~d~~~~~i~lS~k~~~~~~~~-------------------------~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV 210 (390)
T PRK06676 156 KIIELDPEKNRVILSRRAVVEEERA-------------------------AKKEELLSSLKEGDVVEGTVARLTDFGAFV 210 (390)
T ss_pred EEEEEECCCCEEEEEeHHHhhhhhh-------------------------hHHHHHHhhCCCCCEEEEEEEEEecceEEE
Confidence 9999999999999999976553320 001134677899999999999999999999
Q ss_pred EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEE
Q 005707 281 SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHA 350 (681)
Q Consensus 281 eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~ 350 (681)
+++ |++||||.++++|.++. ++...|++||.|+|+|+++| ++++.||+|+...+||.. ..+.|+|.
T Consensus 211 ~l~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~- 286 (390)
T PRK06676 211 DIG-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVK- 286 (390)
T ss_pred EeC-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEE-
Confidence 996 89999999999998753 45778999999999999997 489999999999999862 45788998
Q ss_pred eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 351 ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 351 ~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
.+.++|+||++.+|+.||+|.+++++.
T Consensus 287 ~i~~~G~fV~l~~gi~Glv~~se~~~~ 313 (390)
T PRK06676 287 RLTDFGAFVEVLPGVEGLVHISQISHK 313 (390)
T ss_pred EEeCceEEEEECCCCeEEEEhHHcCcc
Confidence 799999999999999999999999875
No 13
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.1e-31 Score=289.30 Aligned_cols=237 Identities=28% Similarity=0.388 Sum_probs=202.5
Q ss_pred ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTL 123 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~da 123 (681)
..+++++++|++||+|.+++++.... ....++|+.+.|+|+++|++.+ +++||.| .+....
T Consensus 118 ~~G~~V~~~G~~gflp~~el~~~~~~--~~~~~vG~~v~~~Vl~~d~~~~---~i~lS~k--------------~~~~~~ 178 (390)
T PRK06676 118 KGGLVVDVEGVRGFIPASLISTRFVE--DFSDFKGKTLEVKIIELDPEKN---RVILSRR--------------AVVEEE 178 (390)
T ss_pred CCeEEEEECCEEEEEEHHHcCCccCC--ChHHcCCCEEEEEEEEEECCCC---EEEEEeH--------------HHhhhh
Confidence 46889999999999999999876322 2345699999999999999888 8999987 000000
Q ss_pred HHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707 124 AESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203 (681)
Q Consensus 124 ek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl 203 (681)
. ..... . .+..+++|+++.|+|+++.++|+||++++ ++||||+++++|.++.++.+.|++||.|+|+|+
T Consensus 179 ~----~~~~~-~-----~~~~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl 247 (390)
T PRK06676 179 R----AAKKE-E-----LLSSLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVL 247 (390)
T ss_pred h----hhHHH-H-----HHhhCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEE
Confidence 0 00000 0 14568899999999999999999999976 999999999999999999999999999999999
Q ss_pred EEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeC
Q 005707 204 EANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLP 283 (681)
Q Consensus 204 ~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg 283 (681)
.+|+++++|.||+|.+..+||. ....++++|+++.|+|+++.++|+||++.
T Consensus 248 ~vd~~~~~i~lS~k~~~~~~~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l~ 298 (390)
T PRK06676 248 SIDWETERISLSLKDTLPGPWE-----------------------------GVEEKLPEGDVIEGTVKRLTDFGAFVEVL 298 (390)
T ss_pred EEeCCCCEEEEEEeecccCccc-----------------------------cchhhhcCCcEEEEEEEEEeCceEEEEEC
Confidence 9999999999999998888872 34678999999999999999999999999
Q ss_pred CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc
Q 005707 284 EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL 341 (681)
Q Consensus 284 ~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~ 341 (681)
+|+.||+|.++++|.++. ++...|++||.|.|+|+++| ++++.|++|+...+||..
T Consensus 299 ~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~ 356 (390)
T PRK06676 299 PGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEE 356 (390)
T ss_pred CCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhh
Confidence 999999999999988753 45778999999999999998 699999999999999974
No 14
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=7.3e-32 Score=299.95 Aligned_cols=236 Identities=25% Similarity=0.315 Sum_probs=198.7
Q ss_pred ceeEEecc-CCceeEEeCcccCcccccc-cchhhcccceeEEEEEecCCCCCC-CCcceecCCCCCcccccccccccCCC
Q 005707 44 SQRFLLPL-PSSVRFFSQFQSGSALQHK-SALHIISATGINVAVEESDSPAAD-DDSAGASDIPSDVETSESSSIKSEAS 120 (681)
Q Consensus 44 ~~~l~~dl-~glrGfIP~sq~~~~~~~~-~~~~~lvG~~i~VkVievD~~~~~-~~~lvlSer~s~v~~ae~ss~~sea~ 120 (681)
..++.+++ .|+.||||.+++++..... ..+.. +|+.+.|+|+++|.+.+. -.++.||.| .+
T Consensus 215 ~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~-vGd~i~vkVl~id~~~~~~~~ri~lS~K--------------~~- 278 (491)
T PRK13806 215 PFGAFVELAPGVEGMVHISELSWSRVQKADEAVS-VGDTVRVKVLGIERAKKGKGLRISLSIK--------------QA- 278 (491)
T ss_pred CCeEEEEcCCCcEEEEEHHHCCCccccChhHhcC-CCCEEEEEEEEEecccCCcceEEEEEeh--------------hh-
Confidence 46889998 5899999999999862211 22233 899999999999997631 016888876 00
Q ss_pred hhhHHhhhchhhhhcCCCCCC--cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCE
Q 005707 121 PTLAESRRSRTARKSEMPPVK--NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQE 197 (681)
Q Consensus 121 ~daek~~~kr~~rk~e~~~lt--~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~ 197 (681)
...+|. ...+++|+++.|+|+++.++|+||+++.+++||||+++++| .++.++.+.|++||.
T Consensus 279 ---------------~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~ 343 (491)
T PRK13806 279 ---------------GGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA 343 (491)
T ss_pred ---------------hcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCE
Confidence 011222 45789999999999999999999999877999999999998 567888999999999
Q ss_pred EEEEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecce
Q 005707 198 VKVRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSG 277 (681)
Q Consensus 198 VkVkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~G 277 (681)
|+|+|+.+|+++++|.||+|++..+||. ....+|++|+++.|+|+++++||
T Consensus 344 v~vkVl~iD~e~~ri~Ls~K~~~~~p~~-----------------------------~~~~~~~vG~~v~G~V~~i~~~G 394 (491)
T PRK13806 344 VAVKIKDIDPAKRRISLSLRDAEGDPWA-----------------------------DVAERFAPGTTVTGTVEKRAQFG 394 (491)
T ss_pred EEEEEEEEEccCCEEEEEEeecccChhH-----------------------------HhhhhCCCCCEEEEEEEEEecCc
Confidence 9999999999999999999999999993 45678999999999999999999
Q ss_pred EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC-----CCcCCc
Q 005707 278 AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED-----DVGSNL 341 (681)
Q Consensus 278 aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~-----~DP~e~ 341 (681)
+||++.+|++||||+++++|.+. .++...|++||.|+|+|+.+| ++||.||+|... .+||..
T Consensus 395 ~FV~l~~gv~Gli~~se~s~~~~--~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~~~~~~~~~~~~~ 463 (491)
T PRK13806 395 LFVNLAPGVTGLLPASVISRAGK--PATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDDWKQ 463 (491)
T ss_pred eEEEcCCCcEEEEEHHHcCcccc--cchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehhhhhhhhhhHHHh
Confidence 99999999999999999999875 345789999999999999997 589999999762 366763
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.97 E-value=7.6e-30 Score=292.04 Aligned_cols=270 Identities=21% Similarity=0.269 Sum_probs=220.4
Q ss_pred eeEEeccC-CceeEEeCcccCccccc-ccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChh
Q 005707 45 QRFLLPLP-SSVRFFSQFQSGSALQH-KSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 45 ~~l~~dl~-glrGfIP~sq~~~~~~~-~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
.+++++++ ++.||+|.+++.+.... ...... +|+.+.|.|+.+|.+.+ +++||.++. .. .
T Consensus 316 ~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~-vGd~V~v~V~~vd~~~g---~i~LS~k~~------------~~--~ 377 (647)
T PRK00087 316 NEVFVDVGYKSEGVIPLRELTLDEISSLKESVK-VGDEIEVKVLKLEDEDG---YVVLSKKEA------------DR--E 377 (647)
T ss_pred CEEEEEECCCeEEEEEHHHhcccccCChhhccC-CCCEEEEEEEEEECCCC---cEEEEeehh------------cc--h
Confidence 56788885 67899999998865211 122233 89999999999998877 899998711 00 0
Q ss_pred hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEE
Q 005707 123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkV 202 (681)
..+ ..+ ...++.|+++.|+|+++.++|+||++++ ++||||.+++++.+..++... +|+.++|+|
T Consensus 378 ~~~----~~l---------~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~~--vG~~v~v~V 441 (647)
T PRK00087 378 KAW----KEL---------EEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSEY--KGQELEVKI 441 (647)
T ss_pred hHH----HHH---------HHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHHh--CCCEEEEEE
Confidence 011 001 1246899999999999999999999998 999999999999988887653 899999999
Q ss_pred EEEeccCCc-eEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEE
Q 005707 203 IEANAETGR-ISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFIS 281 (681)
Q Consensus 203 l~VD~ekgr-I~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVe 281 (681)
+.+|+++++ +.+|+|........ ......+.++++|+++.|+|+++.++|+||+
T Consensus 442 l~vd~e~~~~l~lS~k~~~~~~~~-------------------------~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~ 496 (647)
T PRK00087 442 IEFNRKRRKKVVLSRKAILEEEKE-------------------------KKKEETWNSLEEGDVVEGEVKRLTDFGAFVD 496 (647)
T ss_pred EEEEcCCCcEEEEEeHHHhhhhhh-------------------------hHHHHHHHhCCCCCEEEEEEEEEeCCcEEEE
Confidence 999999998 99999976431110 0112456778999999999999999999999
Q ss_pred eCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCCc--------ceeeeEEEEe
Q 005707 282 LPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSNL--------QLTQGVIHAA 351 (681)
Q Consensus 282 Ig~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e~--------~lv~G~V~~~ 351 (681)
+ +|++||||.++++|.++. ++...|++||.|.|+|+++| ++++.||+|+...+||.. +.+.|+|. .
T Consensus 497 l-~gv~Gll~~sels~~~~~--~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~-~ 572 (647)
T PRK00087 497 I-GGVDGLLHVSEISWGRVE--KPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVV-R 572 (647)
T ss_pred E-CCEEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEE-E
Confidence 9 699999999999998754 45788999999999999997 499999999999999873 45688888 7
Q ss_pred ecccEEEEEEcCCeEEEeeCCccccc
Q 005707 352 TNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 352 i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
+.+||+||++.+++.||+|.+++++.
T Consensus 573 i~~~G~fV~l~~~i~Gli~~sel~~~ 598 (647)
T PRK00087 573 IAPFGAFVELEPGVDGLVHISQISWK 598 (647)
T ss_pred EECCeEEEEECCCCEEEEEhhhcCcc
Confidence 99999999999999999999999875
No 16
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=2.6e-29 Score=266.11 Aligned_cols=224 Identities=19% Similarity=0.248 Sum_probs=184.9
Q ss_pred ceeEEeccCC-ceeEEeCcccCcccc-cccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCCh
Q 005707 44 SQRFLLPLPS-SVRFFSQFQSGSALQ-HKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASP 121 (681)
Q Consensus 44 ~~~l~~dl~g-lrGfIP~sq~~~~~~-~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~ 121 (681)
..++++|+++ .+||+|.+++++... ....+.. +|+.++|+|+++|.+.. +++||.|+.
T Consensus 44 ~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~-~G~~v~~~Vi~~~~~~~---~i~lS~k~~---------------- 103 (318)
T PRK07400 44 PRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQ-PNETREFFILSDENEDG---QLTLSIRRI---------------- 103 (318)
T ss_pred CCEEEEEECCCeEEEEEHHHhccccccCHHHccC-CCCEEEEEEEEEeCCCC---eEEEehhhh----------------
Confidence 4689999965 799999999987631 1222333 69999999999998877 899998810
Q ss_pred hhHHhhhchhhhhcCCCCCC-c-CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEE
Q 005707 122 TLAESRRSRTARKSEMPPVK-N-EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVK 199 (681)
Q Consensus 122 daek~~~kr~~rk~e~~~lt-~-~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~Vk 199 (681)
... ..|. + ...+.|+++.|+|+++.++|+||+++| ++||||+++++|.+.. ..+ +|+.|.
T Consensus 104 --~~~-----------~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~G-v~gfip~s~ls~~~~~---~~~-vG~~i~ 165 (318)
T PRK07400 104 --EYM-----------RAWERVRQLQKEDATVRSEVFATNRGGALVRIEG-LRGFIPGSHISTRKPK---EEL-VGEELP 165 (318)
T ss_pred --hhh-----------hHHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCccCCc---ccc-CCCEEE
Confidence 000 0011 1 134569999999999999999999975 9999999999986433 334 999999
Q ss_pred EEEEEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEE
Q 005707 200 VRLIEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAF 279 (681)
Q Consensus 200 VkVl~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaF 279 (681)
|+|+.+|+++++|.||+|.+.... .+.++++|+++.|+|++|++||+|
T Consensus 166 ~kVl~id~~~~~i~lS~K~~~~~~--------------------------------~~~~~k~G~vv~G~V~~I~~~G~f 213 (318)
T PRK07400 166 LKFLEVDEERNRLVLSHRRALVER--------------------------------KMNRLEVGEVVVGTVRGIKPYGAF 213 (318)
T ss_pred EEEEEEEcccCEEEEEhhHhhhhh--------------------------------hhccCCCCCEEEEEEEEEECCeEE
Confidence 999999999999999999654322 266799999999999999999999
Q ss_pred EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCcCC
Q 005707 280 ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVGSN 340 (681)
Q Consensus 280 VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP~e 340 (681)
|+++ |+.||||+++++|.+.. ++...|++||.|+|+|+++| ++++.||+|++..|||+
T Consensus 214 V~i~-gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~ 273 (318)
T PRK07400 214 IDIG-GVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGD 273 (318)
T ss_pred EEEC-CEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhh
Confidence 9996 89999999999999854 45889999999999999998 59999999999999997
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.97 E-value=2.5e-29 Score=287.78 Aligned_cols=234 Identities=22% Similarity=0.318 Sum_probs=200.3
Q ss_pred ceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCc-ceecCCCCCcccccccccccCCChh
Q 005707 44 SQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDS-AGASDIPSDVETSESSSIKSEASPT 122 (681)
Q Consensus 44 ~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~-lvlSer~s~v~~ae~ss~~sea~~d 122 (681)
..+++++++|++||+|.+++++... .++..++|+.+.|+|+++|++++ + +++|.| .....
T Consensus 402 ~~G~~V~lggi~gfiP~sel~~~~~--~d~~~~vG~~v~v~Vl~vd~e~~---~~l~lS~k--------------~~~~~ 462 (647)
T PRK00087 402 KGGLLVDYGGVRAFLPASHVELGYV--EDLSEYKGQELEVKIIEFNRKRR---KKVVLSRK--------------AILEE 462 (647)
T ss_pred CCeEEEEECCEEEEEEHHHhCcccc--CCHHHhCCCEEEEEEEEEEcCCC---cEEEEEeH--------------HHhhh
Confidence 3578999999999999999987632 23345699999999999999988 7 999987 00000
Q ss_pred hHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEE
Q 005707 123 LAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202 (681)
Q Consensus 123 aek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkV 202 (681)
. +..... ..+.++++|+++.|+|+++.++|+||++ ++++||||+++++|.++.++.+.|++||.|+|+|
T Consensus 463 -~-----~~~~~~----~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV 531 (647)
T PRK00087 463 -E-----KEKKKE----ETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYI 531 (647)
T ss_pred -h-----hhhHHH----HHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEE
Confidence 0 000000 1255789999999999999999999999 5699999999999999999999999999999999
Q ss_pred EEEeccCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEe
Q 005707 203 IEANAETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISL 282 (681)
Q Consensus 203 l~VD~ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeI 282 (681)
+++|+++++|.||+|++..+||. ....+|++|+++.|+|+++.++|+||+|
T Consensus 532 ~~id~~~~~I~lS~K~~~~~p~~-----------------------------~~~~~~~~G~~v~g~V~~i~~~G~fV~l 582 (647)
T PRK00087 532 LDIDKENKKLSLSLKKLLPDPWE-----------------------------NVEEKYPVGSIVLGKVVRIAPFGAFVEL 582 (647)
T ss_pred EEEECCCCEEEEEeeccccChhh-----------------------------hhhhhccCCeEEEEEEEEEECCeEEEEE
Confidence 99999999999999999998882 3456789999999999999999999999
Q ss_pred CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707 283 PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG 338 (681)
Q Consensus 283 g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP 338 (681)
.+|+.||+|.++++|.++. ++...|++||.|+|+|+++| ++|+.|++|...++|
T Consensus 583 ~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 583 EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 9999999999999998753 45788999999999999997 599999999999888
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=1e-27 Score=254.00 Aligned_cols=197 Identities=21% Similarity=0.336 Sum_probs=172.8
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch-h
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD-I 222 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~-d 222 (681)
.++.|+++.|+|.++.++|+||+||++.+||||+++++|+++.++.+.|++||.|+|+|+++|.+++++.||+|.+.. .
T Consensus 28 ~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~ 107 (318)
T PRK07400 28 HFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMR 107 (318)
T ss_pred hcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhh
Confidence 589999999999999999999999998999999999999999999999999999999999999999999999998753 5
Q ss_pred hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc
Q 005707 223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN 302 (681)
Q Consensus 223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~ 302 (681)
+|. .....+..|+++.|+|+++.++|+||+++ |+.||||.++++|...
T Consensus 108 ~w~-----------------------------~l~~~~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~-- 155 (318)
T PRK07400 108 AWE-----------------------------RVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKP-- 155 (318)
T ss_pred HHH-----------------------------HHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCC--
Confidence 552 23344567999999999999999999995 9999999999998542
Q ss_pred cCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc-CC----cceeeeEEEEeecccEEEEEEcCCeEEEeeCCccc
Q 005707 303 MMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG-SN----LQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKS 375 (681)
Q Consensus 303 ~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP-~e----~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~~els 375 (681)
... .+|+.|.|+|+++| ++|+.||+|+...+. +. ++++.|+|. .+.+||+||.+ .|+.||+|.++++
T Consensus 156 ---~~~-~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~-~I~~~G~fV~i-~gv~Gllhisels 229 (318)
T PRK07400 156 ---KEE-LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVR-GIKPYGAFIDI-GGVSGLLHISEIS 229 (318)
T ss_pred ---ccc-cCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEE-EEECCeEEEEE-CCEEEEEEHHHcc
Confidence 233 49999999999997 489999999765443 22 477899999 89999999998 6899999999999
Q ss_pred ccc
Q 005707 376 ATA 378 (681)
Q Consensus 376 ~~~ 378 (681)
+..
T Consensus 230 ~~~ 232 (318)
T PRK07400 230 HEH 232 (318)
T ss_pred ccc
Confidence 874
No 19
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.69 E-value=1.3e-18 Score=184.32 Aligned_cols=149 Identities=15% Similarity=0.267 Sum_probs=127.6
Q ss_pred CCCC-CCcEEEEEEEEEecCeeEEEEC--CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 143 EDLI-PGATFTGKVRSIQPFGAFIDFG--AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 143 ~~Lk-vGdIVeGkV~sV~d~GaFVdLg--ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
..+. +|++|.|+|++|.+||+||+|. ++++||||+++|+|.++.++.+++++||.|.|+|+.+|+++++|.||+|++
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v 91 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRV 91 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence 3454 7999999999999999999995 569999999999999999999999999999999999999999999999999
Q ss_pred chhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEE------eCCCeEEEEeC
Q 005707 220 DDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFIS------LPEGEEGFLPT 292 (681)
Q Consensus 220 ~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVe------Ig~GIeGLLpi 292 (681)
..+||. ....+|+.|++++|+|+++. ++|+|++ ..++..+|.|.
T Consensus 92 ~~~pw~-----------------------------~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~ 142 (319)
T PTZ00248 92 SPEDIE-----------------------------ACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHA 142 (319)
T ss_pred ccchHH-----------------------------HHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCH
Confidence 999993 56788999999999999995 5999998 55688999998
Q ss_pred CCCCcccccccCCCCccc---CCCEEEEEEEEE
Q 005707 293 SEESDDGFANMMGGSSLQ---VGQEVSVRVLRI 322 (681)
Q Consensus 293 SELSd~~ie~~~p~~~fk---VGqkVkVrVL~I 322 (681)
.++....+. .+...|. +++.+...++.+
T Consensus 143 y~af~~~v~--~~~evl~~l~i~~ev~~~l~~~ 173 (319)
T PTZ00248 143 LDALKEALT--NPDNVFEGLDIPEEVKESLLQD 173 (319)
T ss_pred HHHHHHHhc--CchhhhccCCCCHHHHHHHHHH
Confidence 877655432 2333444 777777666655
No 20
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.69 E-value=1.8e-15 Score=178.90 Aligned_cols=293 Identities=20% Similarity=0.205 Sum_probs=225.6
Q ss_pred CCceeEEeCcccCccc---ccccchhhcccceeEEEEEecCCCCCCCCcceecCCCCCcccccccccccCCChhhHHhhh
Q 005707 52 PSSVRFFSQFQSGSAL---QHKSALHIISATGINVAVEESDSPAADDDSAGASDIPSDVETSESSSIKSEASPTLAESRR 128 (681)
Q Consensus 52 ~glrGfIP~sq~~~~~---~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s~v~~ae~ss~~sea~~daek~~~ 128 (681)
.-++|=||.-.+++.. +....++. +|+.++..|...|.... +. .-
T Consensus 1009 p~v~~RIplld~s~~~~~le~~e~~F~-~g~al~~~V~~~~~~~t-----v~-~i------------------------- 1056 (1710)
T KOG1070|consen 1009 PFVDGRIPLLDTSLDLHVLELPESLFP-LGKALDEYVVRNDKSKT-----VR-AI------------------------- 1056 (1710)
T ss_pred ccccceeeeeeccchhhhhhCchhhcc-cccceeeEEecccceeE-----EE-ec-------------------------
Confidence 5667778887777542 22233444 89999999999983322 21 10
Q ss_pred chhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEec-cccCCccccCcccccccCCEEEEEEEEEec
Q 005707 129 SRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHV-SRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207 (681)
Q Consensus 129 kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPi-SELS~~~v~d~~e~fkVGd~VkVkVl~VD~ 207 (681)
. .-+. .....+|++.-|+|..+.+.++.++++.++.|-++. .++++++..+|...|..++.+.+.++.++.
T Consensus 1057 G--~~~~------~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~ 1128 (1710)
T KOG1070|consen 1057 G--FSKS------DKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSA 1128 (1710)
T ss_pred c--cccC------CCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEec
Confidence 0 0000 112338999999999999999999999989995554 499999999999999999999999999999
Q ss_pred cCCceEEEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeE
Q 005707 208 ETGRISLTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEE 287 (681)
Q Consensus 208 ekgrI~LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIe 287 (681)
.++.+.||++......- + -.+.+...+...+++.|+++.|+|+++.+.|+||.+..+++
T Consensus 1129 ~n~~leLslr~sr~~~t-----~----------------~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~ 1187 (1710)
T KOG1070|consen 1129 LNKGLELSLRESRTKIT-----P----------------VDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVE 1187 (1710)
T ss_pred ccccceeecccccccCc-----c----------------ccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceE
Confidence 88889999986554111 0 01222334678999999999999999999999999999999
Q ss_pred EEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC-CCcCC----------cceeeeEEEEeecc
Q 005707 288 GFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED-DVGSN----------LQLTQGVIHAATNP 354 (681)
Q Consensus 288 GLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~-~DP~e----------~~lv~G~V~~~i~~ 354 (681)
+|++++++++... ..+...|.+|+.|.++|++++ .+|+.|+||... .|+.. ++-..|+|. ...+
T Consensus 1188 a~v~is~~~ds~~--k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~-~~~~ 1264 (1710)
T KOG1070|consen 1188 AFVPISGLSDSFE--KEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVE-VVDP 1264 (1710)
T ss_pred EEEEccccccchh--hhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEE-EecC
Confidence 9999999998773 456899999999999999996 589999999874 22322 234578888 8999
Q ss_pred cEEEEEEcCCe--EEEeeCCccccccc------------cCCCCCCCccccceeeccccccCCCCCCC
Q 005707 355 FVLAFRSNKDI--SSFLDERDKSATAA------------KKSEKPTPIEIGGEVSQMEAGSSIPKVQD 408 (681)
Q Consensus 355 fGlfV~l~~gI--~GfIp~~els~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 408 (681)
||+|+++..++ .|++|..+..+... +.+.......+..+|+.+++-+++..+..
T Consensus 1265 ~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~~~~~dd 1332 (1710)
T KOG1070|consen 1265 FGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSYLSSEDD 1332 (1710)
T ss_pred CceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhccCChhh
Confidence 99999998765 99999998887554 56667777788888887777777765543
No 21
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.62 E-value=2.7e-15 Score=177.58 Aligned_cols=169 Identities=24% Similarity=0.388 Sum_probs=148.6
Q ss_pred CCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 140 VKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
++..++++|++|.|+|..+.+.|+.|.+. +.+.|+||.+++++-...-+...|.+|..+++||+.++.+.+++.|++|.
T Consensus 502 ~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~ 581 (1710)
T KOG1070|consen 502 LRVNDIEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKK 581 (1710)
T ss_pred cccccccccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEech
Confidence 34677999999999999999999999884 44999999999999988888888999999999999999999999999997
Q ss_pred cchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc
Q 005707 219 SDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD 298 (681)
Q Consensus 219 l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~ 298 (681)
.+.+-.. | .-..+.+..+|.++.|+|.++.++||||.|.+|+.||+|.+++++.
T Consensus 582 slv~~~~------------p--------------lp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~ 635 (1710)
T KOG1070|consen 582 SLVNTQL------------P--------------LPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDD 635 (1710)
T ss_pred hhhcccC------------C--------------CccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhh
Confidence 7654421 0 1134777889999999999999999999999999999999999999
Q ss_pred cccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707 299 GFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD 336 (681)
Q Consensus 299 ~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~ 336 (681)
++. .+.+.|.+||+|.++|+++| ++|+.|++|....
T Consensus 636 ~v~--~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~ 673 (1710)
T KOG1070|consen 636 FVL--SDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC 673 (1710)
T ss_pred hhc--ChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence 864 45899999999999999997 6899999998753
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.56 E-value=3.2e-15 Score=138.44 Aligned_cols=80 Identities=38% Similarity=0.759 Sum_probs=76.9
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS 223 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp 223 (681)
.+++|++++|+|++|++||+||+|.++-+||||+|+++++|+.++.+++++||.|+|+|+++|. +++|.||+|.+...|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~p 80 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEP 80 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhCc
Confidence 5789999999999999999999999999999999999999999999999999999999999997 999999999998877
Q ss_pred H
Q 005707 224 K 224 (681)
Q Consensus 224 ~ 224 (681)
.
T Consensus 81 e 81 (129)
T COG1098 81 E 81 (129)
T ss_pred c
Confidence 5
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.52 E-value=8.3e-15 Score=155.54 Aligned_cols=120 Identities=19% Similarity=0.224 Sum_probs=102.7
Q ss_pred cccCCc-cCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 256 KTTKFV-KGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 256 ~~sklk-vGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
...+|+ +|++|.|+|++|.+||+||+|. +|++||||++|++|.++. ++...|++||.|.|+||++| +++|.||
T Consensus 10 ~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD~ekg~IdLS 87 (319)
T PTZ00248 10 YEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVDKEKGYIDLS 87 (319)
T ss_pred hhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEEE
Confidence 456787 7999999999999999999996 699999999999999864 45899999999999999997 6999999
Q ss_pred EeccCCCcCCc--------ceeeeEEEEeecccEEEEE------EcCCeEEEeeCCccccc
Q 005707 331 MKKEDDVGSNL--------QLTQGVIHAATNPFVLAFR------SNKDISSFLDERDKSAT 377 (681)
Q Consensus 331 LK~~~~DP~e~--------~lv~G~V~~~i~~fGlfV~------l~~gI~GfIp~~els~~ 377 (681)
+|++..+||.. +.+.|+|......||++++ ..+.+.+|.|..+..+.
T Consensus 88 ~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~ 148 (319)
T PTZ00248 88 KKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKE 148 (319)
T ss_pred eeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 99999999872 5578888843367999997 57788888887666554
No 24
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.50 E-value=1.3e-14 Score=134.36 Aligned_cols=79 Identities=33% Similarity=0.584 Sum_probs=74.3
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCC
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDV 337 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~D 337 (681)
.+++|+++.|+|+.|++||+||+|++|-.||+|+||+.+.++.++ .+.+++||.|.|+||.+| +||+.||||.+.+.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI--~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~ 79 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDI--HDHLKVGQEVKVKVLDIDENGKISLSIRKLEEE 79 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhH--HHHhcCCCEEEEEEEeeccCCCcceehHHhhhC
Confidence 478999999999999999999999999999999999999998877 799999999999999997 79999999999877
Q ss_pred cC
Q 005707 338 GS 339 (681)
Q Consensus 338 P~ 339 (681)
|-
T Consensus 80 pe 81 (129)
T COG1098 80 PE 81 (129)
T ss_pred cc
Confidence 64
No 25
>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=2.2e-13 Score=116.07 Aligned_cols=71 Identities=21% Similarity=0.383 Sum_probs=66.3
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc---ccccccCCEEEEEEEEEeccCCceEEE
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV---GSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~---~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
+++|+++.|+|++++++|+||+|+.+++||||+++++|+++.++ .+.|++||.|+|+|+++|+++++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 57899999999999999999999988999999999999987765 578999999999999999999999885
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=99.44 E-value=6e-13 Score=111.20 Aligned_cols=73 Identities=37% Similarity=0.725 Sum_probs=70.5
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
+++|+++.|+|.++.++|+||+|+++++||||++++++.+..++...|++||.++|+|+++|.+++++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 6889999999999999999999998899999999999999999999999999999999999999999999986
No 27
>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=99.43 E-value=4e-13 Score=115.66 Aligned_cols=75 Identities=35% Similarity=0.540 Sum_probs=72.2
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+.++++|+++.|+|+++.++|+||++++++.||+|+++++++++.++...|++||.|+|+|+.+|.++++|.||+
T Consensus 9 ~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 9 FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 678999999999999999999999998889999999999999999999999999999999999999999999985
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=99.40 E-value=6.5e-13 Score=113.22 Aligned_cols=71 Identities=23% Similarity=0.303 Sum_probs=62.9
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC-CCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM-GGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~-p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
|++|+++.|+|++++++|+||+|+++++||+|+++++|.++.+.. +...|++||.|+|+|+++| +++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 579999999999999999999999999999999999998865432 4589999999999999997 4777764
No 29
>PRK08582 hypothetical protein; Provisional
Probab=99.39 E-value=1.9e-12 Score=123.17 Aligned_cols=81 Identities=36% Similarity=0.694 Sum_probs=76.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS 223 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp 223 (681)
.+++|++|.|+|+.|+++|+||+|++++.||||+++++|+++.++...|++||.|+|+|+.+|. .++|.||++++..+|
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~ 80 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRP 80 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCc
Confidence 4789999999999999999999999889999999999999999999999999999999999997 499999999998888
Q ss_pred Hh
Q 005707 224 KL 225 (681)
Q Consensus 224 ~e 225 (681)
|.
T Consensus 81 ~~ 82 (139)
T PRK08582 81 KR 82 (139)
T ss_pred hh
Confidence 83
No 30
>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=99.38 E-value=1.6e-12 Score=107.73 Aligned_cols=70 Identities=30% Similarity=0.527 Sum_probs=67.3
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|+++.|+|+++.++|+||+|++++.||+|++++++++..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 7899999999999999999988899999999999998999999999999999999999999999999985
No 31
>PRK08582 hypothetical protein; Provisional
Probab=99.36 E-value=3.2e-12 Score=121.60 Aligned_cols=81 Identities=36% Similarity=0.602 Sum_probs=74.5
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccCCC
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKEDDV 337 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~~D 337 (681)
.+++|++|.|+|++|+++|+||+|+++++||||+++++|.++.+ +...|++||.|+|+|+++| .++|.||+|++..+
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~--~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~ 79 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKD--INDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDR 79 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccc--cccccCCCCEEEEEEEEECCCCcEEEEEEecccC
Confidence 37899999999999999999999999999999999999988643 4688999999999999998 59999999999999
Q ss_pred cCCc
Q 005707 338 GSNL 341 (681)
Q Consensus 338 P~e~ 341 (681)
||..
T Consensus 80 ~~~~ 83 (139)
T PRK08582 80 PKRQ 83 (139)
T ss_pred chhh
Confidence 9874
No 32
>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=99.36 E-value=4e-12 Score=108.56 Aligned_cols=71 Identities=25% Similarity=0.371 Sum_probs=65.6
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD 220 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~ 220 (681)
+|+.|+++.|+|++|.++|+||+++ ++++||||.++++|. ..|++||.+.|+|+++|++++++.||+|+..
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 4789999999999999999999997 569999999999986 5689999999999999999999999999654
No 33
>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=99.35 E-value=3.1e-12 Score=108.58 Aligned_cols=70 Identities=20% Similarity=0.340 Sum_probs=66.6
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc--ccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF--VKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~--v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|+++.|+|+++.++|+||.|+.+++|+||.++++|.. ..++.+.|++||.|+|+|+.+|+++++|.||++
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999988899999999999864 788999999999999999999999999999986
No 34
>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=99.35 E-value=5.6e-12 Score=105.41 Aligned_cols=73 Identities=15% Similarity=0.311 Sum_probs=69.1
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
+++|+++.|+|+++.++|+||+|+.+++|++|.+++++++..++...|++||.|+|+|+++|..++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 4789999999999999999999998899999999999998888888999999999999999999999999975
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=99.34 E-value=3.8e-12 Score=105.67 Aligned_cols=69 Identities=29% Similarity=0.504 Sum_probs=66.0
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
|+++.|+|+++.++|+||+|+++++||+|.+++++.+..++...|++||.++|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999998889999999999999988999999999999999999999999999985
No 36
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.34 E-value=4.4e-12 Score=105.98 Aligned_cols=72 Identities=36% Similarity=0.660 Sum_probs=65.4
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK 332 (681)
++++|+++.|+|+++.++|+||+|+++++||||.+++++.+. ..+...|++||.|.|+|+++| ++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRI--DDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEE--SSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccc--cccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 478999999999999999999999999999999999999753 345789999999999999998 588999986
No 37
>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=3.5e-12 Score=107.78 Aligned_cols=71 Identities=25% Similarity=0.381 Sum_probs=66.6
Q ss_pred CCCCcEEEEEEEEEec-CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 145 LIPGATFTGKVRSIQP-FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d-~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|++|++|.|+|+++.+ +|+||+|+.+.+|++|+++++|++..++.+.|++||.|+|+|+++|. +++.||++
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 5789999999999986 89999999889999999999999999999999999999999999975 89999985
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=99.34 E-value=5.6e-12 Score=107.63 Aligned_cols=70 Identities=27% Similarity=0.446 Sum_probs=63.3
Q ss_pred CCccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED 335 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~ 335 (681)
+++.|+++.|+|++|.++|+||+++ +|+.||+|.++++|. ..|++||.+.|+|+++| ++++.||+|+..
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 4789999999999999999999997 699999999999875 46899999999999997 588999999874
Q ss_pred C
Q 005707 336 D 336 (681)
Q Consensus 336 ~ 336 (681)
.
T Consensus 73 ~ 73 (74)
T cd05694 73 V 73 (74)
T ss_pred c
Confidence 3
No 39
>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=99.32 E-value=4.1e-12 Score=107.39 Aligned_cols=71 Identities=23% Similarity=0.305 Sum_probs=65.1
Q ss_pred CccCcEEEEEEEEEec-ceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707 260 FVKGQDLEGTVKNLTR-SGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK 332 (681)
Q Consensus 260 lkvGdIV~G~VknVt~-~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK 332 (681)
+++|+++.|+|+++.+ +|+||++++|.+|++|+++++|.+.. ++...|++||.|+|+|++++++|+.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~~~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKKDGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEecCCEEEEEeC
Confidence 4689999999999986 89999999999999999999999854 44678999999999999999999999986
No 40
>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=8.9e-12 Score=105.22 Aligned_cols=70 Identities=31% Similarity=0.531 Sum_probs=65.2
Q ss_pred CCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+.|+++.|+|+++.+||+||++.+ +.+||+|+++++|.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 579999999999999999999965 3799999999999999999999999999999999999876 999986
No 41
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.31 E-value=1.3e-10 Score=120.30 Aligned_cols=178 Identities=20% Similarity=0.162 Sum_probs=147.4
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCC-eEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAF-TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI 222 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLggg-V~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d 222 (681)
.+.+|++..+.|....++|+|++=+.+ ..-++|.++...+ .+.+||.|.|.|+- ...+++.++++
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-------e~evGdev~vFiY~--D~~~rl~aTt~----- 67 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-------ELEVGDEVTVFIYV--DSEDRLIATTR----- 67 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC-------ccccCcEEEEEEEE--CCCCceeheee-----
Confidence 467899999999999999999998764 3788888766433 26799999999986 45678888887
Q ss_pred hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEe-cceEEEEeCCCeEEEEeCCCCCccccc
Q 005707 223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLT-RSGAFISLPEGEEGFLPTSEESDDGFA 301 (681)
Q Consensus 223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt-~~GaFVeIg~GIeGLLpiSELSd~~ie 301 (681)
...+.+|+.-.++|+.+. +-|+||+.+-.-+-|+|.+++...+
T Consensus 68 ----------------------------------~p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~-- 111 (287)
T COG2996 68 ----------------------------------EPKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK-- 111 (287)
T ss_pred ----------------------------------cceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc--
Confidence 334778999999999998 8899999998899999999987543
Q ss_pred ccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc-----CCCc----CCcceeeeEEEEeecccEEEEEEcCCeEEEeeC
Q 005707 302 NMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE-----DDVG----SNLQLTQGVIHAATNPFVLAFRSNKDISSFLDE 371 (681)
Q Consensus 302 ~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~-----~~DP----~e~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~ 371 (681)
+-++++||++-|+ |.+| ++||.-+++.- ..+| +.++.+.|+|+ .....|.|+-+++++-||||+
T Consensus 112 ----~~wpq~Gd~l~v~-l~~Dkk~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVY-r~~~~G~fv~~e~~~~GfIh~ 185 (287)
T COG2996 112 ----SLWPQKGDKLLVY-LYVDKKGRIWGTLAIEKILENLATPAYNNLKNQEVDATVY-RLLESGTFVITENGYLGFIHK 185 (287)
T ss_pred ----ccCCCCCCEEEEE-EEEccCCcEEEEecchhHHHhcCCccchhhhcCeeeeEEE-EEeccceEEEEcCCeEEEEcc
Confidence 4579999999999 5666 69999888654 1223 23677899999 789999999999999999999
Q ss_pred Cccccc
Q 005707 372 RDKSAT 377 (681)
Q Consensus 372 ~els~~ 377 (681)
+|.-..
T Consensus 186 sEr~~~ 191 (287)
T COG2996 186 SERFAE 191 (287)
T ss_pred hhhccc
Confidence 998877
No 42
>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=99.31 E-value=5.4e-12 Score=108.60 Aligned_cols=75 Identities=24% Similarity=0.386 Sum_probs=68.5
Q ss_pred ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
..+.++++|+++.|+|+++.++|+||++++|++||+|.+++++.++. ++...|++||.|+|+|+++| ++++.|||
T Consensus 7 ~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 7 TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 45778999999999999999999999999999999999999998754 45789999999999999997 58999986
No 43
>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=99.30 E-value=7.7e-12 Score=103.55 Aligned_cols=68 Identities=37% Similarity=0.576 Sum_probs=65.3
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
|+++.|+|+++.++|+||+|++++.||+|.+++++++..++...|++||.|+|+|+++|+++++|.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999988999999999999999999999999999999999999999999875
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=99.29 E-value=9.9e-12 Score=104.76 Aligned_cols=69 Identities=29% Similarity=0.396 Sum_probs=65.4
Q ss_pred CcEEE-EEEEEE-ecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 148 GATFT-GKVRSI-QPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 148 GdIVe-GkV~sV-~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
|++|+ |+|+++ .++|+||+|.++++||||++++++.+..++...|++||.++|+|+++|+.+++|.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 6999999998779999999999999999899999999999999999999999999985
No 45
>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=99.29 E-value=7.7e-12 Score=106.19 Aligned_cols=70 Identities=20% Similarity=0.374 Sum_probs=62.0
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK 332 (681)
|+++.|+|+++.++|+||+|+++++|+||.++++|..-...++...|++||.|+|+|+++| ++||.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999999999999999999863112245788999999999999998 488999986
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=99.29 E-value=1.8e-11 Score=102.65 Aligned_cols=74 Identities=26% Similarity=0.453 Sum_probs=68.9
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECC--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
++.|+++.|+|+++.++|+||+|.+ +++||||+++++++++.++...|++||.|+|+|+++|..++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 3579999999999999999999963 4999999999999999999999999999999999999999999999873
No 47
>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=1.7e-11 Score=101.71 Aligned_cols=72 Identities=28% Similarity=0.515 Sum_probs=68.8
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
|+++.|+|+++.++|+||+|+++++|++|.++++++++.++.+.|++||.++|+|+.+|.+++++.||++.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999998889999999999999999999999999999999999999999999999864
No 48
>PRK07252 hypothetical protein; Provisional
Probab=99.27 E-value=2e-11 Score=113.66 Aligned_cols=78 Identities=29% Similarity=0.642 Sum_probs=73.7
Q ss_pred CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchhh
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDIS 223 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~dp 223 (681)
++|+++.|+|++|.++|+||+|.+++.||||+++++++++.++...|++||.|+|+|+++|.+++++.||++.+..+.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~ 79 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK 79 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 579999999999999999999988899999999999999999989999999999999999999999999999887644
No 49
>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=99.26 E-value=3.1e-11 Score=100.93 Aligned_cols=74 Identities=36% Similarity=0.641 Sum_probs=69.2
Q ss_pred CCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
++|+++.|+|+++.++|+||+|.+ +..|++|++++++++..++...|++||.|+|+|+++|.+++++.|++|..
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 369999999999999999999974 69999999999999888889999999999999999999999999999854
No 50
>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=99.25 E-value=2.9e-11 Score=100.37 Aligned_cols=70 Identities=29% Similarity=0.507 Sum_probs=67.0
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|+++.|+|.++.++|+||+|+++.+|+||.+++++.+..++.+.|++||.++|+|+++|++++++.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 7899999999999999999988899999999999999999999999999999999999988899999985
No 51
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.23 E-value=2.4e-11 Score=100.05 Aligned_cols=68 Identities=38% Similarity=0.600 Sum_probs=63.2
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC-ccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD-NFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~-~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
|+++.|+|+++.++|+||+|.++++||+|+++++| .+..++...|++||.|+|+|+++|.++++|.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999888999999999997 567788889999999999999999999998874
No 52
>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=99.23 E-value=2.4e-11 Score=100.67 Aligned_cols=68 Identities=31% Similarity=0.452 Sum_probs=62.0
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK 332 (681)
|+++.|+|+++.++|+||+|+++++||+|.+++++.+.. ++...|++||.++|+|+++|+ +++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999999999999999999988743 457889999999999999974 89999986
No 53
>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=99.23 E-value=5.7e-11 Score=99.37 Aligned_cols=71 Identities=17% Similarity=0.179 Sum_probs=64.1
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK 332 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK 332 (681)
+++|+++.|+|+++.++|+||+++++++|++|.++++|++.. ++...|++||.|+|+|+++|. +++.||+|
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 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 468999999999999999999999999999999999987632 447889999999999999984 89999985
No 54
>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=99.21 E-value=4.1e-11 Score=99.47 Aligned_cols=67 Identities=30% Similarity=0.536 Sum_probs=60.5
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
|+++.|+|++|.++|+||+|++|++||+|.++++|.++. ++...|++||.++|+|+++| ++++.|+|
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999999999999999988753 34678999999999999997 48898875
No 55
>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=99.20 E-value=8.1e-11 Score=100.30 Aligned_cols=73 Identities=32% Similarity=0.506 Sum_probs=66.0
Q ss_pred CcEEEEEEEEEecceEEEEeC---CCeEEEEeCCCCCcccc-cccCCCCcccCCCEEEEEEEEEeCCeEEEEEeccCCC
Q 005707 263 GQDLEGTVKNLTRSGAFISLP---EGEEGFLPTSEESDDGF-ANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDV 337 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg---~GIeGLLpiSELSd~~i-e~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~~~D 337 (681)
|+++.|+|+++.+||+||+|+ ++++||+|.++++|.++ . ++...|++||.|+|+|+++|++++.|++|.+.++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k~~~~~ 77 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQD 77 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEEeCCEEEEEEEecccC
Confidence 789999999999999999998 47999999999999874 3 4477899999999999999999999999998654
No 56
>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=99.20 E-value=7.5e-11 Score=95.68 Aligned_cols=69 Identities=41% Similarity=0.801 Sum_probs=65.6
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|+++.|+|+++.++|+||+++.+..||+|.++++++++.++...|++||.|+|+|+.+|. ++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999999889999999999999988998999999999999999998 899999985
No 57
>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=99.20 E-value=7.8e-11 Score=100.41 Aligned_cols=72 Identities=40% Similarity=0.682 Sum_probs=66.6
Q ss_pred CcEEEEEEEEEecCeeEEEEC---CCeEEEEeccccCCccc-cCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 148 GATFTGKVRSIQPFGAFIDFG---AFTDGLVHVSRLSDNFV-KDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLg---ggV~GLVPiSELS~~~v-~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
|+++.|+|+++.++|+||+|+ .+..||+|+++++|.+. .++...|++||.|+|+|+++| ++++.+|+|.+.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 789999999999999999998 35999999999999986 888899999999999999999 8999999997654
No 58
>PRK05807 hypothetical protein; Provisional
Probab=99.20 E-value=9.3e-11 Score=111.26 Aligned_cols=75 Identities=35% Similarity=0.640 Sum_probs=70.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD 220 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~ 220 (681)
.+++|++|.|+|+.+.++|+||+|. +..||||++++++.++.++...|++||.|+|+|+.+|. .++|.||++.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 4778999999999999999999995 48999999999999999999999999999999999998 799999999875
No 59
>PRK08059 general stress protein 13; Validated
Probab=99.19 E-value=8.1e-11 Score=109.49 Aligned_cols=82 Identities=41% Similarity=0.760 Sum_probs=76.5
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
+..+++|++|.|+|.++.++|+||+|+.++.|++|+++++++++.++...|++||.|+|+|+++|.+++++.||++.+..
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 34688999999999999999999999988999999999999999888889999999999999999999999999998876
Q ss_pred hh
Q 005707 222 IS 223 (681)
Q Consensus 222 dp 223 (681)
++
T Consensus 82 ~~ 83 (123)
T PRK08059 82 AP 83 (123)
T ss_pred Cc
Confidence 55
No 60
>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=99.19 E-value=6e-11 Score=100.01 Aligned_cols=67 Identities=25% Similarity=0.414 Sum_probs=60.2
Q ss_pred CcEEE-EEEEEE-ecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 263 GQDLE-GTVKNL-TRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 263 GdIV~-G~VknV-t~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
|+++. |+|+++ .++|+||++.+|++||+|.+++++.+.. .+...|++||.+.|+|+.+| ++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78899 999999 6999999999999999999999988754 34788999999999999998 47899885
No 61
>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=99.18 E-value=1.1e-10 Score=98.69 Aligned_cols=69 Identities=25% Similarity=0.378 Sum_probs=60.8
Q ss_pred ccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTM 331 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSL 331 (681)
..|+++.|+|+++.+||+||++.+ +.+||+|+++++|.++. ++...|++||.|+|+|+++|. +|+.|||
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 589999999999999999999953 37999999999998764 457889999999999999984 5888886
No 62
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.17 E-value=1.1e-10 Score=97.42 Aligned_cols=71 Identities=32% Similarity=0.528 Sum_probs=64.0
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc-cccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN-FVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~-~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
+.+|+++.|+|+++.++|+||+|.++++||+|.+++.|. +..++...|++||.|+|+|+++|.+++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999999999999999999998789999999999875 44577788999999999999999999988764
No 63
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.17 E-value=4.1e-11 Score=141.14 Aligned_cols=84 Identities=23% Similarity=0.357 Sum_probs=76.1
Q ss_pred cccCCccCcEEE-EEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEec
Q 005707 256 KTTKFVKGQDLE-GTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKK 333 (681)
Q Consensus 256 ~~sklkvGdIV~-G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~ 333 (681)
.+.+.++|++|. |+|++|.+||+||+|.+|++||||+++++|.++. ++...|++||.|+|+|+++| ++||.|++|.
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~ 824 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA 824 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence 345678999995 6999999999999999999999999999999865 44788999999999999998 5899999999
Q ss_pred cCCCcCCc
Q 005707 334 EDDVGSNL 341 (681)
Q Consensus 334 ~~~DP~e~ 341 (681)
+..|||+.
T Consensus 825 l~~~Pw~~ 832 (891)
T PLN00207 825 LLPEANSE 832 (891)
T ss_pred cccCchhh
Confidence 99999994
No 64
>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=5.1e-11 Score=107.40 Aligned_cols=76 Identities=25% Similarity=0.430 Sum_probs=68.7
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-------------------cCcccccccCCEEEEEEEEE
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-------------------KDVGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-------------------~d~~e~fkVGd~VkVkVl~V 205 (681)
|++|++|.|+|+++.++|+||.|++++.|++|+++++|++. .++.+.|++||.|+|+|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 57899999999999999999999988999999999999763 34678899999999999999
Q ss_pred ecc---CCceEEEEeccc
Q 005707 206 NAE---TGRISLTMRESD 220 (681)
Q Consensus 206 D~e---kgrI~LSlK~l~ 220 (681)
|+. +++|.||+++..
T Consensus 81 d~~~~~~~~i~LSlr~~~ 98 (100)
T cd05693 81 DKSKSGKKRIELSLEPEL 98 (100)
T ss_pred cCCcCCCcEEEEEecHHH
Confidence 997 789999999643
No 65
>PRK07252 hypothetical protein; Provisional
Probab=99.16 E-value=1.6e-10 Score=107.61 Aligned_cols=76 Identities=29% Similarity=0.489 Sum_probs=68.8
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCCCc
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDDVG 338 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~DP 338 (681)
++|+++.|+|++|.++|+||+|++++.||+|.+++++.++.+ +...|++||.|.|+|+++| ++++.|++|....+.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~--~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~ 79 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDN--IHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK 79 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccC--hhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 579999999999999999999999999999999999988643 4788999999999999998 599999999996643
No 66
>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=99.15 E-value=1.7e-10 Score=96.70 Aligned_cols=71 Identities=31% Similarity=0.446 Sum_probs=63.5
Q ss_pred ccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEec
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMKK 333 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK~ 333 (681)
++|+++.|+|+++.++|+||+|.+ |++||||.+++++.++. ++...|++||.|+|+|+++|. +++.|++|+
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 579999999999999999999974 69999999999998754 347789999999999999984 889999974
No 67
>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=99.15 E-value=1.6e-11 Score=143.09 Aligned_cols=158 Identities=21% Similarity=0.315 Sum_probs=106.8
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS 105 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s 105 (681)
.+.+||||+-.+|.|||||.|++.||-.+|-+. ....+....... . . .+.. .-.+.
T Consensus 539 ~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~-~~l~~~~~~~~~---~----~---------~~~~---~~~l~---- 594 (709)
T TIGR02063 539 ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIK-KALFGGENTTTE---K----E---------REYL---EAKLE---- 594 (709)
T ss_pred CCCCccccccccccccCCccccchHHHHHHHHH-HHHcCCCCCCcc---c----c---------chhh---HHHHH----
Confidence 467999999999999999999999987764221 111110000000 0 0 0000 00011
Q ss_pred CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcc
Q 005707 106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNF 184 (681)
Q Consensus 106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~ 184 (681)
..+.+.+.+.+.+..+++..... ... .|..-++|+++.|+|++|+++|+||+|.+ +++||||++++.+++
T Consensus 595 --~~~~~~~~~er~a~~aer~~~~~--~~~-----~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~ 665 (709)
T TIGR02063 595 --EIAEHSSKTERRADEAERDVNDW--KKA-----EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY 665 (709)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHH--HHH-----HhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc
Confidence 11344555555655555544431 222 14456789999999999999999999976 699999999998765
Q ss_pred c-----------cCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 185 V-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 185 v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+ .+....|++||.|+|+|+++|..+++|.|++
T Consensus 666 ~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l 708 (709)
T TIGR02063 666 YVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFEL 708 (709)
T ss_pred EEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence 3 2345679999999999999999999999986
No 68
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.15 E-value=3.3e-09 Score=110.10 Aligned_cols=145 Identities=26% Similarity=0.350 Sum_probs=117.3
Q ss_pred CCCCCcEEEEEEEEEe-cCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707 144 DLIPGATFTGKVRSIQ-PFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI 222 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~-d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d 222 (681)
.+.+|+--.++|+.+. +-|+||++|-.-+.+||.+++.... .-.+++||.+-|.+.- |+ ++||...++.-..-
T Consensus 70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~wpq~Gd~l~v~l~~-Dk-k~Ri~g~~a~~~~l 143 (287)
T COG2996 70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SLWPQKGDKLLVYLYV-DK-KGRIWGTLAIEKIL 143 (287)
T ss_pred eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc----ccCCCCCCEEEEEEEE-cc-CCcEEEEecchhHH
Confidence 5677999999999999 8899999998899999999986531 2347899999999874 54 55888887732211
Q ss_pred hHhhhhccccccCCccccccccCCCCCCccccccccCCc---cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc
Q 005707 223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV---KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDG 299 (681)
Q Consensus 223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklk---vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ 299 (681)
. .....+- .++.++|+|.++...|.||-+.++.-||||.+|..
T Consensus 144 ~-------------------------------~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~--- 189 (287)
T COG2996 144 E-------------------------------NLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF--- 189 (287)
T ss_pred H-------------------------------hcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc---
Confidence 1 1222233 49999999999999999999999999999999865
Q ss_pred ccccCCCCcccCCCEEEEEEEEE-eCCeEEEEEeccC
Q 005707 300 FANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTMKKED 335 (681)
Q Consensus 300 ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSLK~~~ 335 (681)
..++.|+.+++||+.+ ++|+|.||+++..
T Consensus 190 -------~~prlG~~l~~rVi~~reDg~lnLSl~p~~ 219 (287)
T COG2996 190 -------AEPRLGERLTARVIGVREDGKLNLSLRPRA 219 (287)
T ss_pred -------ccccCCceEEEEEEEEccCCeeeccccccc
Confidence 3568999999999999 5799999999873
No 69
>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=99.15 E-value=1.1e-10 Score=94.57 Aligned_cols=68 Identities=44% Similarity=0.819 Sum_probs=64.3
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
|+++.|+|+++.++|+||+++.+..||+|.+++++.++.++...|++||.++|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999988999999999999988889889999999999999999999998875
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=99.14 E-value=1.6e-10 Score=96.19 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=60.0
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
|++++|+|+++.++|+||+|.++++||+|.++++..+.. ...|++|+.++|+|+.+|+++++|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999997779999999999865544 677999999999999999999998876
No 71
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.13 E-value=1e-10 Score=137.83 Aligned_cols=83 Identities=29% Similarity=0.518 Sum_probs=77.7
Q ss_pred CCCCCCcEEE-EEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 143 EDLIPGATFT-GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 143 ~~LkvGdIVe-GkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
...++|++|. |+|++|.+||+||+|.++++||||+++|+|+++.++.+.|++||.|+|+|+++|. +++|.||+|.+..
T Consensus 749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~ 827 (891)
T PLN00207 749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLP 827 (891)
T ss_pred cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecccc
Confidence 4578999996 6999999999999998779999999999999999999999999999999999997 7999999999999
Q ss_pred hhHhh
Q 005707 222 ISKLQ 226 (681)
Q Consensus 222 dp~ek 226 (681)
+||..
T Consensus 828 ~Pw~~ 832 (891)
T PLN00207 828 EANSE 832 (891)
T ss_pred Cchhh
Confidence 99953
No 72
>PRK05807 hypothetical protein; Provisional
Probab=99.13 E-value=3e-10 Score=107.83 Aligned_cols=74 Identities=34% Similarity=0.535 Sum_probs=67.5
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEeccC
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKED 335 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~~ 335 (681)
.+++|++|.|+|+.|+++|+||+| ++..||||++++++.++.+ +...|++||.|+|+|+++| .++|.||||.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~--~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKD--IREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccC--ccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 478999999999999999999999 6899999999999988654 3688999999999999998 589999999985
No 73
>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=99.12 E-value=2.8e-10 Score=94.38 Aligned_cols=70 Identities=30% Similarity=0.542 Sum_probs=63.7
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEecc
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMKKE 334 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK~~ 334 (681)
|+++.|+|+++.++|+||++.++++|++|.+++++.++. ++...|++||.++|+|+++|. +++.|++|..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999999999999999999988754 357889999999999999984 7899999875
No 74
>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=99.12 E-value=2.7e-10 Score=95.03 Aligned_cols=69 Identities=36% Similarity=0.540 Sum_probs=59.6
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEE
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTL 329 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~L 329 (681)
|++|+++.|+|+++.++|+||+|.++++||+|.+++.|... ..++...|++||.|+|+|+++|. +++.|
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~-~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~ 71 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNK-NIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCccc-ccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence 57899999999999999999999999999999999987521 23456789999999999999974 66655
No 75
>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=99.11 E-value=3.1e-10 Score=93.87 Aligned_cols=67 Identities=28% Similarity=0.402 Sum_probs=61.3
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|+++.|+|+.+.++|+||++ ++++||||.+++++.+..++.. .+|+.++|+|+++|+++++|.||+|
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-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 5699999999999988777765 3899999999999999999999975
No 76
>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=99.11 E-value=1.6e-10 Score=95.61 Aligned_cols=66 Identities=30% Similarity=0.480 Sum_probs=59.6
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
|+++.|+|+++.++|+||+|+++++||+|.+++++.+.. ++...|++||.|+|+|+++| ++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999999999999999999988754 45788999999999999998 4777764
No 77
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.11 E-value=3.6e-10 Score=91.13 Aligned_cols=72 Identities=43% Similarity=0.756 Sum_probs=67.2
Q ss_pred CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
++|+++.|+|.++.++|+||++++++.|++|.+++.+.+..++...|++||.+.|+|+.+|..++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 369999999999999999999997799999999999988788888899999999999999998899999875
No 78
>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=99.11 E-value=3.1e-10 Score=94.89 Aligned_cols=72 Identities=31% Similarity=0.526 Sum_probs=64.6
Q ss_pred ccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE 334 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~ 334 (681)
++|+++.|+|+++.++|+||+|.+ +++|++|.++++|.+.. .+...|++||.|+|+|+++| ++++.|++|+.
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 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 369999999999999999999985 89999999999998743 35688999999999999998 58999999875
No 79
>PRK11642 exoribonuclease R; Provisional
Probab=99.11 E-value=5.7e-11 Score=140.20 Aligned_cols=164 Identities=19% Similarity=0.244 Sum_probs=111.3
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS 105 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s 105 (681)
.+.+||||+..+|.||+||+|+|.||-.+|-+.- ...+... ....+.. ..... . ... . +
T Consensus 551 ~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~-~L~~~~~-~~~~~~~----~~~~~---~--~~~---~--l----- 609 (813)
T PRK11642 551 ENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKY-LLAKEQG-HKGNTTE----TGGYH---Y--SME---E--M----- 609 (813)
T ss_pred CCCCccccccccccccCchhhhhHHHHHHHHHHH-HHhCCCC-ccccccc----ccccc---c--CHH---H--H-----
Confidence 5789999999999999999999999877753321 1000000 0000000 00000 0 000 0 0
Q ss_pred CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcc
Q 005707 106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNF 184 (681)
Q Consensus 106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~ 184 (681)
...++++|.+++.+.++++...... +.. +..-++|+++.|+|++|+++|+||+|.. +++||||+++|.++|
T Consensus 610 -~~~~~~~s~~er~A~~aeR~~~~~~--~~~-----~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~ 681 (813)
T PRK11642 610 -LQLGQHCSMTERRADEATRDVADWL--KCD-----FMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDY 681 (813)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHH--HHh-----hhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcc
Confidence 1225567777777777776555422 221 3344689999999999999999999975 499999999999874
Q ss_pred cc-----------CcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 185 VK-----------DVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 185 v~-----------d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
+. +....|++||.|+|+|+.+|..+++|.|++..
T Consensus 682 y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l~~ 726 (813)
T PRK11642 682 YRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLIS 726 (813)
T ss_pred eEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEEEEec
Confidence 32 23467999999999999999999999999863
No 80
>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=3e-10 Score=92.58 Aligned_cols=68 Identities=49% Similarity=0.780 Sum_probs=64.3
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
|+++.|+|..+.++|+||+|+.+..||+|.+++++.++.++...|++||.|+|+|+++|. ++++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 789999999999999999998889999999999999888888899999999999999998 89999885
No 81
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.10 E-value=2.9e-10 Score=92.24 Aligned_cols=68 Identities=34% Similarity=0.526 Sum_probs=61.6
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK 332 (681)
|+++.|+|+++.++|+||+++++..||+|.+++++.++. ++...|++||.|.|+|+++|. +++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 789999999999999999999999999999999987743 346789999999999999985 89999986
No 82
>PRK08059 general stress protein 13; Validated
Probab=99.10 E-value=3.8e-10 Score=105.03 Aligned_cols=80 Identities=26% Similarity=0.475 Sum_probs=72.0
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE 334 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~ 334 (681)
+.++++|+++.|+|.++.++|+||++.++++||+|.+++++.++. ++...|++||.|.|+|+++| ++++.|++|..
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence 346899999999999999999999999999999999999988753 34678999999999999997 48999999999
Q ss_pred CCCc
Q 005707 335 DDVG 338 (681)
Q Consensus 335 ~~DP 338 (681)
..+|
T Consensus 80 ~~~~ 83 (123)
T PRK08059 80 EEAP 83 (123)
T ss_pred ccCc
Confidence 8777
No 83
>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=7.9e-11 Score=106.18 Aligned_cols=77 Identities=27% Similarity=0.395 Sum_probs=66.4
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-----------------cCCCCcccCCCEEEEEEEEE
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-----------------MMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-----------------~~p~~~fkVGqkVkVrVL~I 322 (681)
+++|++|.|+|++|.++|+||.|++|+.|++|+++++|.+... ..+...|++||.|.|+|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 5789999999999999999999999999999999999864211 12467899999999999999
Q ss_pred eC-----CeEEEEEeccCC
Q 005707 323 SR-----GQVTLTMKKEDD 336 (681)
Q Consensus 323 Dk-----gKI~LSLK~~~~ 336 (681)
|+ ++|.||+|+...
T Consensus 81 d~~~~~~~~i~LSlr~~~v 99 (100)
T cd05693 81 DKSKSGKKRIELSLEPELV 99 (100)
T ss_pred cCCcCCCcEEEEEecHHHC
Confidence 74 589999998654
No 84
>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=99.09 E-value=3.4e-10 Score=92.11 Aligned_cols=68 Identities=44% Similarity=0.737 Sum_probs=63.9
Q ss_pred CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
+|+++.|+|.++.++|+||++++ +.|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECC-eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 48999999999999999999985 999999999999888888899999999999999999999998875
No 85
>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=99.09 E-value=2.5e-10 Score=93.98 Aligned_cols=67 Identities=30% Similarity=0.411 Sum_probs=57.3
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
|+++.|+|+++.++|+||+|.++++||+|.++++|... ..++...|++||.|+|+|+++| ++|+.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~-~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQR-VRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccc-cCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999999999999999997321 2245678999999999999998 4677653
No 86
>PHA02945 interferon resistance protein; Provisional
Probab=99.07 E-value=6.2e-10 Score=98.12 Aligned_cols=77 Identities=21% Similarity=0.324 Sum_probs=70.0
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEecccc--CCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRL--SDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSEL--S~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
|.-.++|+++.|+|.. .++|+||.| .++.+||||++++ +.+|+++ ++.+ +||++.|+|+.+|+.++.|.||+|
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK 82 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYK 82 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence 5567899999999999 999999999 4579999999955 9999999 8888 999999999999999999999999
Q ss_pred ccch
Q 005707 218 ESDD 221 (681)
Q Consensus 218 ~l~~ 221 (681)
+...
T Consensus 83 ~V~~ 86 (88)
T PHA02945 83 RMCR 86 (88)
T ss_pred Eccc
Confidence 7643
No 87
>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=99.07 E-value=6.1e-11 Score=137.26 Aligned_cols=155 Identities=20% Similarity=0.271 Sum_probs=107.8
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS 105 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s 105 (681)
.+.+||||+-.+|.|||||.|++.||-.+|-+ -+... |....- ....+ .--+
T Consensus 487 ~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L-~a~l~--------------~~~~~~-~~~~~-------~~~l----- 538 (654)
T TIGR00358 487 EPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLI-KAVLA--------------KEQTDT-ERYQP-------QDEL----- 538 (654)
T ss_pred CCCCccccccccccccCCccccchHHHHHHHH-HHHHc--------------CCCCcc-cchhh-------HHHH-----
Confidence 57899999999999999999999998766422 11111 110000 00000 0001
Q ss_pred CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCCcc
Q 005707 106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNF 184 (681)
Q Consensus 106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~ 184 (681)
...+++++.+++.+.++++...+. .... |..-++|++++|+|++++++|+||+|. .+++||||++++.+++
T Consensus 539 -~~~~~~~~~~er~a~~aer~~~~~--~~~~-----yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~ 610 (654)
T TIGR00358 539 -LQIAEHCSDTERRARDAERDVADW--LKCR-----YLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDY 610 (654)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHH--HHHH-----hhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcc
Confidence 112445666666666666555432 1121 344467999999999999999999997 6799999999999874
Q ss_pred c-----------cCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 185 V-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 185 v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+ .+....|++||.|+|+|+++|..+++|.+++
T Consensus 611 y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l 653 (654)
T TIGR00358 611 YVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFEL 653 (654)
T ss_pred eEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence 2 2334679999999999999999999999975
No 88
>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=99.06 E-value=5.9e-10 Score=96.31 Aligned_cols=74 Identities=16% Similarity=0.190 Sum_probs=67.1
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCC----ccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSD----NFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~----~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
+++|++|.|+|+++.++|++|+++++.+|+||++++++ .+..++.+.+++||.++|+|+++|++ +++.||++..
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~ 81 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSL 81 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCcc
Confidence 57899999999999999999999988999999999986 45567778899999999999999876 9999999854
No 89
>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=99.03 E-value=8.9e-10 Score=91.42 Aligned_cols=68 Identities=35% Similarity=0.573 Sum_probs=61.8
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK 332 (681)
|+++.|+|.++.++|+||+|+.+.+|++|.+++++.+.. ++...|++||.++|+|+++++ +++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999999999999999999988754 457889999999999999973 78999986
No 90
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.02 E-value=4.5e-10 Score=115.91 Aligned_cols=81 Identities=21% Similarity=0.520 Sum_probs=76.2
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
-..+|++|-|+|+.|.+||+||.| .++++||+|+||++.+|++++++++++||.+-|+|+.||+.++.|.||+|....
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 467899999999999999999999 467999999999999999999999999999999999999999999999999887
Q ss_pred hhH
Q 005707 222 ISK 224 (681)
Q Consensus 222 dp~ 224 (681)
+..
T Consensus 88 ~q~ 90 (269)
T COG1093 88 HQR 90 (269)
T ss_pred HHH
Confidence 664
No 91
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.99 E-value=1.3e-09 Score=90.74 Aligned_cols=64 Identities=20% Similarity=0.261 Sum_probs=56.0
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
|+++.|+|+++.++|+||+|.++++||+|.++++..+. . ...|++|++|.|+|+.+| +++|.||
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-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC---c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999889999999999976542 1 678999999999999998 4677764
No 92
>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=2.3e-09 Score=94.55 Aligned_cols=74 Identities=28% Similarity=0.477 Sum_probs=66.3
Q ss_pred CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCC---ccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSD---NFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~---~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
.+++|++|.|+|+++.++ |+||+|+++.+||||+++++| .++.++.+.+++||.|.|+|+......+...|+.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 467899999999999997 999999988999999999999 66788888999999999999998777777777765
No 93
>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=98.97 E-value=3e-09 Score=90.32 Aligned_cols=70 Identities=30% Similarity=0.701 Sum_probs=61.9
Q ss_pred CCcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEeccCCceEE
Q 005707 147 PGATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 147 vGdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
+|+++.|+|+++.++|+||+|+. +++|++|.++++++++. +....|++||.|+|+|+.+|.+++++.+
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 48999999999999999999986 69999999999876432 3457799999999999999999999998
Q ss_pred EE
Q 005707 215 TM 216 (681)
Q Consensus 215 Sl 216 (681)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 85
No 94
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.97 E-value=1.4e-09 Score=88.22 Aligned_cols=66 Identities=32% Similarity=0.537 Sum_probs=58.7
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLT 330 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LS 330 (681)
|+++.|+|++++++|+||+++++.+||+|.+++.+.++. ++...|++||.|.|+|+++|. +++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789999999999999999999999999999999988754 346779999999999999984 777764
No 95
>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=98.96 E-value=2e-09 Score=93.05 Aligned_cols=75 Identities=19% Similarity=0.161 Sum_probs=64.1
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE 334 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~ 334 (681)
.++|++|.|+|+.+.++|+||+++.+.+|+||.+++++.+++ .......|++||.+.|+|+++++ +++.||+|..
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 469999999999999999999999999999999999863221 11235679999999999999975 8999999875
No 96
>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=98.95 E-value=3.6e-09 Score=90.92 Aligned_cols=73 Identities=14% Similarity=0.098 Sum_probs=68.7
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
.++|++|.|+|+++.+.|++|+++++.+|++|.++++..+..++...|++||.+.|+|+.+|.+ +++.||++.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 4789999999999999999999998899999999999888888889999999999999999986 899999985
No 97
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.95 E-value=2.7e-09 Score=111.42 Aligned_cols=80 Identities=25% Similarity=0.535 Sum_probs=73.8
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECC--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGA--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgg--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
-+++|++|.|+|+++.++|+||+|.. ++.||||+++++++++.++.+.|++||.|.|+|+.+|.++++|.||+|....
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~ 84 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 35789999999999999999999963 6999999999999999999999999999999999999999999999997765
Q ss_pred hh
Q 005707 222 IS 223 (681)
Q Consensus 222 dp 223 (681)
+.
T Consensus 85 ~e 86 (262)
T PRK03987 85 HQ 86 (262)
T ss_pred ch
Confidence 44
No 98
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.93 E-value=3.4e-09 Score=86.37 Aligned_cols=67 Identities=34% Similarity=0.608 Sum_probs=59.9
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTM 331 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSL 331 (681)
|+++.|+|.++.++|+||+++++..||+|.+++.+.++. ++...|++||.|.|+|+++| .+++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 789999999999999999999999999999999988743 34678999999999999998 47888875
No 99
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.93 E-value=3.5e-09 Score=85.35 Aligned_cols=70 Identities=41% Similarity=0.648 Sum_probs=61.8
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEEEe
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLTMK 332 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LSLK 332 (681)
++|+++.|+|.++.++|+||++++++.|++|.+++.+.+. .++...|++||.|.|+|++++. +++.|+++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~--~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRV--KDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcccc--CCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 3699999999999999999999999999999999998752 2335679999999999999974 88999875
No 100
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.91 E-value=4.9e-09 Score=86.68 Aligned_cols=65 Identities=26% Similarity=0.549 Sum_probs=56.2
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK 332 (681)
|+++.|+|+++.++|+||++ +|++||||.+++++.+..+. ...+||.+.|+|+++| ++++.||+|
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-EGVRAFLPASQVDLRPVEDL----DEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCCh----HHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 69999999999998764322 2248999999999998 488999975
No 101
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.90 E-value=1.7e-09 Score=124.99 Aligned_cols=82 Identities=48% Similarity=0.804 Sum_probs=77.6
Q ss_pred CCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
..+.+|++|++++|+|++|.++|+||+||-+.+|+||++++++.++.+|.+++++||.|+|+|+++|..++||.|||+..
T Consensus 651 ~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~ 730 (780)
T COG2183 651 ESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD 730 (780)
T ss_pred hhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeecc
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999999999965
Q ss_pred ch
Q 005707 220 DD 221 (681)
Q Consensus 220 ~~ 221 (681)
..
T Consensus 731 ~~ 732 (780)
T COG2183 731 EE 732 (780)
T ss_pred CC
Confidence 44
No 102
>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=98.88 E-value=6.4e-09 Score=86.94 Aligned_cols=63 Identities=27% Similarity=0.421 Sum_probs=58.6
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc--ccCcccccccCCEEEEEEEEEeccCC
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF--VKDVGSIVSVGQEVKVRLIEANAETG 210 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~--v~d~~e~fkVGd~VkVkVl~VD~ekg 210 (681)
|+++.|+|+++.++|+||+++++++|++|++++++++ ..++.+.|++||.|+|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 7899999999999999999998899999999999885 78888899999999999999987654
No 103
>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=98.88 E-value=6e-09 Score=91.95 Aligned_cols=74 Identities=27% Similarity=0.343 Sum_probs=59.4
Q ss_pred CCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccc-ccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707 259 KFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFA-NMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie-~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK 332 (681)
++++|+++.|+|+++.++ |+||+|++|.+||||.++++|.+.. ..++...|++||.|.|+|++.. .+.-.||.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 578999999999999997 9999999999999999999983211 1234678999999999999984 233444443
No 104
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.88 E-value=6e-09 Score=121.63 Aligned_cols=76 Identities=37% Similarity=0.625 Sum_probs=72.2
Q ss_pred CCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 143 ~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
..+++|++|.|+|+++.+||+||+|.++.+||||+++++|.++.++.+.|++||.|+|+|+++|.+ ++|.||+|.+
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 468899999999999999999999988899999999999999999999999999999999999987 9999999865
No 105
>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=98.87 E-value=1.2e-08 Score=86.58 Aligned_cols=70 Identities=27% Similarity=0.550 Sum_probs=59.6
Q ss_pred cCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707 262 KGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RGQVTL 329 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kgKI~L 329 (681)
+|+++.|+|++++++|+||++++ |++|++|.+++.++++.. ......|++||.|+|+|..+| ++++.|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48999999999999999999998 899999999998764321 123578999999999999997 588888
Q ss_pred EE
Q 005707 330 TM 331 (681)
Q Consensus 330 SL 331 (681)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 76
No 106
>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=98.86 E-value=5.6e-09 Score=82.76 Aligned_cols=65 Identities=51% Similarity=0.845 Sum_probs=60.2
Q ss_pred EEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 151 FTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 151 VeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
+.|+|+++.++|+||+++.+..|++|.+++++.+..++...|++||.|+|+|+++|.+++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999977999999999999888888889999999999999999988888775
No 107
>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=98.85 E-value=6.1e-09 Score=120.87 Aligned_cols=71 Identities=32% Similarity=0.578 Sum_probs=65.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccC----CccccCcccccccCCEEEEEEEEEeccCCceEEE
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS----DNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS----~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
.+++|++|.|+|+++.+||+||+|.++++||||+++|+ |.++.++.+.|++||.|+|+|+++|. ++||.|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 47899999999999999999999987799999999996 46889999999999999999999995 7888875
No 108
>PHA02945 interferon resistance protein; Provisional
Probab=98.84 E-value=1.3e-08 Score=89.93 Aligned_cols=73 Identities=26% Similarity=0.378 Sum_probs=63.9
Q ss_pred CccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCC--CcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEec
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEE--SDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKK 333 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSEL--Sd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~ 333 (681)
-.+|+++.|+|+. .++|+||.|.+ |.+||+|.++. +..++.+ ++.+ .||+|.|+|+++| +|.|.||||.
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~---rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY---RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee---eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 4689999999999 99999999975 99999999955 8887643 6778 9999999999998 5889999998
Q ss_pred cCCC
Q 005707 334 EDDV 337 (681)
Q Consensus 334 ~~~D 337 (681)
...+
T Consensus 84 V~~~ 87 (88)
T PHA02945 84 MCRH 87 (88)
T ss_pred cccC
Confidence 7543
No 109
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.84 E-value=1.1e-08 Score=83.30 Aligned_cols=66 Identities=38% Similarity=0.595 Sum_probs=57.8
Q ss_pred cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--CeEEEE
Q 005707 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--GQVTLT 330 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--gKI~LS 330 (681)
+|+++.|+|.++.++|+||+++ +++|++|.+++++.+.. .+...|++||.|+|+|+++|. +++.||
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-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999997 79999999999987643 346789999999999999984 777764
No 110
>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=2.4e-08 Score=85.41 Aligned_cols=68 Identities=35% Similarity=0.579 Sum_probs=61.5
Q ss_pred CCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 140 VKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 140 lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+.+.+++.|+++.|+|.+++++|+||++.++..||+|.+++. ..|++||.++|+|.++ .+++++.+++
T Consensus 9 ~~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred cchhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 346789999999999999999999999988899999999873 3489999999999999 8889999986
No 111
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.82 E-value=1e-08 Score=107.14 Aligned_cols=76 Identities=33% Similarity=0.566 Sum_probs=68.0
Q ss_pred CccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccC
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKED 335 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~ 335 (681)
.++|+++.|+|++|.++|+||+|.+ |++||||.+++++.++.+ +...|++||.|.|+|+++| ++++.||+|...
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~--i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~ 83 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKN--IRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVN 83 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccC--HHHhCCCCCEEEEEEEEEecccCeEEEEEEecc
Confidence 4689999999999999999999985 899999999999988654 3788999999999999998 488999999876
Q ss_pred CC
Q 005707 336 DV 337 (681)
Q Consensus 336 ~D 337 (681)
.+
T Consensus 84 ~~ 85 (262)
T PRK03987 84 EH 85 (262)
T ss_pred cc
Confidence 54
No 112
>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=98.81 E-value=2.8e-08 Score=85.03 Aligned_cols=66 Identities=26% Similarity=0.442 Sum_probs=59.1
Q ss_pred cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE-eCCeEEEEE
Q 005707 256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTM 331 (681)
Q Consensus 256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSL 331 (681)
.+.+++.|+.+.|+|++++++|+||++.++++||+|.+++. ..|++||.++++|.++ +++++.|++
T Consensus 10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~----------~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL----------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc----------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 36679999999999999999999999999999999999853 4689999999999999 458888876
No 113
>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=98.81 E-value=1.4e-08 Score=84.94 Aligned_cols=64 Identities=20% Similarity=0.246 Sum_probs=55.9
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
|+++.|+|+++.++|+||++++|++|++|.+++++.+.....+.+.|++||.|.|+|+++|..+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 7899999999999999999999999999999998874222345788999999999999998644
No 114
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.79 E-value=1.5e-08 Score=118.32 Aligned_cols=76 Identities=32% Similarity=0.490 Sum_probs=69.7
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE 334 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~ 334 (681)
..++++|+++.|+|++|.+||+||+|.+|.+||+|+++++|.++. ++...|++||.|+|+|+++|. +|+.||+|.+
T Consensus 616 ~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~ 692 (693)
T PRK11824 616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVE--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692 (693)
T ss_pred cccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcccc--CccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 356899999999999999999999999999999999999999865 457899999999999999974 9999999975
No 115
>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=98.79 E-value=9.9e-09 Score=119.16 Aligned_cols=70 Identities=33% Similarity=0.463 Sum_probs=62.2
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC---c-ccccccCCCCcccCCCEEEEEEEEEe-CCeEEEE
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES---D-DGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLT 330 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELS---d-~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LS 330 (681)
.+++|++|.|+|++|.+||+||+|.+|++||||+++++ | .++. ++.+.|++||.|+|+|+++| ++|+.|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~--~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVE--NVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcC--CHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 47899999999999999999999999999999999986 4 4543 45889999999999999998 5888875
No 116
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.76 E-value=5.3e-08 Score=96.78 Aligned_cols=75 Identities=17% Similarity=0.295 Sum_probs=66.1
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeC----------CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLP----------EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg----------~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
...+++|++|.|+|+++.++|+||+|. .++.|++|.+++++....+ +...|++||.|.|+|++++ ++
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~--~~~~~~~GD~V~akV~~i~-~~ 135 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVES--LTDAFKIGDIVRAKVISYT-DP 135 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhh--HHhccCCCCEEEEEEEecC-Cc
Confidence 456789999999999999999999985 4789999999999876543 4788999999999999999 89
Q ss_pred EEEEEecc
Q 005707 327 VTLTMKKE 334 (681)
Q Consensus 327 I~LSLK~~ 334 (681)
+.||+|..
T Consensus 136 i~LS~k~~ 143 (189)
T PRK09521 136 LQLSTKGK 143 (189)
T ss_pred EEEEEecC
Confidence 99999853
No 117
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.76 E-value=5.2e-09 Score=108.16 Aligned_cols=76 Identities=34% Similarity=0.598 Sum_probs=69.5
Q ss_pred ccCcEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD 336 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~--GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~ 336 (681)
.+|++|-|+|++|.+||+||.|.+ |++||+|+||++..++.++ ++.+++||++-|+||++| +|.|.||||...+
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknI--rd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNI--RDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHH--HHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 479999999999999999999974 9999999999999998776 899999999999999998 5889999999876
Q ss_pred Cc
Q 005707 337 VG 338 (681)
Q Consensus 337 DP 338 (681)
+-
T Consensus 88 ~q 89 (269)
T COG1093 88 HQ 89 (269)
T ss_pred HH
Confidence 53
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=98.75 E-value=3.4e-08 Score=84.87 Aligned_cols=72 Identities=18% Similarity=0.134 Sum_probs=64.2
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE 334 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~ 334 (681)
++|++|.|+|+++.+.|++|+++.+.+|++|.++++..... .....|++||.+.|+|+++++ +++.||++..
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~ 77 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLGDDMNVLLTTADN 77 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeCCCCCEEEEECCC
Confidence 68999999999999999999999999999999999876533 336789999999999999986 7899999763
No 119
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.66 E-value=4.1e-08 Score=112.44 Aligned_cols=79 Identities=29% Similarity=0.492 Sum_probs=72.9
Q ss_pred ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEec
Q 005707 255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKK 333 (681)
Q Consensus 255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~ 333 (681)
....++++|+++.|+|+++.+||+||.|.+|-+||||++++++.+++.. ...+++||.|.|+|+.+|+ ||+.|++|.
T Consensus 612 ~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv--~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~ 689 (692)
T COG1185 612 AITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKV--EDVLKEGDEVKVKVIEIDKQGRIRLSIKA 689 (692)
T ss_pred HHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcc--cceeecCceEEEEEeeecccCCccceehh
Confidence 4568899999999999999999999999999999999999999987655 7999999999999999985 999999987
Q ss_pred cC
Q 005707 334 ED 335 (681)
Q Consensus 334 ~~ 335 (681)
..
T Consensus 690 ~~ 691 (692)
T COG1185 690 VL 691 (692)
T ss_pred cc
Confidence 53
No 120
>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=98.66 E-value=1.1e-07 Score=79.37 Aligned_cols=64 Identities=19% Similarity=0.329 Sum_probs=55.4
Q ss_pred CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEE
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTM 216 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSl 216 (681)
..|++++|+|.++.++|+||++++ .+|+||.++++. .+.|++|+.|+|.|++++.++ ..|.||+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 469999999999999999999987 999999999963 345899999999999999755 4677774
No 121
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.63 E-value=4.7e-08 Score=109.53 Aligned_cols=71 Identities=18% Similarity=0.282 Sum_probs=64.1
Q ss_pred cCCCC--CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEEEe
Q 005707 142 NEDLI--PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLTMR 217 (681)
Q Consensus 142 ~~~Lk--vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LSlK 217 (681)
+..++ .|+++.|+|+++.++|+||+|++ +.||||.+++. |.+.|++|+.|+|+|+.++++++ +|.||++
T Consensus 127 ~~eyk~~~GeIV~G~V~ri~~~giiVDLgg-vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt 199 (470)
T PRK09202 127 YEEYKDRVGEIITGVVKRVERGNIIVDLGR-AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRT 199 (470)
T ss_pred HHHHHhhcCCEEEEEEEEEecCCEEEEECC-eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 66676 89999999999999999999976 99999999985 67789999999999999999877 8999998
Q ss_pred cc
Q 005707 218 ES 219 (681)
Q Consensus 218 ~l 219 (681)
..
T Consensus 200 ~p 201 (470)
T PRK09202 200 HP 201 (470)
T ss_pred cH
Confidence 54
No 122
>PRK05054 exoribonuclease II; Provisional
Probab=98.63 E-value=1.7e-08 Score=116.93 Aligned_cols=148 Identities=11% Similarity=0.018 Sum_probs=98.3
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS 105 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s 105 (681)
.+.+||||+-.+|.|||||.|++.||-.+|-+. +. |.|.... ... .
T Consensus 481 ~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~-a~--------------l~~~~~~--------~~~---~-------- 526 (644)
T PRK05054 481 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK-AV--------------IKGETAE--------RPQ---D-------- 526 (644)
T ss_pred CCcCccccccccccccCChhhhhHHHHHHHHHH-HH--------------HcCCCCC--------ccH---H--------
Confidence 567999999999999999999999987764221 11 1111000 000 0
Q ss_pred CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCC--cEEEEEEEEEecCeeEEEEC-CCeEEEEeccccCC
Q 005707 106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPG--ATFTGKVRSIQPFGAFIDFG-AFTDGLVHVSRLSD 182 (681)
Q Consensus 106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvG--dIVeGkV~sV~d~GaFVdLg-ggV~GLVPiSELS~ 182 (681)
..+++.+.++..+..+++...+.. +.. |..=.+| +.+.|.|++|+.+|+||+|. .++.||||.+.|.+
T Consensus 527 --~~~~~~s~~er~a~~aer~~~~~~--~~~-----y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~ 597 (644)
T PRK05054 527 --EITVQLAERRRLNRMAERDVGDWL--YAR-----YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHA 597 (644)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHHH--HHH-----HHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCC
Confidence 012234444445555554333311 111 2233455 59999999999999999994 55999999999975
Q ss_pred c--cc-c--C-------cccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 183 N--FV-K--D-------VGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 183 ~--~v-~--d-------~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+ ++ . + -...|++||.|+|+|..+|..+++|.+..
T Consensus 598 ~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~ 643 (644)
T PRK05054 598 VRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARP 643 (644)
T ss_pred CccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEE
Confidence 3 11 1 1 12469999999999999999999998864
No 123
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.62 E-value=4.3e-08 Score=113.72 Aligned_cols=79 Identities=29% Similarity=0.473 Sum_probs=72.7
Q ss_pred ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEe
Q 005707 255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMK 332 (681)
Q Consensus 255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK 332 (681)
..+.+|++|+++.|+|+|+.+||+||+|+-+.+|++|++.+++.++. +|.+.+++||.|+|+|+.+| ++||.|||+
T Consensus 651 ~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr 728 (780)
T COG2183 651 ESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVDTARKRIALSMR 728 (780)
T ss_pred hhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEecccCeeeeEee
Confidence 45679999999999999999999999999999999999999999864 46899999999999999998 699999998
Q ss_pred ccC
Q 005707 333 KED 335 (681)
Q Consensus 333 ~~~ 335 (681)
...
T Consensus 729 ~~~ 731 (780)
T COG2183 729 LDE 731 (780)
T ss_pred ccC
Confidence 763
No 124
>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=98.61 E-value=8.7e-08 Score=75.91 Aligned_cols=63 Identities=35% Similarity=0.616 Sum_probs=54.7
Q ss_pred EEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEE
Q 005707 266 LEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLT 330 (681)
Q Consensus 266 V~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LS 330 (681)
+.|+|+++.++|+||+++.++.|++|.+++++.++. ++...|++||.|.|+|+++| ++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999999999999999999987643 34678999999999999997 4667654
No 125
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.61 E-value=1.8e-08 Score=117.96 Aligned_cols=160 Identities=19% Similarity=0.306 Sum_probs=109.9
Q ss_pred eeeeeeccccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCc
Q 005707 18 TAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDS 97 (681)
Q Consensus 18 ~~~~~~~~~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~ 97 (681)
..|.+. +.+||||+-.+|.|||||.|++.|+=.+|.+.- ...+........ + .
T Consensus 533 a~Ys~~---~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~-~l~~~~~~~~~~----------------~-------~ 585 (706)
T COG0557 533 AEYSPD---NVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKA-LLSGEPIPEKKT----------------S-------E 585 (706)
T ss_pred CeecCC---CCCceeccccchhccCCchhhchHHHHHHHHHH-HhcCCCCCccch----------------h-------H
Confidence 344444 789999999999999999999999876643321 111100000000 0 0
Q ss_pred ceecCCCCCcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCCCcEEEEEEEEEecCeeEEEECCC-eEEEEe
Q 005707 98 AGASDIPSDVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIPGATFTGKVRSIQPFGAFIDFGAF-TDGLVH 176 (681)
Q Consensus 98 lvlSer~s~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~LkvGdIVeGkV~sV~d~GaFVdLggg-V~GLVP 176 (681)
..+ ...+.+++-+++++.++++.... .... .+..-.+|+.+.|.|.+|..+|+||.|.+. ++|+||
T Consensus 586 ~~l------~~i~~~~s~~er~a~~aer~~~~--~~~~-----~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~ 652 (706)
T COG0557 586 EEL------DELAAHISSAERRAQEAERDVID--LLKA-----EYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVH 652 (706)
T ss_pred HHH------HHHHHHhCHHHHHHHHHHHHHHH--HHHH-----HHHHHhcCCEEEEEEEEEEeccEEEEecccccccceE
Confidence 001 11134456666666666665433 1222 256677899999999999999999999654 999999
Q ss_pred ccccCCccc-----------cCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 177 VSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 177 iSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
++.+..+++ ......|+.|+.|+|+|+.+|...++|.+++.
T Consensus 653 ~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v 704 (706)
T COG0557 653 ISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELV 704 (706)
T ss_pred cccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceEEEec
Confidence 999996543 22334699999999999999999999998764
No 126
>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=98.61 E-value=6.9e-08 Score=112.73 Aligned_cols=70 Identities=39% Similarity=0.659 Sum_probs=65.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
.+++|++|.|+|+++.+||+||+|.++.+||||+++++|.++.++.+.|++||.|+|+|+++|. +++|.|
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 5789999999999999999999998889999999999999999999999999999999999997 677654
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=98.60 E-value=1.8e-07 Score=83.48 Aligned_cols=75 Identities=29% Similarity=0.591 Sum_probs=64.9
Q ss_pred cEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccC-----------cccccccCCEEEEEEEEEeccC-----Cce
Q 005707 149 ATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD-----------VGSIVSVGQEVKVRLIEANAET-----GRI 212 (681)
Q Consensus 149 dIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d-----------~~e~fkVGd~VkVkVl~VD~ek-----grI 212 (681)
+++.|+|+++.++|+||+|.+ +.||+|+++++++++.. ....|++||.|+|+|.++|.+. +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 479999999999999999986 99999999999876643 3477999999999999999764 589
Q ss_pred EEEEeccchhhH
Q 005707 213 SLTMRESDDISK 224 (681)
Q Consensus 213 ~LSlK~l~~dp~ 224 (681)
.||++.....++
T Consensus 80 ~ls~k~~~~g~~ 91 (99)
T cd04460 80 GLTMRQPGLGKL 91 (99)
T ss_pred EEEEecCCCCcH
Confidence 999998776665
No 128
>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=98.57 E-value=2.7e-07 Score=82.37 Aligned_cols=76 Identities=26% Similarity=0.346 Sum_probs=64.0
Q ss_pred cEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEeC-------CeE
Q 005707 264 QDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRISR-------GQV 327 (681)
Q Consensus 264 dIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~IDk-------gKI 327 (681)
+++.|+|+.+.++|+||++. +++||+|.+++.+.++... .....|++||.|.|+|.++|. +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47899999999999999998 6999999999987765322 124789999999999999973 589
Q ss_pred EEEEeccCCCcCC
Q 005707 328 TLTMKKEDDVGSN 340 (681)
Q Consensus 328 ~LSLK~~~~DP~e 340 (681)
.||+|.....||+
T Consensus 80 ~ls~k~~~~g~~~ 92 (99)
T cd04460 80 GLTMRQPGLGKLE 92 (99)
T ss_pred EEEEecCCCCcHH
Confidence 9999998777754
No 129
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.54 E-value=5.2e-08 Score=109.20 Aligned_cols=123 Identities=17% Similarity=0.273 Sum_probs=90.1
Q ss_pred EEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEE-EeccchhhHhhhhccccccCCccccccccCCCCCC
Q 005707 172 DGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLT-MRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQ 250 (681)
Q Consensus 172 ~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS-lK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~ 250 (681)
.+.++.++... ....+.+|+.+.+.|...+ -+|+.++ .|+.....|. .
T Consensus 72 ~~eI~L~eAk~-----~~~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkir------------------------e 120 (470)
T PRK09202 72 TKEISLEEARK-----IDPDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIR------------------------E 120 (470)
T ss_pred cceeeHHHHhh-----hCccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHH------------------------H
Confidence 35566555422 2233789999999998876 3444333 3333333331 1
Q ss_pred ccccccccCCc--cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--C-
Q 005707 251 KRDEMKTTKFV--KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--G- 325 (681)
Q Consensus 251 ~k~~~~~sklk--vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--g- 325 (681)
..+...+..|+ .|+++.|+|+++.++|+||+++ |++||||.+++. |...|++||.|+|+|+++++ +
T Consensus 121 ~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~kg 191 (470)
T PRK09202 121 AERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEARG 191 (470)
T ss_pred HHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCCC
Confidence 12235678887 9999999999999999999996 999999999874 46789999999999999974 3
Q ss_pred -eEEEEEecc
Q 005707 326 -QVTLTMKKE 334 (681)
Q Consensus 326 -KI~LSLK~~ 334 (681)
+|.||.+..
T Consensus 192 ~qIilSRt~p 201 (470)
T PRK09202 192 PQIILSRTHP 201 (470)
T ss_pred CeEEEEeCcH
Confidence 799999654
No 130
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.53 E-value=1.2e-07 Score=108.59 Aligned_cols=77 Identities=36% Similarity=0.645 Sum_probs=72.4
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
...+++|+++.|+|+++.+||+||.|.++-+|++|++++++.++....+.+++||.|+|+|+.+|+ ++++.||++..
T Consensus 614 ~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 614 TREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred HhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence 478999999999999999999999998889999999999999999999999999999999999985 78999999854
No 131
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.52 E-value=2.4e-07 Score=92.19 Aligned_cols=73 Identities=19% Similarity=0.358 Sum_probs=66.7
Q ss_pred CCCCCCcEEEEEEEEEecCeeEEEECC----------CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCce
Q 005707 143 EDLIPGATFTGKVRSIQPFGAFIDFGA----------FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212 (681)
Q Consensus 143 ~~LkvGdIVeGkV~sV~d~GaFVdLgg----------gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI 212 (681)
..+++|++|.|+|+++.++|+||+|++ +..|++|.+++++.+..++.+.|++||.|+|+|+.++ +++
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i 136 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPL 136 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcE
Confidence 467899999999999999999999952 4789999999999888888999999999999999997 789
Q ss_pred EEEEec
Q 005707 213 SLTMRE 218 (681)
Q Consensus 213 ~LSlK~ 218 (681)
.||++.
T Consensus 137 ~LS~k~ 142 (189)
T PRK09521 137 QLSTKG 142 (189)
T ss_pred EEEEec
Confidence 999984
No 132
>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=98.50 E-value=1.7e-07 Score=109.55 Aligned_cols=72 Identities=31% Similarity=0.491 Sum_probs=64.0
Q ss_pred cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEE
Q 005707 256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTL 329 (681)
Q Consensus 256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~L 329 (681)
....+++|+++.|+|++|.+||+||+|.+|++||||+++++|.++. ++...|++||.|+|+|+++|. +|+.|
T Consensus 612 ~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~--~~~~~~kvGD~V~VkVi~id~~gki~L 684 (684)
T TIGR03591 612 ITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVE--KVEDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred hhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCccc--ChhhccCCCCEEEEEEEEECCCCCccC
Confidence 3456789999999999999999999999999999999999998865 347889999999999999984 77654
No 133
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.47 E-value=4.7e-07 Score=93.19 Aligned_cols=73 Identities=18% Similarity=0.240 Sum_probs=66.8
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc----cCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV----KDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v----~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
..++|++|.|+|+++.++|+||+|+....|+||++++++.++ .++...|++||.|+|+|+++++++ .+.||++
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~-~~~LS~k 136 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTR-DVVLTLK 136 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCC-cEEEEEc
Confidence 458899999999999999999999988999999999999887 788889999999999999998654 5999997
No 134
>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=98.45 E-value=8.4e-08 Score=111.24 Aligned_cols=147 Identities=10% Similarity=0.019 Sum_probs=96.5
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccCcccccccchhhcccceeEEEEEecCCCCCCCCcceecCCCC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSGSALQHKSALHIISATGINVAVEESDSPAADDDSAGASDIPS 105 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~~~~~~~~~~~~lvG~~i~VkVievD~~~~~~~~lvlSer~s 105 (681)
.+.+||||+-.+|.|||||.|++.||-.+|-+. .. |.|+.... . +
T Consensus 477 ~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~-~~--------------l~~~~~~~---------~------~----- 521 (639)
T TIGR02062 477 EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK-AV--------------IKGETATR---------P------Q----- 521 (639)
T ss_pred CCcCcchhccccccccCChhhhhHHHHHHHHHH-HH--------------HcCCCCCC---------C------H-----
Confidence 467999999999999999999999987764221 11 11110000 0 0
Q ss_pred CcccccccccccCCChhhHHhhhchhhhhcCCCCCCcCCCCC--CcEEEEEEEEEecCeeEEEE-CCCeEEEEeccccCC
Q 005707 106 DVETSESSSIKSEASPTLAESRRSRTARKSEMPPVKNEDLIP--GATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSD 182 (681)
Q Consensus 106 ~v~~ae~ss~~sea~~daek~~~kr~~rk~e~~~lt~~~Lkv--GdIVeGkV~sV~d~GaFVdL-gggV~GLVPiSELS~ 182 (681)
...+++.+.++..+..+++...+.. ... |..-++ |+.+.|.|.++..+|+||+| ..++.||||.+.+.+
T Consensus 522 -~~~~~~~s~~er~a~~aeR~~~~~~--~~~-----yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~ 593 (639)
T TIGR02062 522 -EDITVQLAERRRLNRIAERDVADWL--YAR-----FLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHA 593 (639)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHH--HHH-----HHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCC
Confidence 0012233444444445554333211 111 223345 45999999999999999999 566999999999965
Q ss_pred --ccc-cC-------c--ccccccCCEEEEEEEEEeccCCceEEE
Q 005707 183 --NFV-KD-------V--GSIVSVGQEVKVRLIEANAETGRISLT 215 (681)
Q Consensus 183 --~~v-~d-------~--~e~fkVGd~VkVkVl~VD~ekgrI~LS 215 (681)
+++ -+ + ...|+.||.|+|+|..+|..+++|.+.
T Consensus 594 ~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 594 NREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR 638 (639)
T ss_pred CCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence 222 11 1 126999999999999999999998874
No 135
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.43 E-value=9e-07 Score=73.81 Aligned_cols=61 Identities=28% Similarity=0.493 Sum_probs=52.9
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTLT 330 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~LS 330 (681)
+.|+++.|+|.++.++|+||+++ +.+|+||.+++.. ...|++||.|+++|+++++ ++|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP--------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 47999999999999999999997 5999999998863 3468999999999999963 457776
No 136
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.40 E-value=2.3e-06 Score=88.19 Aligned_cols=75 Identities=24% Similarity=0.276 Sum_probs=65.6
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccc--cccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGF--ANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE 334 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~i--e~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~ 334 (681)
.++||+|.|+|+++.++|+||+|+.+..|+||.++++|.++ +..++...|++||.|.|+|+++++ +++.||+|..
T Consensus 61 P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~ 138 (235)
T PRK04163 61 PKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK 138 (235)
T ss_pred CCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence 47999999999999999999999999999999999998764 223457789999999999999975 5799999864
No 137
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.38 E-value=4.3e-07 Score=101.80 Aligned_cols=83 Identities=27% Similarity=0.452 Sum_probs=73.9
Q ss_pred CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccc
Q 005707 141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESD 220 (681)
Q Consensus 141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~ 220 (681)
...+|+.|.+++|+|+.+.++|+||.|.++..||+|+++|+..++.+|.+.+.+||.|.|+.+..|+. +.+.++.+.++
T Consensus 662 ~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~-g~~~ls~ralL 740 (760)
T KOG1067|consen 662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPR-GGIMLSSRALL 740 (760)
T ss_pred cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCc-cceeehhhhhc
Confidence 36689999999999999999999999998899999999999999999999999999999999999974 55566666666
Q ss_pred hhhH
Q 005707 221 DISK 224 (681)
Q Consensus 221 ~dp~ 224 (681)
++|.
T Consensus 741 p~p~ 744 (760)
T KOG1067|consen 741 PDPA 744 (760)
T ss_pred CCcc
Confidence 6664
No 138
>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=98.31 E-value=2.5e-06 Score=84.23 Aligned_cols=79 Identities=32% Similarity=0.554 Sum_probs=66.0
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEe-----c
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEAN-----A 207 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD-----~ 207 (681)
....|++++|+|++++++|+||+++. ++|++|.+++.+++.. +....|++|+.|+++|.++| +
T Consensus 78 ~p~~gEvv~G~V~~v~~~GifV~lg~-~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 156 (179)
T TIGR00448 78 KPELGEIVEGEVIEIVEFGAFVSLGP-FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP 156 (179)
T ss_pred eccCCCEEEEEEEEEEeeEEEEEeCC-ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence 45679999999999999999999965 9999999999865432 23467999999999999998 5
Q ss_pred cCCceEEEEeccchhh
Q 005707 208 ETGRISLTMRESDDIS 223 (681)
Q Consensus 208 ekgrI~LSlK~l~~dp 223 (681)
+..+|.+|+|+.-.-+
T Consensus 157 ~~~~I~lt~k~~~LG~ 172 (179)
T TIGR00448 157 EGSKIGLTMRQPLLGK 172 (179)
T ss_pred CcceEEEEeccCcCCc
Confidence 6678999999754433
No 139
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.20 E-value=2.2e-06 Score=93.51 Aligned_cols=70 Identities=16% Similarity=0.284 Sum_probs=60.6
Q ss_pred cCCC--CCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC--ceEEEEe
Q 005707 142 NEDL--IPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG--RISLTMR 217 (681)
Q Consensus 142 ~~~L--kvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg--rI~LSlK 217 (681)
|..+ +.|+++.|+|.++.++|+||++|+ ++|+||.+++.. .+.|++||.++|.|++++..++ .|.||+.
T Consensus 127 ~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 127 YNEFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred HHHHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 6677 899999999999999999999987 999999877743 5669999999999999997654 5888887
Q ss_pred c
Q 005707 218 E 218 (681)
Q Consensus 218 ~ 218 (681)
.
T Consensus 200 ~ 200 (362)
T PRK12327 200 H 200 (362)
T ss_pred C
Confidence 4
No 140
>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=98.20 E-value=2.4e-06 Score=92.56 Aligned_cols=72 Identities=18% Similarity=0.433 Sum_probs=60.5
Q ss_pred cCCC--CCCcEEEEEEEEEecCe-eEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC--CceEEEE
Q 005707 142 NEDL--IPGATFTGKVRSIQPFG-AFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET--GRISLTM 216 (681)
Q Consensus 142 ~~~L--kvGdIVeGkV~sV~d~G-aFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek--grI~LSl 216 (681)
+..+ +.|+++.|+|.++.+.| +||+||+ ++|+||.+++.. .+.|++||.++|.|+.++... ..|.||+
T Consensus 124 ~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~-~ea~LP~~E~ip------~E~~~~Gd~ik~~V~~V~~~~kg~qIivSR 196 (341)
T TIGR01953 124 YDEFSSKEGEIISGTVKRVNRRGNLYVELGK-TEGILPKKEQIP------GEKFRIGDRIKAYVYEVRKTAKGPQIILSR 196 (341)
T ss_pred HHHHHhhcCCEEEEEEEEEecCCcEEEEECC-eEEEecHHHcCC------CcCCCCCCEEEEEEEEEEcCCCCCeEEEEe
Confidence 4455 59999999999999988 6999965 999999999873 445999999999999999654 5799999
Q ss_pred eccc
Q 005707 217 RESD 220 (681)
Q Consensus 217 K~l~ 220 (681)
+...
T Consensus 197 t~~~ 200 (341)
T TIGR01953 197 THPE 200 (341)
T ss_pred CcHH
Confidence 8543
No 141
>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=98.16 E-value=9.2e-06 Score=80.25 Aligned_cols=78 Identities=27% Similarity=0.312 Sum_probs=63.7
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc-c--------CCCCcccCCCEEEEEEEEEe-------
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN-M--------MGGSSLQVGQEVSVRVLRIS------- 323 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~-~--------~p~~~fkVGqkVkVrVL~ID------- 323 (681)
-.+|+++.|+|++++++|+||+++ .++|++|.+++.++.... . .....|++||.|+++|++++
T Consensus 79 p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 79 PELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred ccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 347999999999999999999996 699999999987654321 0 12467999999999999996
Q ss_pred CCeEEEEEeccCCCc
Q 005707 324 RGQVTLTMKKEDDVG 338 (681)
Q Consensus 324 kgKI~LSLK~~~~DP 338 (681)
..++.||||+....+
T Consensus 158 ~~~I~lt~k~~~LG~ 172 (179)
T TIGR00448 158 GSKIGLTMRQPLLGK 172 (179)
T ss_pred cceEEEEeccCcCCc
Confidence 368999999875555
No 142
>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=98.14 E-value=7e-06 Score=96.43 Aligned_cols=74 Identities=26% Similarity=0.471 Sum_probs=61.8
Q ss_pred cCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CC
Q 005707 258 TKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RG 325 (681)
Q Consensus 258 sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kg 325 (681)
.+-++|+++.|+|++|++||+||+|.+ |++||+|.+++.++++.. ......|++||.|+|+|.++| ++
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 334679999999999999999999998 899999999998654311 122467999999999999998 58
Q ss_pred eEEEEE
Q 005707 326 QVTLTM 331 (681)
Q Consensus 326 KI~LSL 331 (681)
+|.|++
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 898876
No 143
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.10 E-value=2.8e-06 Score=95.46 Aligned_cols=83 Identities=19% Similarity=0.310 Sum_probs=75.8
Q ss_pred cccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe-CCeEEEEEecc
Q 005707 256 KTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS-RGQVTLTMKKE 334 (681)
Q Consensus 256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID-kgKI~LSLK~~ 334 (681)
...++..|-++.|+|+.+.++|+||+|+++..||||.++|+..++ .+|...|++||.|.++.+..| ++.+.|+.|.+
T Consensus 662 ~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~i--akpsd~levGq~I~vk~ie~d~~g~~~ls~ral 739 (760)
T KOG1067|consen 662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKI--AKPSDLLEVGQEIQVKYIERDPRGGIMLSSRAL 739 (760)
T ss_pred cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccc--cChHHHHhhcceeEEEEEeecCccceeehhhhh
Confidence 355788999999999999999999999999999999999999885 577899999999999999998 68899999999
Q ss_pred CCCcCC
Q 005707 335 DDVGSN 340 (681)
Q Consensus 335 ~~DP~e 340 (681)
+++|.-
T Consensus 740 Lp~p~~ 745 (760)
T KOG1067|consen 740 LPDPAT 745 (760)
T ss_pred cCCccc
Confidence 998854
No 144
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.06 E-value=1e-05 Score=80.57 Aligned_cols=77 Identities=32% Similarity=0.673 Sum_probs=64.1
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-----------cCcccccccCCEEEEEEEEEeccC---
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVRLIEANAET--- 209 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-----------~d~~e~fkVGd~VkVkVl~VD~ek--- 209 (681)
....|++|.|.|+.+.++|+||.||. .+||+|.+++.++++ +.....+++|+.|+++|+.+....
T Consensus 78 kP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~ 156 (183)
T COG1095 78 KPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP 156 (183)
T ss_pred EeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence 34579999999999999999999997 999999999998844 123347899999999999987655
Q ss_pred --CceEEEEeccch
Q 005707 210 --GRISLTMRESDD 221 (681)
Q Consensus 210 --grI~LSlK~l~~ 221 (681)
.+|.++|++.-.
T Consensus 157 ~~~~I~lTmrq~~L 170 (183)
T COG1095 157 RESKIGLTMRQPGL 170 (183)
T ss_pred ccceEEEEeccccC
Confidence 478899986544
No 145
>PRK11642 exoribonuclease R; Provisional
Probab=98.05 E-value=1.2e-05 Score=95.92 Aligned_cols=72 Identities=21% Similarity=0.392 Sum_probs=61.1
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCC-eEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe--CCeEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEG-EEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS--RGQVT 328 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~G-IeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID--kgKI~ 328 (681)
++|+++.|+|++|++||+||+|.++ ++||||.+++.++++... .....|++||.|+|+|+.+| +++|.
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 6899999999999999999999874 999999999987643211 12467999999999999997 68899
Q ss_pred EEEe
Q 005707 329 LTMK 332 (681)
Q Consensus 329 LSLK 332 (681)
|++-
T Consensus 722 f~l~ 725 (813)
T PRK11642 722 FSLI 725 (813)
T ss_pred EEEe
Confidence 9884
No 146
>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=98.05 E-value=3e-06 Score=91.86 Aligned_cols=114 Identities=26% Similarity=0.465 Sum_probs=80.6
Q ss_pred cCcccccccCCEEEEEEEEEeccCCceEEE-EeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCc--c
Q 005707 186 KDVGSIVSVGQEVKVRLIEANAETGRISLT-MRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFV--K 262 (681)
Q Consensus 186 ~d~~e~fkVGd~VkVkVl~VD~ekgrI~LS-lK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklk--v 262 (681)
......+++||.|.+.|...+ -+|+.++ .|+...+.. | ...++..+..|+ .
T Consensus 78 ~~~d~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qki------------------r------e~ere~i~~ey~~k~ 131 (341)
T TIGR01953 78 REIDPDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKI------------------R------EAERERVYDEFSSKE 131 (341)
T ss_pred HhhccccccCCEEEEEecccC--CCHHHHHHHHHHHHHHH------------------H------HHHHHHHHHHHHhhc
Confidence 334455889999998885432 2443333 222111110 0 112235677774 9
Q ss_pred CcEEEEEEEEEecce-EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeEEEEEecc
Q 005707 263 GQDLEGTVKNLTRSG-AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQVTLTMKKE 334 (681)
Q Consensus 263 GdIV~G~VknVt~~G-aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI~LSLK~~ 334 (681)
|+++.|+|.++.+.| +||+++ +++|+||.+++. |.+.|++||.++|+|+++++ .+|.||.+..
T Consensus 132 GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i--------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 132 GEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI--------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred CCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC--------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 999999999999988 699996 999999998765 34669999999999999973 4699999764
No 147
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.05 E-value=2e-05 Score=78.16 Aligned_cols=75 Identities=29% Similarity=0.617 Sum_probs=63.7
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc-----------CcccccccCCEEEEEEEEEeccCC--
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK-----------DVGSIVSVGQEVKVRLIEANAETG-- 210 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~-----------d~~e~fkVGd~VkVkVl~VD~ekg-- 210 (681)
....|+++.|+|+++.++|+||+++. .+|++|.+++.+++.. +....|++|+.|+++|++++...+
T Consensus 78 ~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~ 156 (187)
T PRK08563 78 KPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156 (187)
T ss_pred eccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence 46689999999999999999999986 9999999999876432 345678999999999999987653
Q ss_pred ---ceEEEEecc
Q 005707 211 ---RISLTMRES 219 (681)
Q Consensus 211 ---rI~LSlK~l 219 (681)
+|.+|++..
T Consensus 157 ~~~~I~ls~~~~ 168 (187)
T PRK08563 157 RGSKIGLTMRQP 168 (187)
T ss_pred CCCEEEEEecCC
Confidence 788899864
No 148
>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=98.04 E-value=1.7e-05 Score=70.80 Aligned_cols=73 Identities=16% Similarity=0.194 Sum_probs=64.2
Q ss_pred CCCCcEEEEEEEEEecCeeEEEE--------CCCeEEEEeccccCCcccc--CcccccccCCEEEEEEEEEeccCCceEE
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDF--------GAFTDGLVHVSRLSDNFVK--DVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdL--------gggV~GLVPiSELS~~~v~--d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
.++|++|-|+|+++....++|+| .....|++|.+++...+.. ++.+.|++||.|+|+|++++. .+.+.|
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L 82 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL 82 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence 47899999999999999999999 6778999999999877665 678899999999999999864 466889
Q ss_pred EEec
Q 005707 215 TMRE 218 (681)
Q Consensus 215 SlK~ 218 (681)
|++.
T Consensus 83 st~~ 86 (92)
T cd05791 83 STAE 86 (92)
T ss_pred EecC
Confidence 9874
No 149
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.01 E-value=3.3e-06 Score=92.11 Aligned_cols=71 Identities=21% Similarity=0.402 Sum_probs=60.4
Q ss_pred cccccCC--ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC----CeE
Q 005707 254 EMKTTKF--VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR----GQV 327 (681)
Q Consensus 254 ~~~~skl--kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk----gKI 327 (681)
...+..| +.|+++.|+|.++.++|+||+++ +++||||.+++. |...|++||.++|+|+++++ -+|
T Consensus 124 e~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP~~E~i--------p~e~~~~Gd~Ika~V~~V~~~~kgp~I 194 (362)
T PRK12327 124 EIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVLPPAEQI--------PGETYKHGDRIKVYVVKVEKTTKGPQI 194 (362)
T ss_pred HHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEecHHHcC--------CCCCCCCCCEEEEEEEEEecCCCCCeE
Confidence 3668888 89999999999999999999997 799999987653 36789999999999999973 258
Q ss_pred EEEEec
Q 005707 328 TLTMKK 333 (681)
Q Consensus 328 ~LSLK~ 333 (681)
.||...
T Consensus 195 ivSRt~ 200 (362)
T PRK12327 195 FVSRTH 200 (362)
T ss_pred EEEeCC
Confidence 888743
No 150
>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=97.99 E-value=2e-05 Score=92.00 Aligned_cols=71 Identities=21% Similarity=0.469 Sum_probs=60.0
Q ss_pred ccCcEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEe--CCeEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLP-EGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRIS--RGQVT 328 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg-~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~ID--kgKI~ 328 (681)
++|+++.|+|++|+++|+||+|+ .+++||+|.+++.|+++.. ......|++||.|+|+|.++| +++|.
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~ 650 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII 650 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 57999999999999999999998 6899999999998864211 112467999999999999997 58888
Q ss_pred EEE
Q 005707 329 LTM 331 (681)
Q Consensus 329 LSL 331 (681)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 875
No 151
>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=97.91 E-value=2.4e-05 Score=69.77 Aligned_cols=75 Identities=12% Similarity=0.109 Sum_probs=64.2
Q ss_pred CccCcEEEEEEEEEecceEEEEe--------CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEE
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISL--------PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLT 330 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeI--------g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LS 330 (681)
.++|++|-|+|+.+....++|+| .....|++|.+++.....+.....+.|++||.|+++|+++++ ..+.||
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Ls 83 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLS 83 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEE
Confidence 37899999999999999999999 778999999998876655433457889999999999999965 779999
Q ss_pred Eecc
Q 005707 331 MKKE 334 (681)
Q Consensus 331 LK~~ 334 (681)
++..
T Consensus 84 t~~~ 87 (92)
T cd05791 84 TAEN 87 (92)
T ss_pred ecCC
Confidence 9753
No 152
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.87 E-value=3.5e-05 Score=67.97 Aligned_cols=73 Identities=10% Similarity=0.103 Sum_probs=66.8
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEE-CCCeEEEEe-ccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDF-GAFTDGLVH-VSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdL-gggV~GLVP-iSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
+.-.++|+++. .|+.+.+.|+||.| +.+++|+|. .++++.++++.+.+.+ +|..+.|+|+.+|+++|-|.||.
T Consensus 11 y~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 11 YVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred EecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 56678999998 99999999999999 344999998 9999999999999999 99999999999999999999984
No 153
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.83 E-value=8.1e-05 Score=73.80 Aligned_cols=76 Identities=28% Similarity=0.380 Sum_probs=62.0
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccc---------cCCCCcccCCCEEEEEEEEEeC-----
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFAN---------MMGGSSLQVGQEVSVRVLRISR----- 324 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~---------~~p~~~fkVGqkVkVrVL~IDk----- 324 (681)
+..+|+++.|+|+++.++|+||+++ .++||+|.+++.+++... ......+++||.|+++|++++.
T Consensus 78 ~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~ 156 (187)
T PRK08563 78 KPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156 (187)
T ss_pred eccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence 4557999999999999999999998 699999999988764321 0124678999999999999962
Q ss_pred --CeEEEEEeccC
Q 005707 325 --GQVTLTMKKED 335 (681)
Q Consensus 325 --gKI~LSLK~~~ 335 (681)
.++.||||..-
T Consensus 157 ~~~~I~ls~~~~~ 169 (187)
T PRK08563 157 RGSKIGLTMRQPG 169 (187)
T ss_pred CCCEEEEEecCCC
Confidence 37999998763
No 154
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.78 E-value=6.7e-05 Score=74.85 Aligned_cols=80 Identities=28% Similarity=0.392 Sum_probs=64.4
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccC---------CCCcccCCCEEEEEEEEEe---C
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMM---------GGSSLQVGQEVSVRVLRIS---R 324 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~---------p~~~fkVGqkVkVrVL~ID---k 324 (681)
.-+...|++|.|.|+++.++|+||.|+ -.+||+|.+.+.++++.... -...|++|+.|++||+.+. +
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence 334558999999999999999999999 89999999999887432110 1237999999999999994 2
Q ss_pred ----CeEEEEEeccCCC
Q 005707 325 ----GQVTLTMKKEDDV 337 (681)
Q Consensus 325 ----gKI~LSLK~~~~D 337 (681)
-++.||||+.-..
T Consensus 155 ~~~~~~I~lTmrq~~LG 171 (183)
T COG1095 155 RPRESKIGLTMRQPGLG 171 (183)
T ss_pred ccccceEEEEeccccCC
Confidence 6799999987443
No 155
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.74 E-value=0.00013 Score=60.43 Aligned_cols=61 Identities=31% Similarity=0.384 Sum_probs=38.1
Q ss_pred CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
+|++...+|..+.++|+|++.+.+.+.|||.+++... +++||.|.|.|+. ...+|+.+|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFvY~--D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFVYL--DKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE---TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEEEE--CCCCCEEEecC
Confidence 5899999999999999999998889999999988543 7899999999997 34578888875
No 156
>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=97.65 E-value=0.00028 Score=62.63 Aligned_cols=64 Identities=16% Similarity=0.302 Sum_probs=52.9
Q ss_pred CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc-----------ccccccCCEEEEEEEEEeccCCc
Q 005707 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV-----------GSIVSVGQEVKVRLIEANAETGR 211 (681)
Q Consensus 147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~-----------~e~fkVGd~VkVkVl~VD~ekgr 211 (681)
.|+++.|+|+++.++|+||.+|. +++|+|...+..+...++ ...+.+|+.|++||+.+..+.+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 75 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATD 75 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCc
Confidence 48999999999999999999988 999999999976644333 23478999999999998765443
No 157
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.52 E-value=7.2e-05 Score=77.98 Aligned_cols=81 Identities=23% Similarity=0.363 Sum_probs=75.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEE--CCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccch
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDF--GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDD 221 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdL--gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~ 221 (681)
-..++++|-+.|+.|.+-|+||.| .++++|+|-.++||..+++.+..+.++|..=-|.|+.||+++|.|.||.+...+
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 456799999999999999999999 577999999999999999999999999999999999999999999999998877
Q ss_pred hhH
Q 005707 222 ISK 224 (681)
Q Consensus 222 dp~ 224 (681)
...
T Consensus 93 ed~ 95 (304)
T KOG2916|consen 93 EDK 95 (304)
T ss_pred HHH
Confidence 654
No 158
>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=97.48 E-value=0.00025 Score=61.16 Aligned_cols=70 Identities=26% Similarity=0.280 Sum_probs=57.3
Q ss_pred CcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEE-EEEEEEEeCCeEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEV-SVRVLRISRGQVTLTMK 332 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkV-kVrVL~IDkgKI~LSLK 332 (681)
|++|.|+|...++.+++|++.+ |+.|++|..+++|..-++...-.++++||++ .+.|++.-.+.+.||.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEeccccEEEEecC
Confidence 7899999999999999999998 9999999999999322222235789999999 89999434577888765
No 159
>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=97.36 E-value=0.00053 Score=59.21 Aligned_cols=68 Identities=18% Similarity=0.189 Sum_probs=56.8
Q ss_pred CcEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccC--cccccccCCEE-EEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKD--VGSIVSVGQEV-KVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d--~~e~fkVGd~V-kVkVl~VD~ekgrI~LSlK 217 (681)
|++|.|+|..-++.+++|++.+ ++.|+||..++++..-++ .-..+++||++ ++.|+ |...+.|.+|.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 7899999999999999999965 799999999999932222 23568999999 99999 777788888865
No 160
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.33 E-value=0.00045 Score=61.12 Aligned_cols=72 Identities=15% Similarity=0.215 Sum_probs=61.0
Q ss_pred cccCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEe-CCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 256 KTTKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLP-TSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 256 ~~sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLp-iSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
.+.--++|+++. .|+.+.+.|+||.|-+ |++|++. .+|++..++..+ .+.+ +|..+.|+|+++| +|-|.||.
T Consensus 10 cy~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi--~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 10 CYVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKL--KKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred EEecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhh--hhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 445567899998 8999999999999865 8999998 999999887655 6677 9999999999998 47788774
No 161
>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=97.32 E-value=0.00062 Score=75.89 Aligned_cols=74 Identities=26% Similarity=0.489 Sum_probs=57.9
Q ss_pred CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCcc------------ccCcccccccCCEEEEEEEEEeccC
Q 005707 144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNF------------VKDVGSIVSVGQEVKVRLIEANAET 209 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~------------v~d~~e~fkVGd~VkVkVl~VD~ek 209 (681)
...+|.+|.|+|+++.++ |+||+||.+..||||++++.+.+ ..++.+.+++||.|-|.|+.--...
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~ 101 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN 101 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence 345799999999999998 99999999999999999997531 3345567999999999999833333
Q ss_pred CceEEEEe
Q 005707 210 GRISLTMR 217 (681)
Q Consensus 210 grI~LSlK 217 (681)
+.-.||..
T Consensus 102 Kgp~lT~~ 109 (414)
T TIGR00757 102 KGARLTTD 109 (414)
T ss_pred CCCeEEEE
Confidence 44444443
No 162
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.32 E-value=0.00072 Score=55.99 Aligned_cols=61 Identities=36% Similarity=0.388 Sum_probs=37.9
Q ss_pred cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK 332 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK 332 (681)
+|++...+|..++++|+|++.+.+-+-|||.++.. ..+++||.|.|.|-.-..+|+..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP----------EPLKVGDEVEVFVYLDKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG----------------TTSEEEEEEEE-TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC----------CCCCCCCEEEEEEEECCCCCEEEecC
Confidence 48899999999999999999998899999988764 34799999999977755789999886
No 163
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.23 E-value=0.00088 Score=73.58 Aligned_cols=68 Identities=19% Similarity=0.243 Sum_probs=57.5
Q ss_pred CCCCcEEEEEEEEEecC-eeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCC---ceEEEEecc
Q 005707 145 LIPGATFTGKVRSIQPF-GAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETG---RISLTMRES 219 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~-GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekg---rI~LSlK~l 219 (681)
-++|+++.|+|.++... ++||+||+ +.|+||..+.. +.+.|++||.++|.|.+|+...+ .|.||+...
T Consensus 136 ~~~Geiv~g~V~r~~~~~~i~vdlg~-~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p 207 (374)
T PRK12328 136 KKVGKIVFGTVVRVDNEENTFIEIDE-IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTSP 207 (374)
T ss_pred HhcCcEEEEEEEEEecCCCEEEEcCC-eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence 35899999999999974 58999986 99999987764 45679999999999999998765 788888743
No 164
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.18 E-value=0.0019 Score=64.32 Aligned_cols=74 Identities=19% Similarity=0.262 Sum_probs=58.0
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcccc------------CcccccccCCEEEEEEEEEeccCC-
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVK------------DVGSIVSVGQEVKVRLIEANAETG- 210 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~------------d~~e~fkVGd~VkVkVl~VD~ekg- 210 (681)
....|++++|+|+++.++|+||.+|. .++|||.++|.++..- +-...+..|+.|++||+.+..+.+
T Consensus 78 rPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 156 (176)
T PTZ00162 78 KPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN 156 (176)
T ss_pred ecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence 46689999999999999999999976 7899999999854221 123468999999999988765443
Q ss_pred -ceEEEEec
Q 005707 211 -RISLTMRE 218 (681)
Q Consensus 211 -rI~LSlK~ 218 (681)
++.+|||+
T Consensus 157 ~~~i~T~~~ 165 (176)
T PTZ00162 157 LFAIATINS 165 (176)
T ss_pred cEEEEEecC
Confidence 46667774
No 165
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.18 E-value=0.001 Score=75.91 Aligned_cols=163 Identities=21% Similarity=0.395 Sum_probs=109.1
Q ss_pred CCCcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 139 PVKNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 139 ~lt~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
.-++.+++.|..+.|+|.++..||+||+|..++.|++|.++++.. ..|.+|+.+-|.+..+-+.++.|.+....
T Consensus 114 ~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~ 187 (715)
T COG1107 114 SCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVG 187 (715)
T ss_pred ccchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecC
Confidence 345889999999999999999999999999999999999998762 13789999999999998888988887776
Q ss_pred cchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcE--EEEEEEEEecc-eE-EEEeCCCeEEEEeCCC
Q 005707 219 SDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQD--LEGTVKNLTRS-GA-FISLPEGEEGFLPTSE 294 (681)
Q Consensus 219 l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdI--V~G~VknVt~~-Ga-FVeIg~GIeGLLpiSE 294 (681)
+......+ .++. -.+....-+.+ ..|+. +.|.|+.|... |= ...|- .-.|+++..-
T Consensus 188 ~~~Y~~~~--------~~ke----------~~r~~i~~id~-~ig~tV~I~GeV~qikqT~GPTVFtlt-Detg~i~aAA 247 (715)
T COG1107 188 LDRYREVQ--------VEKE----------LPRTLIDDLDE-MIGKTVRIEGEVTQIKQTSGPTVFTLT-DETGAIWAAA 247 (715)
T ss_pred Cccchhhh--------hhhh----------cccccHHHHHh-hcCceEEEEEEEEEEEEcCCCEEEEEe-cCCCceehhh
Confidence 55222110 0000 00111122333 56776 58999998544 32 22343 4456777654
Q ss_pred CCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 295 ESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 295 LSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
+....+ ...-.+++|+.|.+. =.++ .|++.+-+
T Consensus 248 Fe~aGv---RAyP~IevGdiV~Vi-G~V~~r~g~lQiE~ 282 (715)
T COG1107 248 FEEAGV---RAYPEIEVGDIVEVI-GEVTRRDGRLQIEI 282 (715)
T ss_pred hccCCc---ccCCCCCCCceEEEE-EEEeecCCcEEEee
Confidence 443332 224568999998753 2233 47776643
No 166
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.15 E-value=0.0022 Score=66.53 Aligned_cols=73 Identities=23% Similarity=0.383 Sum_probs=64.3
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCcc----ccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNF----VKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~----v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
..++||+|-|+|..+...+-.|||++...+++|.+++.+.. ..+++..|++||.|.|+|..+|+ .+.+.|++|
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k 137 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLK 137 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEee
Confidence 56789999999999999999999999999999999996544 35778899999999999999985 577788875
No 167
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.11 E-value=0.0027 Score=56.54 Aligned_cols=72 Identities=18% Similarity=0.134 Sum_probs=61.1
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
.++||+|-|+|+.+...+.+|+|+....|+||..++... .+..+..+++||.|.|+|..+|+. ....||+..
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~ 75 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVD 75 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeC
Confidence 468999999999999999999999889999999887543 344566799999999999999865 457888874
No 168
>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=97.10 E-value=0.00086 Score=74.78 Aligned_cols=65 Identities=26% Similarity=0.342 Sum_probs=52.3
Q ss_pred cCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccc----------ccCCCCcccCCCEEEEEEEEE
Q 005707 258 TKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFA----------NMMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 258 sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie----------~~~p~~~fkVGqkVkVrVL~I 322 (681)
....+|+++.|+|++|.++ |+||+|+.+..||+|.+++.+.... ..+....+++||.|.|.|.+-
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence 3467999999999999999 9999999999999999998653100 011234699999999999884
No 169
>PRK05054 exoribonuclease II; Provisional
Probab=97.04 E-value=0.0018 Score=75.84 Aligned_cols=69 Identities=16% Similarity=0.297 Sum_probs=54.5
Q ss_pred CcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccc-----c-----cCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFA-----N-----MMGGSSLQVGQEVSVRVLRIS--RGQVTL 329 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie-----~-----~~p~~~fkVGqkVkVrVL~ID--kgKI~L 329 (681)
|+.+.|.|+.|+.+|+||+|.+ |++||||.+.|.+.+.. + ......|+.||.|+|+|.++| +++|.+
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~ 641 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA 641 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence 4599999999999999999965 79999999998653110 0 011357999999999999998 577776
Q ss_pred EE
Q 005707 330 TM 331 (681)
Q Consensus 330 SL 331 (681)
.+
T Consensus 642 ~~ 643 (644)
T PRK05054 642 RP 643 (644)
T ss_pred EE
Confidence 54
No 170
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.99 E-value=0.012 Score=61.11 Aligned_cols=80 Identities=24% Similarity=0.243 Sum_probs=68.0
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc--ccCCCCcccCCCEEEEEEEEEeC-CeEEEEEeccCCC
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFA--NMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKEDDV 337 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie--~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~~~D 337 (681)
++||+|-|+|..+...+-.|+|+.-..+++|.+++.+..++ ....+..|++||.|.++|..+|+ +.+.|++|....-
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~G 142 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLG 142 (239)
T ss_pred CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCc
Confidence 57999999999999999999999889999999999766654 23467899999999999999985 8899999776444
Q ss_pred cCC
Q 005707 338 GSN 340 (681)
Q Consensus 338 P~e 340 (681)
++.
T Consensus 143 kL~ 145 (239)
T COG1097 143 KLK 145 (239)
T ss_pred ccc
Confidence 433
No 171
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.94 E-value=0.0036 Score=55.64 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=47.6
Q ss_pred cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe
Q 005707 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID 323 (681)
+|+++.|+|++++++|+||.++ .+++|+|...+..+..-+. .....+++|+.|++||+.+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~ 70 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence 5899999999999999999997 8889988877654321110 11356899999999999884
No 172
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.85 E-value=0.004 Score=61.99 Aligned_cols=75 Identities=19% Similarity=0.248 Sum_probs=57.0
Q ss_pred CCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-cccc---------cCCCCcccCCCEEEEEEEEEe----C
Q 005707 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-GFAN---------MMGGSSLQVGQEVSVRVLRIS----R 324 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~ie~---------~~p~~~fkVGqkVkVrVL~ID----k 324 (681)
+.-+|+++.|+|++++++|+||.++ -.++|+|.+.+.+. .++. ......++.|+.|++||+.+. .
T Consensus 78 rPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 156 (176)
T PTZ00162 78 KPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN 156 (176)
T ss_pred ecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence 3458999999999999999999997 66799999888643 1111 111356999999999999983 2
Q ss_pred CeEEEEEecc
Q 005707 325 GQVTLTMKKE 334 (681)
Q Consensus 325 gKI~LSLK~~ 334 (681)
.++.+|||+-
T Consensus 157 ~~~i~T~~~~ 166 (176)
T PTZ00162 157 LFAIATINSD 166 (176)
T ss_pred cEEEEEecCC
Confidence 4566688764
No 173
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.50 E-value=0.0085 Score=67.21 Aligned_cols=68 Identities=9% Similarity=0.051 Sum_probs=56.3
Q ss_pred CCCCcEEEEEEEEEecCeeEEEEC---C--CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccC---CceEEEE
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFG---A--FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAET---GRISLTM 216 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLg---g--gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ek---grI~LSl 216 (681)
-++|+++.|+|.++...+++|+|+ | ++.|+||..+.. +.+.|++|+.|+|.|..|.... -+|.||+
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 348999999999999999999994 3 389999987763 4566999999999999998753 2688888
Q ss_pred ec
Q 005707 217 RE 218 (681)
Q Consensus 217 K~ 218 (681)
..
T Consensus 224 t~ 225 (449)
T PRK12329 224 AN 225 (449)
T ss_pred CC
Confidence 74
No 174
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.47 E-value=0.012 Score=59.17 Aligned_cols=73 Identities=21% Similarity=0.346 Sum_probs=64.0
Q ss_pred cCCCCCCcEEEEEEEEEecCeeEEEECC----------CeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCc
Q 005707 142 NEDLIPGATFTGKVRSIQPFGAFIDFGA----------FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGR 211 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~GaFVdLgg----------gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgr 211 (681)
...++.|++|-|+|+++....+.|++.+ ...|-+|++++.+.++.+..+.|++||.|+++|++.- ..
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~ 135 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP 135 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CC
Confidence 4568899999999999999999887731 2568899999999999999999999999999999962 67
Q ss_pred eEEEEe
Q 005707 212 ISLTMR 217 (681)
Q Consensus 212 I~LSlK 217 (681)
+.||++
T Consensus 136 ~~Lst~ 141 (188)
T COG1096 136 IQLSTK 141 (188)
T ss_pred eEEEec
Confidence 888887
No 175
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.43 E-value=0.0063 Score=69.74 Aligned_cols=76 Identities=17% Similarity=0.287 Sum_probs=61.7
Q ss_pred ccccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 255 MKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 255 ~~~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
-.+.++..|..++|+|.++.+||+||++...+.||+|.++++.. ..|.+|+.+-|.|..+..++-.++++..
T Consensus 115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~--------~~~~vgdeiiV~v~~vr~~~geidf~~~ 186 (715)
T COG1107 115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD--------PDYAVGDEIIVQVSDVRPEKGEIDFEPV 186 (715)
T ss_pred cchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC--------CCCCCCCeEEEEeeccCCCCCccceeec
Confidence 45788999999999999999999999999999999999988752 4679999999999999644333444444
Q ss_pred CCCc
Q 005707 335 DDVG 338 (681)
Q Consensus 335 ~~DP 338 (681)
..++
T Consensus 187 ~~~~ 190 (715)
T COG1107 187 GLDR 190 (715)
T ss_pred CCcc
Confidence 3333
No 176
>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=96.43 E-value=0.0068 Score=53.61 Aligned_cols=60 Identities=15% Similarity=0.197 Sum_probs=41.7
Q ss_pred CCCcEEEEEEEEEecCeeEEEEC------------------CCeEEEEeccccCCcccc--CcccccccCCEEEEEEEEE
Q 005707 146 IPGATFTGKVRSIQPFGAFIDFG------------------AFTDGLVHVSRLSDNFVK--DVGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~GaFVdLg------------------ggV~GLVPiSELS~~~v~--d~~e~fkVGd~VkVkVl~V 205 (681)
++|++|.|+|+++++.-++++|- ....|+|+.+++...... .+.+.|++||.|+|+|+++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 67999999999999999887762 246799999998765443 3578899999999999974
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=96.30 E-value=0.009 Score=70.10 Aligned_cols=67 Identities=13% Similarity=0.363 Sum_probs=51.8
Q ss_pred CcEEEEEEEEEecceEEEEe-CCCeEEEEeCCCCCc--ccc--c------ccCCCCcccCCCEEEEEEEEEe--CCeEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISL-PEGEEGFLPTSEESD--DGF--A------NMMGGSSLQVGQEVSVRVLRIS--RGQVTL 329 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeI-g~GIeGLLpiSELSd--~~i--e------~~~p~~~fkVGqkVkVrVL~ID--kgKI~L 329 (681)
|+.+.|.|..++.+|+||+| ..|++||||.+.+.+ +.+ + .+.....|+.||.|+|+|.++| +++|.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 45899999999999999999 558999999998865 221 0 1111236999999999999998 455554
No 178
>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=96.30 E-value=0.021 Score=50.98 Aligned_cols=72 Identities=19% Similarity=0.146 Sum_probs=59.6
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC-CeEEEEEecc
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKKE 334 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk-gKI~LSLK~~ 334 (681)
-++||.|-|+|+.+...+.+|+|+.-..|++|...+.... .+.+..|++||.|-|+|..+++ ....|++...
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gat---k~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGAT---KRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHccccc---ccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 3589999999999999999999998899999997764332 1225789999999999999985 5688888653
No 179
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.21 E-value=0.0052 Score=74.48 Aligned_cols=80 Identities=25% Similarity=0.277 Sum_probs=70.7
Q ss_pred CCCCCCcEEEEEEEEEecCe---eEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 143 EDLIPGATFTGKVRSIQPFG---AFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 143 ~~LkvGdIVeGkV~sV~d~G---aFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
+.+..|.+|.++|++|...- +-|.+.+|++|+||...+++..+.+|...+++|+.|.|+|+.+|.++=-+.||++..
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~r~s 1060 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 35779999999999998554 457888889999999999999999999999999999999999999888889998876
Q ss_pred chh
Q 005707 220 DDI 222 (681)
Q Consensus 220 ~~d 222 (681)
...
T Consensus 1061 dlk 1063 (1299)
T KOG1856|consen 1061 DLK 1063 (1299)
T ss_pred Hhh
Confidence 554
No 180
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.14 E-value=0.018 Score=63.63 Aligned_cols=69 Identities=22% Similarity=0.337 Sum_probs=56.1
Q ss_pred cccCC--ccCcEEEEEEEEEecc-eEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC--C---eE
Q 005707 256 KTTKF--VKGQDLEGTVKNLTRS-GAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR--G---QV 327 (681)
Q Consensus 256 ~~skl--kvGdIV~G~VknVt~~-GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk--g---KI 327 (681)
.+..| +.|+++.|+|.++... ++||+|+ +.+|+||..+.. |.+.|++||.++|.|.++++ + +|
T Consensus 130 i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~k~gp~I 200 (374)
T PRK12328 130 IFEKYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDKNNGILI 200 (374)
T ss_pred HHHHHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCCCCCCEE
Confidence 44444 4899999999999864 6999997 899999987643 57889999999999999952 3 67
Q ss_pred EEEEec
Q 005707 328 TLTMKK 333 (681)
Q Consensus 328 ~LSLK~ 333 (681)
.||+..
T Consensus 201 ilSRt~ 206 (374)
T PRK12328 201 ELSRTS 206 (374)
T ss_pred EEEcCC
Confidence 788743
No 181
>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=96.01 E-value=0.012 Score=52.08 Aligned_cols=62 Identities=15% Similarity=0.161 Sum_probs=41.3
Q ss_pred ccCcEEEEEEEEEecceEEEEeC------------------CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLP------------------EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg------------------~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I 322 (681)
++|++|.|+|+++++.-++++|- +...|+++.+++.....+.....+.|++||.|.++|++.
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 58999999999999998888752 256789999887655444445578899999999999974
No 182
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.96 E-value=0.0037 Score=65.61 Aligned_cols=75 Identities=23% Similarity=0.363 Sum_probs=66.6
Q ss_pred ccCcEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEeccCC
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLP--EGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKEDD 336 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg--~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~~~ 336 (681)
.++++|-+.|+.|.+.|+||.|- ++++|++-.+||+..++..+ ....++|..=.|.||++| +|-|.||++...+
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI--~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSI--QKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHH--HHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 47999999999999999999985 59999999999999887655 788999999999999998 4779999988754
Q ss_pred C
Q 005707 337 V 337 (681)
Q Consensus 337 D 337 (681)
+
T Consensus 93 e 93 (304)
T KOG2916|consen 93 E 93 (304)
T ss_pred H
Confidence 4
No 183
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.80 E-value=0.017 Score=69.79 Aligned_cols=63 Identities=27% Similarity=0.369 Sum_probs=50.7
Q ss_pred ccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCccccccc-------CCCCcccCCCEEEEEEEEEe
Q 005707 261 VKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANM-------MGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 261 kvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~-------~p~~~fkVGqkVkVrVL~ID 323 (681)
.+|.||.|+|.+|.+. ++||+|+.|..||||+++.....+.+. +....++.||.|.|.|.+-.
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 4899999999999877 999999999999999998854332111 12346899999999999863
No 184
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.72 E-value=0.033 Score=62.62 Aligned_cols=70 Identities=17% Similarity=0.306 Sum_probs=56.4
Q ss_pred cccCC--ccCcEEEEEEEEEecceEEEEeC----C-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC---
Q 005707 256 KTTKF--VKGQDLEGTVKNLTRSGAFISLP----E-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG--- 325 (681)
Q Consensus 256 ~~skl--kvGdIV~G~VknVt~~GaFVeIg----~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg--- 325 (681)
.+.+| ++|+++.|+|.++.+.+++|+++ . +++|+||.++. .|.+.|++|+.|+|.|.+|.++
T Consensus 144 i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq--------ip~E~y~~Gdrika~i~~V~~~~~k 215 (449)
T PRK12329 144 IQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ--------LPNDNYRANATFKVFLKEVSEGPRR 215 (449)
T ss_pred HHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc--------CCCCcCCCCCEEEEEEEEeecCCCC
Confidence 34444 48999999999999999999993 2 49999998764 3578899999999999999532
Q ss_pred --eEEEEEec
Q 005707 326 --QVTLTMKK 333 (681)
Q Consensus 326 --KI~LSLK~ 333 (681)
+|.||...
T Consensus 216 GpqIilSRt~ 225 (449)
T PRK12329 216 GPQLFVSRAN 225 (449)
T ss_pred CCEEEEEcCC
Confidence 58888743
No 185
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.70 E-value=0.025 Score=68.44 Aligned_cols=60 Identities=25% Similarity=0.560 Sum_probs=49.5
Q ss_pred CCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCcccc---------CcccccccCCEEEEEEEEE
Q 005707 146 IPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNFVK---------DVGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 146 kvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~v~---------d~~e~fkVGd~VkVkVl~V 205 (681)
.+|.||.|+|.+|.+. ++||+||.+..||||+.++...++. .....+++||.|-|.|..-
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 4799999999999974 8999999999999999999644322 2244688999999999874
No 186
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=95.58 E-value=0.033 Score=66.14 Aligned_cols=75 Identities=29% Similarity=0.506 Sum_probs=59.6
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccccc---------CCCCcccCCCEEEEEEEEEe--C
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANM---------MGGSSLQVGQEVSVRVLRIS--R 324 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~---------~p~~~fkVGqkVkVrVL~ID--k 324 (681)
+.+-.+|+.+.|+|.+++.+|+||.|.+ +++|++|.+.+...++... .-...|+.||.|+++|..++ .
T Consensus 617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~ 696 (706)
T COG0557 617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE 696 (706)
T ss_pred HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence 3445689999999999999999999987 5999999999985332111 11346999999999999996 5
Q ss_pred CeEEEEE
Q 005707 325 GQVTLTM 331 (681)
Q Consensus 325 gKI~LSL 331 (681)
+++.+++
T Consensus 697 ~~i~~~~ 703 (706)
T COG0557 697 RKIDFEL 703 (706)
T ss_pred cceEEEe
Confidence 7777765
No 187
>PRK11712 ribonuclease G; Provisional
Probab=95.17 E-value=0.05 Score=62.17 Aligned_cols=73 Identities=27% Similarity=0.478 Sum_probs=54.6
Q ss_pred CCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCc------------cccCcccccccCCEEEEEEEEEeccCC
Q 005707 145 LIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDN------------FVKDVGSIVSVGQEVKVRLIEANAETG 210 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~------------~v~d~~e~fkVGd~VkVkVl~VD~ekg 210 (681)
..+|.||.|+|.+|.+. ++||+||.+..||+|..++... ....+...+++||.|-|.|+.--...+
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~K 115 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK 115 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCC
Confidence 45799999999999984 8999999999999999998321 011234558999999999998543444
Q ss_pred ceEEEEe
Q 005707 211 RISLTMR 217 (681)
Q Consensus 211 rI~LSlK 217 (681)
.-.||..
T Consensus 116 G~~lT~~ 122 (489)
T PRK11712 116 GARLTTD 122 (489)
T ss_pred CCeEEEE
Confidence 4444443
No 188
>PRK11712 ribonuclease G; Provisional
Probab=94.93 E-value=0.041 Score=62.83 Aligned_cols=64 Identities=19% Similarity=0.239 Sum_probs=49.1
Q ss_pred CCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccc----------cccCCCCcccCCCEEEEEEEEE
Q 005707 259 KFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGF----------ANMMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 259 klkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~i----------e~~~p~~~fkVGqkVkVrVL~I 322 (681)
...+|.++.|+|.+|.+. +|||+|+.+..||+|.+++..... ........++.||.|-|.|.+-
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 456899999999999887 899999999999999998731100 0001134589999999998885
No 189
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=94.89 E-value=0.03 Score=68.31 Aligned_cols=77 Identities=23% Similarity=0.357 Sum_probs=62.6
Q ss_pred cccCCccCcEEEEEEEEEecce---EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeE--EEE
Q 005707 256 KTTKFVKGQDLEGTVKNLTRSG---AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQV--TLT 330 (681)
Q Consensus 256 ~~sklkvGdIV~G~VknVt~~G---aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI--~LS 330 (681)
..+.+.+|.+|.++|++|+..- +-|.+..|+.|+|+..++++..+ .+|..++++||.|.|+|+++|..++ .||
T Consensus 979 t~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v--~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls 1056 (1299)
T KOG1856|consen 979 TPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDV--RRPENRVKVGQTVYCKVIKIDKERFSVELS 1056 (1299)
T ss_pred ChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhc--cCHHHhhccCceEEEEeeeeeHhhhhhhhh
Confidence 3455789999999999997553 46789999999999999999654 3578999999999999999997664 456
Q ss_pred Eecc
Q 005707 331 MKKE 334 (681)
Q Consensus 331 LK~~ 334 (681)
+|..
T Consensus 1057 ~r~s 1060 (1299)
T KOG1856|consen 1057 CRTS 1060 (1299)
T ss_pred hhhH
Confidence 5544
No 190
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.66 E-value=0.2 Score=50.68 Aligned_cols=106 Identities=16% Similarity=0.182 Sum_probs=73.0
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCC----------CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPE----------GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~----------GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
..-.++|++|-|.|+.+....+.|++-. -..|-+|++...+.+.++. .+.|++||.|+++|++.- --
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~--~d~f~~GDivrA~Vis~~-~~ 135 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKL--SDAFRIGDIVRARVISTG-DP 135 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccccc--ccccccccEEEEEEEecC-CC
Confidence 4457889999999999999999998752 1456789999998887655 799999999999999985 45
Q ss_pred EEEEEeccCCCcCCcceeeeEEEEeecccEEEEEEcCCeEEEeeCCccc
Q 005707 327 VTLTMKKEDDVGSNLQLTQGVIHAATNPFVLAFRSNKDISSFLDERDKS 375 (681)
Q Consensus 327 I~LSLK~~~~DP~e~~lv~G~V~~~i~~fGlfV~l~~gI~GfIp~~els 375 (681)
+.||.+.- --|.|...-..-|..+.. .|..=.+|.....
T Consensus 136 ~~Lst~~~---------dlGVI~A~CsrC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 136 IQLSTKGN---------DLGVIYARCSRCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred eEEEecCC---------cceEEEEEccCCCcceEE-cCcEEECCCCCCE
Confidence 66666432 126666322222333333 5555555554443
No 191
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.57 E-value=0.32 Score=48.21 Aligned_cols=65 Identities=18% Similarity=0.342 Sum_probs=48.1
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCc-----------ccccccCCEEEEEEEEEeccCC
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDV-----------GSIVSVGQEVKVRLIEANAETG 210 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~-----------~e~fkVGd~VkVkVl~VD~ekg 210 (681)
.--|++++|.|+.|...|+|+++|. ++.++-...+..++--+| ....++|..|+++|+..-.+..
T Consensus 79 pfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~ 154 (170)
T KOG3298|consen 79 PFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET 154 (170)
T ss_pred ecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence 3469999999999999999999998 888876555543222111 2268899999999998654443
No 192
>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=93.40 E-value=0.42 Score=45.26 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=46.4
Q ss_pred CCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccc-------------cCcccccccCCEEEEEEEEEec
Q 005707 147 PGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-------------KDVGSIVSVGQEVKVRLIEANA 207 (681)
Q Consensus 147 vGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v-------------~d~~e~fkVGd~VkVkVl~VD~ 207 (681)
+|+++.|+|++....|+.|.|+-.-+.+||...|..... ..-.-.|..|+.|++||.++.-
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 699999999999999999999888899999999974322 1223346899999999998753
No 193
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=91.41 E-value=0.31 Score=55.84 Aligned_cols=75 Identities=27% Similarity=0.455 Sum_probs=60.4
Q ss_pred CCCCCcEEEEEEEEEecC--eeEEEECCCeEEEEeccccCCccccCc-----ccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 144 DLIPGATFTGKVRSIQPF--GAFIDFGAFTDGLVHVSRLSDNFVKDV-----GSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~--GaFVdLgggV~GLVPiSELS~~~v~d~-----~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
...+|.+|.|+|++|.+. .+|||+|..-.||+|.+++.+ +...+ ...++.||.+-|.|+.-...++--.||.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~ 112 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTT 112 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcccccccee
Confidence 455799999999999986 789999999999999999998 44433 3478999999999998766666556665
Q ss_pred ecc
Q 005707 217 RES 219 (681)
Q Consensus 217 K~l 219 (681)
.-.
T Consensus 113 ~Is 115 (487)
T COG1530 113 DIS 115 (487)
T ss_pred EEe
Confidence 543
No 194
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=91.14 E-value=0.98 Score=44.93 Aligned_cols=63 Identities=24% Similarity=0.287 Sum_probs=43.0
Q ss_pred CccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC----ccccccc-----CCCCcccCCCEEEEEEEEEe
Q 005707 260 FVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES----DDGFANM-----MGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 260 lkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELS----d~~ie~~-----~p~~~fkVGqkVkVrVL~ID 323 (681)
.=+|++++|+|+.++..|+|++++ -+.-|+...-.. ...-++. .-.++.++|..|+++|+...
T Consensus 79 pfKGEVvdgvV~~Vnk~G~F~~~G-Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 79 PFKGEVVDGVVTKVNKMGVFARSG-PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred ecCCcEEEEEEEEEeeeeEEEecc-ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 347999999999999999999998 455554432222 1111110 00236899999999999883
No 195
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=90.56 E-value=0.32 Score=55.75 Aligned_cols=67 Identities=27% Similarity=0.371 Sum_probs=55.2
Q ss_pred ccCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccccccCC---CCcccCCCEEEEEEEEEeC
Q 005707 257 TTKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANMMG---GSSLQVGQEVSVRVLRISR 324 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~~p---~~~fkVGqkVkVrVL~IDk 324 (681)
.....+|.++.|+|++|.+. .+||+++.+-.||+|.+++.+ ++..... ...++.||.+-|.|+.-..
T Consensus 32 ~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~ 103 (487)
T COG1530 32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR 103 (487)
T ss_pred CcEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence 45567899999999999887 899999999999999999988 3322211 3589999999999988753
No 196
>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=89.16 E-value=1.6 Score=40.50 Aligned_cols=58 Identities=21% Similarity=0.295 Sum_probs=47.6
Q ss_pred CcCCCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEe
Q 005707 141 KNEDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206 (681)
Q Consensus 141 t~~~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD 206 (681)
.+.+ ..|.+|.|+|..+.+.-+|+|+|+...+.++...... +.|..|..|.+++.+..
T Consensus 18 ~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 18 QLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred hcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 3445 4799999999999999999999999999999765533 34889999998887753
No 197
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=88.90 E-value=1.9 Score=38.89 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=51.3
Q ss_pred EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
.++|+|+.+.+.+.| |.|.++...+.|++= ..+.-.-.+.+||.|.|.+...|..+++|..-.+.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 589999999999887 688877777777642 22222334679999999999999999999998873
No 198
>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=88.49 E-value=2 Score=37.06 Aligned_cols=61 Identities=26% Similarity=0.341 Sum_probs=47.5
Q ss_pred EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707 150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
.+.|+|+...+.+.| |.+.++..-+.|++= ..+.-.-...+||.|.|.+...|..+++|..
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEEe
Confidence 489999999999987 688877887777642 2232234478999999999999998888864
No 199
>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=86.95 E-value=2.2 Score=39.54 Aligned_cols=54 Identities=13% Similarity=0.211 Sum_probs=46.3
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID 323 (681)
..|.+|.|+|..|.+.-+||++|....+.|++.... .+.|..|.+|.+++...+
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~---------~~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN---------GEKYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc---------ccccccCCEEEEEECCHh
Confidence 489999999999999999999999999999976543 356889999999877664
No 200
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=86.90 E-value=2.1 Score=43.12 Aligned_cols=74 Identities=20% Similarity=0.094 Sum_probs=55.2
Q ss_pred CCCCCCcEEEEEEEEEecCeeEEEEC--------CCeEEEEeccccCCc--cccCcccccccCCEEEEEEEEEeccCCce
Q 005707 143 EDLIPGATFTGKVRSIQPFGAFIDFG--------AFTDGLVHVSRLSDN--FVKDVGSIVSVGQEVKVRLIEANAETGRI 212 (681)
Q Consensus 143 ~~LkvGdIVeGkV~sV~d~GaFVdLg--------ggV~GLVPiSELS~~--~v~d~~e~fkVGd~VkVkVl~VD~ekgrI 212 (681)
--...|+||.++|.++...-+-|+|- ...+|+||..++..- ..-++-+-|++||.|.++|++.+ .+...
T Consensus 64 ~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~-~~~~y 142 (193)
T KOG3409|consen 64 LLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG-DGSNY 142 (193)
T ss_pred cCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC-CCCcE
Confidence 34567999999999999877766652 357899999888632 12344566999999999999965 35566
Q ss_pred EEEEe
Q 005707 213 SLTMR 217 (681)
Q Consensus 213 ~LSlK 217 (681)
.|+..
T Consensus 143 ~LTtA 147 (193)
T KOG3409|consen 143 LLTTA 147 (193)
T ss_pred EEEEe
Confidence 77765
No 201
>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=84.45 E-value=3.4 Score=39.20 Aligned_cols=62 Identities=26% Similarity=0.311 Sum_probs=44.4
Q ss_pred cCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-ccccc----------CCCCcccCCCEEEEEEEEEe
Q 005707 262 KGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDD-GFANM----------MGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~-~ie~~----------~p~~~fkVGqkVkVrVL~ID 323 (681)
+|+++.|+|++-++.|+.|.|+---+-+||.+.|... .++.. .-.-.|..|+.|++||.++.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 6999999999999999999998777889999887632 11100 01235689999999999984
No 202
>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=83.88 E-value=9.3 Score=31.54 Aligned_cols=50 Identities=26% Similarity=0.286 Sum_probs=38.1
Q ss_pred EEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 151 FTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 151 VeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+.|+|+...+ ||++..-++.-+.|+|.+++.... ...++.|+.|.+.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 4799999985 566666666669999999998764 2347799999999988
No 203
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=83.27 E-value=4 Score=41.23 Aligned_cols=71 Identities=14% Similarity=0.149 Sum_probs=54.1
Q ss_pred ccCcEEEEEEEEEecceEEEEe--------CCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE-eCCeEEEEE
Q 005707 261 VKGQDLEGTVKNLTRSGAFISL--------PEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI-SRGQVTLTM 331 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeI--------g~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I-DkgKI~LSL 331 (681)
..|++|.++|..++..-+-|+| .....|+||..++-..-.+..++-+.|++||.|.++|++. +.....||.
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTt 146 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTT 146 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEE
Confidence 4899999999999877666654 3477899999877543333345567899999999999997 456677776
No 204
>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=81.88 E-value=4 Score=34.67 Aligned_cols=63 Identities=17% Similarity=0.355 Sum_probs=43.1
Q ss_pred CcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 263 GdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
|+.+.-.|-.++..|--+--++.+.|+.-.. .+.. .....+.+||++++.||+|| +-++.+||
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~A----tryH--~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLA----SRYH--KEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEE----EEEE--ecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 6778888999888876665666666653221 1110 12567899999999999999 56666654
No 205
>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=81.17 E-value=6.9 Score=32.22 Aligned_cols=57 Identities=32% Similarity=0.445 Sum_probs=42.0
Q ss_pred EEEEEEEec---ceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEE
Q 005707 267 EGTVKNLTR---SGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLT 330 (681)
Q Consensus 267 ~G~VknVt~---~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LS 330 (681)
.|+|+...+ || ||...+ |-+-|+|.+++.... ...+++|+.|.+.+..-+++.....
T Consensus 2 ~G~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~~------~~~~~~G~~V~f~~~~~~~g~~A~~ 62 (65)
T cd04458 2 TGTVKWFDDEKGFG-FITPDDGGEDVFVHISALEGDG------FRSLEEGDRVEFELEEGDKGPQAVN 62 (65)
T ss_pred cEEEEEEECCCCeE-EEecCCCCcCEEEEhhHhhccC------CCcCCCCCEEEEEEEECCCCCeEEE
Confidence 478888755 45 777666 899999999887542 2578999999998777655544433
No 206
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=79.12 E-value=15 Score=30.25 Aligned_cols=53 Identities=34% Similarity=0.485 Sum_probs=38.1
Q ss_pred EEEEEEEEec---ceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 266 LEGTVKNLTR---SGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 266 V~G~VknVt~---~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
..|+|+...+ || ||.-.+ +-+-|+|.+++.... -..++.|+.|++.+.. .+++
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~------~~~l~~G~~V~F~~~~-~~~g 57 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG------FRSLKEGDRVEFEVEE-GKKG 57 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS------STS--TTSEEEEEEEE-CTTS
T ss_pred CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc------cccCCCCCEEEEEEEE-CCCC
Confidence 3689999874 57 566555 459999999887654 2578999999999888 5444
No 207
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=78.61 E-value=8.8 Score=34.72 Aligned_cols=64 Identities=20% Similarity=0.314 Sum_probs=49.4
Q ss_pred EEEEEEEEEecceEEE-EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707 265 DLEGTVKNLTRSGAFI-SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE 334 (681)
Q Consensus 265 IV~G~VknVt~~GaFV-eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~ 334 (681)
.+.|+|+.+.+.+.|. .+.+|..-++|++=--... .-++.+||.|.|-+--.| +|+|..-.|..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~------rIrIl~GD~V~VE~spYDltkGRIiyR~~~~ 74 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKH------RIRILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeee------eEEecCCCEEEEEECcccCCceeEEEEecCC
Confidence 4799999999888875 8999999999986322111 346789999999988876 68888877753
No 208
>PRK09890 cold shock protein CspG; Provisional
Probab=77.20 E-value=13 Score=31.74 Aligned_cols=55 Identities=22% Similarity=0.318 Sum_probs=40.2
Q ss_pred EEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 266 LEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 266 V~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
..|+|+...+ .|. ||.-.+ +-+-|+|++.+.... ...++.||.|.+.+..-++|.
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~------~~~l~~G~~V~f~~~~~~~G~ 62 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE------FRTLNENQKVEFSIEQGQRGP 62 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCC------CCCCCCCCEEEEEEEECCCCc
Confidence 4799999753 343 787765 489999999887543 246899999999876655544
No 209
>PRK15464 cold shock-like protein CspH; Provisional
Probab=72.80 E-value=18 Score=31.13 Aligned_cols=56 Identities=27% Similarity=0.295 Sum_probs=42.1
Q ss_pred EEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeE
Q 005707 266 LEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQV 327 (681)
Q Consensus 266 V~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI 327 (681)
+.|+|+...+ .|. ||.-.+ +-+-|+|++.+.... ...+..||.|.+.|..-.+|.-
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g------~~~l~~G~~V~f~v~~~~kG~~ 63 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD------AEVLIPGLRVEFCRVNGLRGPT 63 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC------CCCCCCCCEEEEEEEECCCCce
Confidence 4799999864 455 887765 579999999886443 2468999999999877656553
No 210
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=72.69 E-value=12 Score=38.97 Aligned_cols=62 Identities=16% Similarity=0.156 Sum_probs=49.4
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEec
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ 207 (681)
..+|+.|-|.|+.-...+..|||+|...+.|+.-.+....-+ -+-.+++||.|.++|...++
T Consensus 63 P~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~Atkr-NrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKR-NRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCcccc-CCCccccccEEEEEEEecCC
Confidence 457999999999999999999999988888887666543211 22348999999999998754
No 211
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=72.42 E-value=19 Score=31.28 Aligned_cols=62 Identities=31% Similarity=0.359 Sum_probs=45.1
Q ss_pred EEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 267 EGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 267 ~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
.|+|+-... .|. ||.-.+ +.+-|+|++.+.... ...+..||.|.+.+..-.+|+-...+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g------~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG------YRTLKAGQSVQFDVHQGPKGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC------CCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence 488888754 444 776654 689999999886443 25789999999998887777755555444
No 212
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=71.97 E-value=13 Score=34.33 Aligned_cols=68 Identities=13% Similarity=0.054 Sum_probs=50.8
Q ss_pred CCCCCcEEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 144 DLIPGATFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
....|+ +.|+|+.....+.| |.+.++..-+.++. +.++. .-.+..||.|.|.+...|..+++|..-..
T Consensus 17 ~p~e~e-~~g~V~~~lG~~~~~V~~~dG~~~la~i~----GK~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 85 (100)
T PRK04012 17 MPEEGE-VFGVVEQMLGANRVRVRCMDGVERMGRIP----GKMKK-RMWIREGDVVIVAPWDFQDEKADIIWRYT 85 (100)
T ss_pred CCCCCE-EEEEEEEEcCCCEEEEEeCCCCEEEEEEc----hhhcc-cEEecCCCEEEEEecccCCCEEEEEEEcC
Confidence 344454 88999999999887 67777777777653 23333 45688999999999999988788877665
No 213
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=71.94 E-value=23 Score=31.28 Aligned_cols=66 Identities=23% Similarity=0.327 Sum_probs=49.2
Q ss_pred CcEEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 148 GATFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
.-.+.|+|..+.+.+.| |.+.++..-+-|++- +.+.-.-.+.+||.|.|.....|..+++|..-.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~G----Kmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISG----KMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccC----cchheeEEeCCCCEEEEEecccccccccEEEEec
Confidence 34589999999998875 888777776666532 2222233478999999999999988898877554
No 214
>PRK10943 cold shock-like protein CspC; Provisional
Probab=71.78 E-value=23 Score=30.26 Aligned_cols=55 Identities=25% Similarity=0.416 Sum_probs=40.4
Q ss_pred EEEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC
Q 005707 265 DLEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG 325 (681)
Q Consensus 265 IV~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg 325 (681)
.+.|+|+.-.+ .|. ||.-.+ +-+-|+|++.+.... ...+..||.|.+.+..-+++
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g------~~~l~~G~~V~f~~~~~~~g 60 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG------FKTLAEGQNVEFEIQDGQKG 60 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC------CCCCCCCCEEEEEEEECCCC
Confidence 46799999754 444 787654 679999999887543 25689999999987665443
No 215
>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=71.18 E-value=18 Score=31.27 Aligned_cols=58 Identities=24% Similarity=0.316 Sum_probs=43.5
Q ss_pred EEEEEEEEEecceEEE-EeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEE
Q 005707 265 DLEGTVKNLTRSGAFI-SLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVT 328 (681)
Q Consensus 265 IV~G~VknVt~~GaFV-eIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~ 328 (681)
.+.|.|+...+.|.|- .+.+|..-++|++---.. -.-++.+||.|.|.+-..| +++|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~------~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRM------HYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchh------ccEEECCCCEEEEEECcccCCcEeEE
Confidence 4789999999888874 889999999998632211 1356889999999877776 45553
No 216
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=70.87 E-value=11 Score=32.00 Aligned_cols=65 Identities=15% Similarity=0.234 Sum_probs=43.0
Q ss_pred CcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 148 GdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
|+.++-.|..+.+.|-.+=-+|.+.|+.- ...++-.-...+-+|+++++.|+.+|.-+-.+.+|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv----~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTV----LASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEE----EEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 67788889998877655444554666522 112222223457799999999999998776666653
No 217
>PRK10943 cold shock-like protein CspC; Provisional
Probab=69.89 E-value=16 Score=31.20 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=37.9
Q ss_pred EEEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 150 TFTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 150 IVeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
.+.|+|+...+ ||++-.-+++-+.|+|++.+..... ..+..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 46899999874 4544444566899999999975432 236799999998876
No 218
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=69.62 E-value=25 Score=29.97 Aligned_cols=55 Identities=25% Similarity=0.422 Sum_probs=40.4
Q ss_pred EEEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC
Q 005707 265 DLEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG 325 (681)
Q Consensus 265 IV~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg 325 (681)
.+.|+|+...+ .|. ||.-.+ +-+-|+|++.+.... ...+..||.|.+.+..-++|
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g------~~~l~~G~~V~f~~~~~~~G 60 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG------FKTLAEGQRVEFEITNGAKG 60 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccC------CCCCCCCCEEEEEEEECCCC
Confidence 35699998753 344 787655 579999999886543 25689999999987765554
No 219
>PRK15464 cold shock-like protein CspH; Provisional
Probab=69.35 E-value=26 Score=30.20 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=37.4
Q ss_pred EEEEEEEEec-Cee-EEEE-CCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 151 FTGKVRSIQP-FGA-FIDF-GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 151 VeGkV~sV~d-~Ga-FVdL-gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+.|+|+-..+ .|+ |+.- .++-+.|+|++.|...-. ..+..|+.|.+.|..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence 5799999984 454 5544 566899999999965422 236799999999887
No 220
>PRK15463 cold shock-like protein CspF; Provisional
Probab=68.75 E-value=26 Score=30.13 Aligned_cols=54 Identities=22% Similarity=0.275 Sum_probs=40.7
Q ss_pred EEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC
Q 005707 266 LEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG 325 (681)
Q Consensus 266 V~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg 325 (681)
+.|+|+.-.+ .|. ||.-.+ +-+-|+|++.+.... ...++.||.|.+.|..-++|
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g------~~~l~~G~~V~f~v~~~~~G 61 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD------AEELTTGLRVEFCRINGLRG 61 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC------CCCCCCCCEEEEEEEECCCC
Confidence 3799999864 454 787755 679999999887543 25689999999987765555
No 221
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=67.85 E-value=29 Score=30.18 Aligned_cols=60 Identities=20% Similarity=0.251 Sum_probs=41.3
Q ss_pred EEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 152 TGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 152 eGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
+|+|+-... ||++..-.++-+.|+|++.|...-. ..+..|+.|.+.|..- .+++....+.
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~--~~G~~A~~V~ 65 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQG--PKGNHASVIV 65 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEEC--CCCceeeEEE
Confidence 488988874 4544444666899999999975422 2367999999998873 3455444444
No 222
>PRK09890 cold shock protein CspG; Provisional
Probab=67.81 E-value=38 Score=29.01 Aligned_cols=50 Identities=22% Similarity=0.325 Sum_probs=36.8
Q ss_pred EEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 151 FTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 151 VeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+.|+|+...+ ||++-.-+++-+.|+|++.+...-+. .+.+|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~----~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFR----TLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCC----CCCCCCEEEEEEEE
Confidence 4799999874 45444445668999999999765322 36799999997765
No 223
>PRK14998 cold shock-like protein CspD; Provisional
Probab=66.31 E-value=32 Score=29.84 Aligned_cols=60 Identities=32% Similarity=0.376 Sum_probs=43.4
Q ss_pred EEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEe
Q 005707 267 EGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMK 332 (681)
Q Consensus 267 ~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK 332 (681)
.|+|+--.. .|. ||.-.+ +-+-|+|++.+.... ...+..|+.|.+.+..-++|+-...+.
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g------~~~l~~G~~V~f~~~~~~~G~~A~~V~ 65 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG------YRTLKAGQSVRFDVHQGPKGNHASVIV 65 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC------CCCCCCCCEEEEEEEECCCCceeEEEE
Confidence 488888754 444 777654 689999999886432 257899999999988877776444443
No 224
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=65.09 E-value=24 Score=30.15 Aligned_cols=51 Identities=24% Similarity=0.343 Sum_probs=37.5
Q ss_pred EEEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 150 TFTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 150 IVeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
.+.|+|+...+ ||++-.-.++-+.|+|++.+..... ..+.+|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCC----CCCCCCCEEEEEEEE
Confidence 36799999874 4554444666899999999975422 236799999998876
No 225
>PRK15463 cold shock-like protein CspF; Provisional
Probab=63.95 E-value=21 Score=30.68 Aligned_cols=50 Identities=26% Similarity=0.286 Sum_probs=37.1
Q ss_pred EEEEEEEEec-Cee-EEEE-CCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 151 FTGKVRSIQP-FGA-FIDF-GAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 151 VeGkV~sV~d-~Ga-FVdL-gggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+.|+|+...+ .|+ |+.- +++-+.|+|++.+...-.. .+.+|+.|.+.|..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~----~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE----ELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCC----CCCCCCEEEEEEEE
Confidence 4799999984 444 4544 5668999999999754222 36799999998776
No 226
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=62.49 E-value=45 Score=28.43 Aligned_cols=54 Identities=31% Similarity=0.453 Sum_probs=39.6
Q ss_pred EEEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCC
Q 005707 266 LEGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRG 325 (681)
Q Consensus 266 V~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkg 325 (681)
..|+|+...+ .|. ||.-.+ +.+-|+|++.+.... ...++.|+.|.+.+..-++|
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g------~~~l~~G~~V~f~~~~~~~G 61 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG------YKSLDEGQKVSFTIESGAKG 61 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccC------CCCCCCCCEEEEEEEECCCC
Confidence 3799998753 333 787665 589999999886543 25689999999987665555
No 227
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=61.96 E-value=52 Score=28.06 Aligned_cols=50 Identities=24% Similarity=0.310 Sum_probs=37.0
Q ss_pred EEEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 151 FTGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 151 VeGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+.|+|+...+ ||++-.-+++-+.|+|++.+...-. ..+.+|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE
Confidence 4899999863 5554444666899999999975422 236799999998776
No 228
>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=61.72 E-value=25 Score=30.90 Aligned_cols=62 Identities=13% Similarity=0.107 Sum_probs=46.5
Q ss_pred EEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 151 FTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 151 VeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
+.|+|+.....+.| |.+.++..-+.+++ +.++. .-.++.||.|.|.+...|..+++|..-..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~----gK~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~ 64 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIR----GKMRK-RVWINEGDIVLVAPWDFQDDKADIIYKYT 64 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEc----hhhcc-cEEEcCCCEEEEEeccccCCEEEEEEEcC
Confidence 57999999998887 67777677666653 22333 45688999999999988887788776654
No 229
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=61.17 E-value=1.5e+02 Score=32.92 Aligned_cols=122 Identities=19% Similarity=0.344 Sum_probs=77.0
Q ss_pred CCCCCCcCCCCCCcEEEEEEEEEec-CeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceE
Q 005707 136 EMPPVKNEDLIPGATFTGKVRSIQP-FGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRIS 213 (681)
Q Consensus 136 e~~~lt~~~LkvGdIVeGkV~sV~d-~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~ 213 (681)
.+++|.-.. +.|.++.|+|..-.+ ||+- +.++. +.+-..++ ...+|..+.++|-.-| +.
T Consensus 221 ~~~p~~~~~-e~~~vl~~~V~~hd~~y~lt~l~l~~---~~l~v~~~----------~a~~g~~~R~~I~a~D-----Vs 281 (352)
T COG4148 221 DFPPWLPRE-EQSSVLEGTVLEHDPRYGLTALALGD---QHLWVPKL----------DAPVGARLRIRIQARD-----VS 281 (352)
T ss_pred ccCcccCcc-ccceEEEEEehhcCCCcceEEEecCc---eEEEeecc----------CCCCCCcEEEEEEccc-----eE
Confidence 344553333 679999999999874 6663 45553 22222222 2468999999998743 55
Q ss_pred EEEeccchhhHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecce----EEEEeCCCeEEE
Q 005707 214 LTMRESDDISKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSG----AFISLPEGEEGF 289 (681)
Q Consensus 214 LSlK~l~~dp~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~G----aFVeIg~GIeGL 289 (681)
+.+++.. ....=.++.|+|+.+.+.+ ++++++ |-.-+
T Consensus 282 lal~~P~--------------------------------------~~SirNiLp~~v~~i~~~~~~V~v~ld~~-g~~l~ 322 (352)
T COG4148 282 LALQKPE--------------------------------------QTSIRNILPGKVVGIEDDDGQVDVQLDCG-GKTLW 322 (352)
T ss_pred EEecCcc--------------------------------------ccchhhccceeEEEEEcCCCcEEEEEEcC-CcEEE
Confidence 5555221 1223346778898887653 344555 66666
Q ss_pred EeCCCCCcccccccCCCCcccCCCEEEEEEEEE
Q 005707 290 LPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 290 LpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I 322 (681)
..+++++.+ .-.+++|+.|.+.|..+
T Consensus 323 Arit~~srd-------~L~l~~G~~v~AqIKsV 348 (352)
T COG4148 323 ARITPWARD-------ELALKPGQWVYAQIKSV 348 (352)
T ss_pred EEccHhhHH-------hhcCCCCCeEEEEEEEE
Confidence 666665543 24789999999999876
No 230
>PRK14998 cold shock-like protein CspD; Provisional
Probab=60.26 E-value=48 Score=28.77 Aligned_cols=59 Identities=22% Similarity=0.287 Sum_probs=40.5
Q ss_pred EEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEE
Q 005707 152 TGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTM 216 (681)
Q Consensus 152 eGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSl 216 (681)
.|+|+-... ||++..-.++-+.|+|++.|...-. ..+..|+.|.+.+..- .+++.....
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~~--~~G~~A~~V 64 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQG--PKGNHASVI 64 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCC----CCCCCCCEEEEEEEEC--CCCceeEEE
Confidence 488998874 4544444666899999999965422 3367999999998873 345444333
No 231
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=58.10 E-value=1.5e+02 Score=37.31 Aligned_cols=69 Identities=19% Similarity=0.085 Sum_probs=40.2
Q ss_pred cccCCCEEEEEEE----------EEeCCeEEEEEecc-CCCcCC-------cceeeeEEE---Eee--cccEEEEEEcCC
Q 005707 308 SLQVGQEVSVRVL----------RISRGQVTLTMKKE-DDVGSN-------LQLTQGVIH---AAT--NPFVLAFRSNKD 364 (681)
Q Consensus 308 ~fkVGqkVkVrVL----------~IDkgKI~LSLK~~-~~DP~e-------~~lv~G~V~---~~i--~~fGlfV~l~~g 364 (681)
.|.+||.|.|.+- .||...+++-.|+. +.+|++ +.+..|-.+ +.. -..|+.|++..+
T Consensus 407 ~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 407 LFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3999999887543 44444444444432 566755 334455333 111 367899999887
Q ss_pred eEEEeeCCcccc
Q 005707 365 ISSFLDERDKSA 376 (681)
Q Consensus 365 I~GfIp~~els~ 376 (681)
..-|+....+.+
T Consensus 487 ~vi~~Sd~t~ee 498 (1024)
T KOG1999|consen 487 DVILLSDLTMEE 498 (1024)
T ss_pred eEEEEecCccce
Confidence 777665544443
No 232
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=57.72 E-value=20 Score=36.60 Aligned_cols=62 Identities=23% Similarity=0.374 Sum_probs=48.3
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccC-----------------cccccccCCEEEEEEEEE
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKD-----------------VGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d-----------------~~e~fkVGd~VkVkVl~V 205 (681)
..-+|+++.|+|+.....|+-|.|+-.-+.|||..-|......+ ..-.|.+|..|+++|.+.
T Consensus 78 rPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 78 RPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred ecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 45689999999999999999999997778999988776543211 123467888888888774
No 233
>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=56.95 E-value=41 Score=28.55 Aligned_cols=55 Identities=29% Similarity=0.343 Sum_probs=40.1
Q ss_pred EEEEEEEec-ceE-EEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeE
Q 005707 267 EGTVKNLTR-SGA-FISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQV 327 (681)
Q Consensus 267 ~G~VknVt~-~Ga-FVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI 327 (681)
.|+|+-... .|. ||.-.+ +-+-|+|++.+.... ...++.||.|.+.+..-++|.-
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g------~~~l~~G~~V~f~~~~~~~G~~ 60 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG------YRTLKAGQKVQFEVVQGPKGAH 60 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC------CCCCCCCCEEEEEEEECCCCce
Confidence 488888753 444 787665 689999999886433 2578999999998766555543
No 234
>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=56.54 E-value=50 Score=28.00 Aligned_cols=49 Identities=22% Similarity=0.301 Sum_probs=35.7
Q ss_pred EEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 152 TGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 152 eGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
+|+|+-... ||++..-.++-+.|+|++.+...-. ..+..|+.|.+.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 488998873 4544444566899999999975422 236799999998776
No 235
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=55.46 E-value=19 Score=35.45 Aligned_cols=56 Identities=25% Similarity=0.340 Sum_probs=46.5
Q ss_pred CCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEec
Q 005707 145 LIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ 207 (681)
-..|..|.|+|-.+...-+|+|+|+...+.+..-.+.. +.|..|..|..++++..-
T Consensus 80 ~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~-------e~Y~~GaRVrlRl~DlEL 135 (173)
T KOG4078|consen 80 DAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNG-------EAYQKGARVRLRLIDLEL 135 (173)
T ss_pred CcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCH-------HHhhcCceEEEEEcChhH
Confidence 34699999999999999999999999898888766543 348899999999988644
No 236
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=54.43 E-value=14 Score=38.56 Aligned_cols=83 Identities=19% Similarity=0.267 Sum_probs=58.1
Q ss_pred CcCCCCCCcEEEEEEEEEec--CeeEEEECC----CeEEEEeccccCCccccCc----ccc--cccCCEEEEEEEEEecc
Q 005707 141 KNEDLIPGATFTGKVRSIQP--FGAFIDFGA----FTDGLVHVSRLSDNFVKDV----GSI--VSVGQEVKVRLIEANAE 208 (681)
Q Consensus 141 t~~~LkvGdIVeGkV~sV~d--~GaFVdLgg----gV~GLVPiSELS~~~v~d~----~e~--fkVGd~VkVkVl~VD~e 208 (681)
++.+++.|+++-|+.....+ ||+||+++- -.++|||.-+|...+-..| ... +-.-..++|.|.++|..
T Consensus 69 sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~ 148 (247)
T COG4044 69 SLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKL 148 (247)
T ss_pred ccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccch
Confidence 57899999999999999985 678888862 3689999888765443223 222 22345688999999887
Q ss_pred CCceEEEEeccchhh
Q 005707 209 TGRISLTMRESDDIS 223 (681)
Q Consensus 209 kgrI~LSlK~l~~dp 223 (681)
.+.|..-+-+.+.+.
T Consensus 149 ~~EIea~ltd~qvd~ 163 (247)
T COG4044 149 AQEIEARLTDKQVDK 163 (247)
T ss_pred hhhhhhhhhHHHHHH
Confidence 776665554444433
No 237
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=54.18 E-value=60 Score=28.91 Aligned_cols=65 Identities=11% Similarity=0.076 Sum_probs=47.6
Q ss_pred EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEecc
Q 005707 150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRES 219 (681)
Q Consensus 150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l 219 (681)
.+.|+|+.....+.| |.+.+|..-++++. ..++. .-.++.||.|.|.....+..+++|..-..+-
T Consensus 6 q~~g~V~~~lG~~~~~V~~~dG~~~la~ip----gK~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCADGKERLARIP----GKMRK-KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEc----hhhcc-cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 378999999998887 67776677776653 22232 4558899999999988887777777666543
No 238
>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=53.92 E-value=32 Score=27.86 Aligned_cols=47 Identities=21% Similarity=0.346 Sum_probs=30.4
Q ss_pred EEEEEEEEEecCe----eEEEECCC--eEEEEeccccCCccccCcccccccCCEEEEEEE
Q 005707 150 TFTGKVRSIQPFG----AFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLI 203 (681)
Q Consensus 150 IVeGkV~sV~d~G----aFVdLggg--V~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl 203 (681)
.+.|+|..+.+.| ++++++++ +.+.++.... ..+ .+++|+.|.+.+-
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~-----~~L--~L~~G~~V~~~ik 58 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA-----EEL--GLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH-----HHC--T-STT-EEEEEE-
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH-----HHc--CCCCCCEEEEEEe
Confidence 5899999999998 56677665 4566654332 111 2779999998763
No 239
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=53.54 E-value=7.2 Score=48.42 Aligned_cols=34 Identities=9% Similarity=0.014 Sum_probs=28.7
Q ss_pred ccccccceeeecccccccccceeEEeccCCceeE
Q 005707 24 KNNCLTRYNSTRKSTKQTISSQRFLLPLPSSVRF 57 (681)
Q Consensus 24 ~~~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGf 57 (681)
.-....||||+-.+|.||+||.|++.|+-.+|.+
T Consensus 766 ~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL 799 (941)
T KOG2102|consen 766 DTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQL 799 (941)
T ss_pred CcchhhchhhcccchhhccCcccccchHHHHHHH
Confidence 4456789999999999999999999997666544
No 240
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=52.83 E-value=31 Score=33.97 Aligned_cols=54 Identities=17% Similarity=0.298 Sum_probs=46.1
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID 323 (681)
..|..|.|+|-.+...-+||+++......|.+..+. .+.|+.|-.|..+++..+
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n---------~e~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN---------GEAYQKGARVRLRLIDLE 134 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC---------HHHhhcCceEEEEEcChh
Confidence 368899999999999999999999899999887654 456899999998888764
No 241
>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=52.04 E-value=62 Score=26.52 Aligned_cols=50 Identities=28% Similarity=0.302 Sum_probs=37.2
Q ss_pred EEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEE
Q 005707 152 TGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 152 eGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~V 205 (681)
.|+|+...+ ||++..-.++-+.|+|.+++...- ...+.+|+.|.+.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 588888875 555555555689999999997642 23467999999988764
No 242
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=51.66 E-value=20 Score=38.38 Aligned_cols=73 Identities=18% Similarity=0.218 Sum_probs=56.2
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCc--cc--------cCcccccccCCEEEEEEEEEeccCCceE
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDN--FV--------KDVGSIVSVGQEVKVRLIEANAETGRIS 213 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~--~v--------~d~~e~fkVGd~VkVkVl~VD~ekgrI~ 213 (681)
.-++|++|-|+|..|...---|+++...++.+..+-+-.. -. ...+.+|+.||.|.+.|-.+- ..|-+.
T Consensus 82 ~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~-~dGs~s 160 (301)
T KOG3013|consen 82 APEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF-HDGSLS 160 (301)
T ss_pred CCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhc-cCCeEE
Confidence 4678999999999999999999999889999988776531 11 234568999999999887764 345555
Q ss_pred EEEe
Q 005707 214 LTMR 217 (681)
Q Consensus 214 LSlK 217 (681)
|-.+
T Consensus 161 LhTR 164 (301)
T KOG3013|consen 161 LHTR 164 (301)
T ss_pred EEec
Confidence 5444
No 243
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=51.13 E-value=1.1e+02 Score=31.97 Aligned_cols=44 Identities=30% Similarity=0.168 Sum_probs=28.7
Q ss_pred cEEEEEEEEEecCeeEEEECC-CeEEEEeccccCCccccCcccccccCCEEEEE
Q 005707 149 ATFTGKVRSIQPFGAFIDFGA-FTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVR 201 (681)
Q Consensus 149 dIVeGkV~sV~d~GaFVdLgg-gV~GLVPiSELS~~~v~d~~e~fkVGd~VkVk 201 (681)
+.++|+|..|...-++++.-+ +-..-++ .+....+++||.|+|.
T Consensus 40 ~tiEGrVvEV~~~~i~iesk~yn~~v~i~---------~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSKQYEEPVSVY---------IDSLSNVKVGDEVKAT 84 (213)
T ss_pred ceeeeEEEEEeCCEEEEEeccCCCceEEE---------ecCCCCcccCcEEEEc
Confidence 468999999999989998842 1121111 1222236899999865
No 244
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=50.26 E-value=86 Score=27.78 Aligned_cols=63 Identities=21% Similarity=0.316 Sum_probs=46.0
Q ss_pred CcEEEEEEEEEecceE-EEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEE
Q 005707 263 GQDLEGTVKNLTRSGA-FISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTM 331 (681)
Q Consensus 263 GdIV~G~VknVt~~Ga-FVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSL 331 (681)
.-.+.|+|......+. .|.+.+|..-+.|++---.. -.-++.+||.|.|.....| +++|..-.
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~------~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK------NRIRILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh------eeEEeCCCCEEEEEecccccccccEEEEe
Confidence 3457899999987765 48899999999998632211 0347889999999988886 46655444
No 245
>COG1278 CspC Cold shock proteins [Transcription]
Probab=48.30 E-value=49 Score=28.67 Aligned_cols=54 Identities=31% Similarity=0.451 Sum_probs=37.5
Q ss_pred EEEEEEEecc-eE-EEEeCCC-eEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCe
Q 005707 267 EGTVKNLTRS-GA-FISLPEG-EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQ 326 (681)
Q Consensus 267 ~G~VknVt~~-Ga-FVeIg~G-IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgK 326 (681)
.|+|+-.++. |. ||.=.+| -+.|+|+|.+.... -..|..||+|.+.|..=.++-
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g------~~~L~eGQ~V~f~~~~g~kgp 59 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG------FRTLREGQKVEFEVEQGRKGP 59 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCC------CcccCCCCEEEEEEecCCCCC
Confidence 4667766422 32 7776666 79999999886544 357899999998876644433
No 246
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=45.42 E-value=2.2e+02 Score=30.28 Aligned_cols=115 Identities=17% Similarity=0.254 Sum_probs=64.0
Q ss_pred EEEEEEEEEecC--eeEEE--ECCC---eEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEeccchh
Q 005707 150 TFTGKVRSIQPF--GAFID--FGAF---TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRESDDI 222 (681)
Q Consensus 150 IVeGkV~sV~d~--GaFVd--Lggg---V~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~l~~d 222 (681)
.+.|+|.++... +..|+ +.++ +...|. ..-..++. +.+|+.|.+.|-.- .|.+....
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT-----~~s~~~L~--l~~G~~v~~~Ika~-----~V~l~~~~---- 192 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAIT-----AQSAERLG--LDEGKEVLVLIKAP-----WVGITQDP---- 192 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeC-----HHHHhhcC--CCCCCeEEEEEECC-----EEEEEcCC----
Confidence 689999999865 45554 4332 333333 22222333 67999998887653 23443210
Q ss_pred hHhhhhccccccCCccccccccCCCCCCccccccccCCccCcEEEEEEEEEecceEEE----EeCCCeEEEEeCCCCCcc
Q 005707 223 SKLQQQKDATASGDKVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFI----SLPEGEEGFLPTSEESDD 298 (681)
Q Consensus 223 p~ek~~~~~p~s~d~~~~k~r~~~k~~~~k~~~~~sklkvGdIV~G~VknVt~~GaFV----eIg~GIeGLLpiSELSd~ 298 (681)
+ .....-..+.|+|..+...|..+ ++++|..-...++..+..
T Consensus 193 ~----------------------------------~~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~ 238 (263)
T PRK10676 193 A----------------------------------VAQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAA 238 (263)
T ss_pred C----------------------------------CCCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHH
Confidence 0 01223457899999997665433 344443322223222221
Q ss_pred cccccCCCCcccCCCEEEEEEEE
Q 005707 299 GFANMMGGSSLQVGQEVSVRVLR 321 (681)
Q Consensus 299 ~ie~~~p~~~fkVGqkVkVrVL~ 321 (681)
.-.|++|+.|.+.|..
T Consensus 239 -------~L~L~~G~~V~a~iKa 254 (263)
T PRK10676 239 -------RLSLQQGDAVTAYFNA 254 (263)
T ss_pred -------hcCCCCCCEEEEEEEc
Confidence 2468999999987643
No 247
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=43.72 E-value=83 Score=33.03 Aligned_cols=60 Identities=22% Similarity=0.247 Sum_probs=46.3
Q ss_pred ccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707 261 VKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 261 kvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID 323 (681)
.+||.|-|.|+.-...+..|+|++.-.+.++.- +....+ .+-.-.|++||.|-++|+.-+
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~l--aFe~At-krNrPnl~vGdliyakv~~a~ 123 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYL--AFEGAT-KRNRPNLQVGDLIYAKVVDAN 123 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeec--cccCcc-ccCCCccccccEEEEEEEecC
Confidence 479999999999999999999997677777753 332221 112467999999999998875
No 248
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=43.70 E-value=1e+02 Score=26.31 Aligned_cols=57 Identities=28% Similarity=0.349 Sum_probs=44.2
Q ss_pred EEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEE
Q 005707 265 DLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTM 331 (681)
Q Consensus 265 IV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSL 331 (681)
-++|+|++|.+...-|.|.+|-.=-+|. +.. -..+++|.+|.+..-..+..|+.=.|
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~lp~-ef~---------~~~L~~G~kV~V~yd~~~gk~vitdi 60 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKLPE-EFD---------FDGLKPGMKVVVFYDEVDGKRVITDI 60 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEECCC-ccc---------ccccCCCCEEEEEEEccCCcEEeeec
Confidence 4789999999999999999998877774 222 25689999999887777766665433
No 249
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=40.16 E-value=1e+02 Score=27.17 Aligned_cols=64 Identities=13% Similarity=0.090 Sum_probs=45.9
Q ss_pred EEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEE-eccCCceEEEEecc
Q 005707 151 FTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA-NAETGRISLTMRES 219 (681)
Q Consensus 151 VeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~V-D~ekgrI~LSlK~l 219 (681)
+-|+|+....++.| |.+.++..-++++.- . ++.- -.++.||.|.|..... |+.+++|..-...-
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~g---K-~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPG---K-LRKN-IWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEch---h-hccC-EEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 45889999998887 687777777776532 2 2222 4588999999999888 67777777666543
No 250
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=39.99 E-value=1.7e+02 Score=27.09 Aligned_cols=63 Identities=11% Similarity=0.128 Sum_probs=45.0
Q ss_pred cCcEEEEEEEEEecceEE-EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEE
Q 005707 262 KGQDLEGTVKNLTRSGAF-ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTM 331 (681)
Q Consensus 262 vGdIV~G~VknVt~~GaF-VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSL 331 (681)
....+.|+|+.....+.| |.+.+|..-+++++--.. ..-++..||.|.|.....+..|-.+..
T Consensus 19 ~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~R-------k~IwI~~GD~VlVe~~~~~~~kg~Iv~ 82 (100)
T PRK04012 19 EEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMK-------KRMWIREGDVVIVAPWDFQDEKADIIW 82 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhc-------ccEEecCCCEEEEEecccCCCEEEEEE
Confidence 344578999999888877 478889999998763221 145789999999998777644433333
No 251
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=39.78 E-value=1.5e+02 Score=28.19 Aligned_cols=97 Identities=22% Similarity=0.233 Sum_probs=65.2
Q ss_pred ccCcEEEEEEEEEecce-EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEEeccCCCcC
Q 005707 261 VKGQDLEGTVKNLTRSG-AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTMKKEDDVGS 339 (681)
Q Consensus 261 kvGdIV~G~VknVt~~G-aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~~~DP~ 339 (681)
+-|=-+.|+|++..+.| ++|++..+-.--++..++-... ... ...+++||.|-++ .+ +.
T Consensus 10 ~DG~YY~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~--~~~-~~~L~~GD~VLA~---~~--------------~~ 69 (124)
T PF15057_consen 10 EDGFYYPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALS--DAM-RHSLQVGDKVLAP---WE--------------PD 69 (124)
T ss_pred CCCcEEeEEEEEccCCCEEEEEECCCCEEEeChHHeEEcc--Ccc-cCcCCCCCEEEEe---cC--------------cC
Confidence 45777889999986555 4678866666666666553221 112 5689999999887 11 22
Q ss_pred CcceeeeEEEE-----eecccEEEEEEcCCeEEEeeCCccccc
Q 005707 340 NLQLTQGVIHA-----ATNPFVLAFRSNKDISSFLDERDKSAT 377 (681)
Q Consensus 340 e~~lv~G~V~~-----~i~~fGlfV~l~~gI~GfIp~~els~~ 377 (681)
...|..|+|.. .....-+-|.+.+|-...+|..+.-+-
T Consensus 70 ~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I 112 (124)
T PF15057_consen 70 DCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWI 112 (124)
T ss_pred CCEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEEC
Confidence 23488888884 234556777888888888888877765
No 252
>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=39.40 E-value=56 Score=26.38 Aligned_cols=47 Identities=23% Similarity=0.366 Sum_probs=31.1
Q ss_pred cEEEEEEEEEecce----EEEEeCCC--eEEEEeCCCCCcccccccCCCCcccCCCEEEEEE
Q 005707 264 QDLEGTVKNLTRSG----AFISLPEG--EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRV 319 (681)
Q Consensus 264 dIV~G~VknVt~~G----aFVeIg~G--IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrV 319 (681)
-.+.|+|..+.+.| +.++++++ +...++..... .-.|++|+.|.+.|
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~---------~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE---------ELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH---------HCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH---------HcCCCCCCEEEEEE
Confidence 36899999999999 67777875 45555532211 23578999999765
No 253
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=38.80 E-value=1.9e+02 Score=32.20 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=11.8
Q ss_pred CcccCCCEEEEEEEE
Q 005707 307 SSLQVGQEVSVRVLR 321 (681)
Q Consensus 307 ~~fkVGqkVkVrVL~ 321 (681)
..|++|+.+.+.|..
T Consensus 333 ~~Lr~Gm~~~v~i~~ 347 (390)
T PRK15136 333 HPLRIGLSTLVTVDT 347 (390)
T ss_pred CCccCCceEEEEEEe
Confidence 468899999988754
No 254
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=38.64 E-value=1.3e+02 Score=27.83 Aligned_cols=64 Identities=14% Similarity=0.104 Sum_probs=44.3
Q ss_pred cEEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEe-ccCCceEEEEe
Q 005707 149 ATFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN-AETGRISLTMR 217 (681)
Q Consensus 149 dIVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD-~ekgrI~LSlK 217 (681)
..+.|+|+.+...+.| |.+.++..-+.++. +.++. .-.++.||.|.|..++.. +.+++|..-..
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~----GK~Rk-~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~ 84 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCLDGKTRLGRIP----GKLKK-RIWIREGDVVIVKPWEFQGDDKCDIVWRYT 84 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEc----hhhcc-cEEecCCCEEEEEEccCCCCccEEEEEEcC
Confidence 3488999999999887 57776677776653 22333 456889999999766665 44566665444
No 255
>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=38.20 E-value=40 Score=27.49 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=30.8
Q ss_pred EEEEEEEEEecCeeEE----EECCC--eEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 150 TFTGKVRSIQPFGAFI----DFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 150 IVeGkV~sV~d~GaFV----dLggg--V~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
.+.|+|.++...|.++ +++++ +...++...+ .++ .+++|+.|.+.+-.
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~-----~~l--~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV-----AEL--GLKPGKEVYAVIKA 61 (69)
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH-----hhC--CCCCCCEEEEEEEC
Confidence 5899999998777654 44443 4444444332 222 37899999988754
No 256
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=37.46 E-value=1.9e+02 Score=26.14 Aligned_cols=68 Identities=19% Similarity=0.331 Sum_probs=40.8
Q ss_pred EEEEEEEEEecCe--eEEEEC---CCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEe
Q 005707 150 TFTGKVRSIQPFG--AFIDFG---AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMR 217 (681)
Q Consensus 150 IVeGkV~sV~d~G--aFVdLg---ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK 217 (681)
.+.|.|.++...| +|++|- +.+..++...++....+......++.|+.|.|.=.-....++.+.+..+
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~ 75 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVK 75 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeC
Confidence 4789999998765 799993 3466777655443222223333378899987754333334455555443
No 257
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=33.99 E-value=2.3e+02 Score=24.23 Aligned_cols=61 Identities=21% Similarity=0.257 Sum_probs=36.7
Q ss_pred EEEEEEEEEecCe-eEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707 150 TFTGKVRSIQPFG-AFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 150 IVeGkV~sV~d~G-aFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
.+.|+|.+....+ ++|.+.++..-.++.. +.++.......+||.|.+.+...+..+++|..
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~----Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHIS----GKMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEc----cceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 4679999988775 4455544333333321 22221122367999999998776666676654
No 258
>COG1278 CspC Cold shock proteins [Transcription]
Probab=33.08 E-value=1.4e+02 Score=26.01 Aligned_cols=49 Identities=24% Similarity=0.343 Sum_probs=34.6
Q ss_pred EEEEEEEec---CeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 152 TGKVRSIQP---FGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 152 eGkV~sV~d---~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
.|+|+-..+ ||++--=.|+-+.|||+|.+...-.+. +..||.|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~----L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRT----LREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcc----cCCCCEEEEEEec
Confidence 577887763 344333345589999999996543333 6789999998876
No 259
>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=32.27 E-value=51 Score=27.31 Aligned_cols=31 Identities=35% Similarity=0.622 Sum_probs=26.3
Q ss_pred CCCcccCCCEEEEEEEEEeCCeEEEEEeccC
Q 005707 305 GGSSLQVGQEVSVRVLRISRGQVTLTMKKED 335 (681)
Q Consensus 305 p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~~ 335 (681)
+.+.+..|+.+.++|+.++.+++.|.+.+..
T Consensus 8 ~gE~I~Ig~~I~I~Vl~i~~~~VklgI~AP~ 38 (54)
T PF02599_consen 8 VGESIVIGDDIEITVLEISGGQVKLGIDAPK 38 (54)
T ss_dssp TT-EEEETTTEEEEEEEEETTEEEEEEEECT
T ss_pred CCCEEEECCCEEEEEEEEcCCEEEEEEECCC
Confidence 4677888999999999999999999997653
No 260
>CHL00010 infA translation initiation factor 1
Probab=31.84 E-value=2.7e+02 Score=24.41 Aligned_cols=64 Identities=23% Similarity=0.261 Sum_probs=39.6
Q ss_pred EEEEEEEEecCee-EEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEEEEec
Q 005707 151 FTGKVRSIQPFGA-FIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISLTMRE 218 (681)
Q Consensus 151 VeGkV~sV~d~Ga-FVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~LSlK~ 218 (681)
+.|+|+++...|. +|.+..+..-.+++. +.++.......+||.|.+.+...+..+++|..-.+.
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~r----Gklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYIS----GKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEec----cceecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 7899999987555 456544333333321 222222233578999999987777667777776553
No 261
>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=31.07 E-value=2.5e+02 Score=24.71 Aligned_cols=59 Identities=12% Similarity=0.158 Sum_probs=42.4
Q ss_pred EEEEEEEEecceEE-EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEEEE
Q 005707 266 LEGTVKNLTRSGAF-ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTLTM 331 (681)
Q Consensus 266 V~G~VknVt~~GaF-VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~LSL 331 (681)
+.|+|+.....+.| |.+.+|..-+++++--.. ..-+++.||.|.|.....|..|-.+..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~r-------k~iwI~~GD~V~Ve~~~~d~~kg~Iv~ 61 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMR-------KRVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhc-------ccEEEcCCCEEEEEeccccCCEEEEEE
Confidence 56899999888776 578889999988753221 146889999999987777654433333
No 262
>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=30.44 E-value=56 Score=27.47 Aligned_cols=59 Identities=20% Similarity=0.245 Sum_probs=38.0
Q ss_pred EEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceE
Q 005707 150 TFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRIS 213 (681)
Q Consensus 150 IVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~ 213 (681)
.+.|+|+.....+.| |.+.++..-++++.- .+.. .-.++.||.|.|.+-..|..+++|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~g---K~r~--~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPG---KFRK--RIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-H---HHHT--CC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc---ceee--eEecCCCCEEEEEecccCCCeEEEE
Confidence 467999999988887 788777766665532 1111 2347899999988876665555553
No 263
>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=30.36 E-value=42 Score=27.38 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=29.8
Q ss_pred cEEEEEEEEEecceEEEE----eCCC--eEEEEeCCCCCcccccccCCCCcccCCCEEEEEEE
Q 005707 264 QDLEGTVKNLTRSGAFIS----LPEG--EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320 (681)
Q Consensus 264 dIV~G~VknVt~~GaFVe----Ig~G--IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL 320 (681)
..+.|+|.++...|.+++ ++++ +...++...+ ..-.|++|+.|.+.+.
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 468999999987766554 4333 2333332211 1346789999997764
No 264
>CHL00010 infA translation initiation factor 1
Probab=29.72 E-value=2.8e+02 Score=24.27 Aligned_cols=63 Identities=17% Similarity=0.264 Sum_probs=39.6
Q ss_pred EEEEEEEEecce-EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe--CCeEEEEEecc
Q 005707 266 LEGTVKNLTRSG-AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS--RGQVTLTMKKE 334 (681)
Q Consensus 266 V~G~VknVt~~G-aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID--kgKI~LSLK~~ 334 (681)
+.|.|..+...| .+|.+.+|..-.++..-.... ..-.+.+||.|.+.+-..+ +++|..-.++.
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~------~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRR------NSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEeccceec------CCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 679999988544 456676776666664321111 1345789999999865555 46666555543
No 265
>PF14985 TM140: TM140 protein family
Probab=28.91 E-value=15 Score=36.49 Aligned_cols=8 Identities=88% Similarity=1.801 Sum_probs=6.6
Q ss_pred hhhhhccc
Q 005707 662 FYNFCLRN 669 (681)
Q Consensus 662 ~~~~~~~~ 669 (681)
||||||-|
T Consensus 45 FyNFCLWn 52 (181)
T PF14985_consen 45 FYNFCLWN 52 (181)
T ss_pred eeeeeeec
Confidence 58999876
No 266
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=27.95 E-value=39 Score=35.66 Aligned_cols=66 Identities=24% Similarity=0.309 Sum_probs=49.6
Q ss_pred ccccCCccCcEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeCCeEEE
Q 005707 255 MKTTKFVKGQDLEGTVKNLTRS--GAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISRGQVTL 329 (681)
Q Consensus 255 ~~~sklkvGdIV~G~VknVt~~--GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDkgKI~L 329 (681)
...-.-++|+++.|+|..|.+. |+.|. +-..+-||+.+++.++ ..+..+++...+|.+.|.+.+.-
T Consensus 100 fyVf~Pk~Gd~LeG~Vn~vS~sHIglLIh--g~FNASIpk~nip~dw-------~fI~md~eee~~v~ntD~gnln~ 167 (253)
T KOG4134|consen 100 FYVFRPKAGDILEGVVNHVSRSHIGLLIH--GVFNASIPKTNIPADW-------EFIAMDQEEEIRVKNTDIGNLNP 167 (253)
T ss_pred EEEECCCCCCeeeeeeeecchhhhceeeh--hhhhccCCCCCCccce-------eeecCCchhhhceeecccccCCC
Confidence 4456678999999999999877 65543 3455778888776655 25688999999999999766543
No 267
>PRK01712 carbon storage regulator; Provisional
Probab=27.07 E-value=95 Score=26.76 Aligned_cols=30 Identities=30% Similarity=0.529 Sum_probs=26.6
Q ss_pred CCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 305 GGSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 305 p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
+.+.+..|+.+.++|+.+..+++.|++.+-
T Consensus 8 ~gE~I~Igd~I~I~V~~i~~~~VrlGI~AP 37 (64)
T PRK01712 8 VGESLMIGDDIEVTVLGVKGNQVRIGINAP 37 (64)
T ss_pred CCCEEEeCCCEEEEEEEEeCCEEEEEEECC
Confidence 467788999999999999999999999764
No 268
>PRK00568 carbon storage regulator; Provisional
Probab=25.23 E-value=97 Score=27.55 Aligned_cols=30 Identities=20% Similarity=0.475 Sum_probs=26.5
Q ss_pred CCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 305 GGSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 305 p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
..+.+..|+.+.++|+.+..+++.|.+.+-
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~g~~VrlGI~AP 37 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISIDRGSVRLGFEAP 37 (76)
T ss_pred CCCeEEeCCCeEEEEEEEcCCEEEEEEECC
Confidence 367788999999999999999999999654
No 269
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=24.64 E-value=16 Score=39.13 Aligned_cols=37 Identities=11% Similarity=0.085 Sum_probs=22.5
Q ss_pred EeceeeeeeccccccceeeecccccccccceeEEeccCCc
Q 005707 15 IPVTAFTIKKNNCLTRYNSTRKSTKQTISSQRFLLPLPSS 54 (681)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~s~~~l~~dl~gl 54 (681)
++..-|.+ ....||+|.-..|.|++||.|++.|+-.+
T Consensus 280 l~~a~y~~---~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~h 316 (325)
T PF00773_consen 280 LPPAEYST---EPSGHFGLGLPAYTHFTSPLRRYADLVVH 316 (325)
T ss_dssp C--EEEES---SGC-BTTTTBSS-B--S-TTTBHHHHHHH
T ss_pred hccccccc---CCCcceeeeccccccccChhhhhHHHHHH
Confidence 34455533 33489999999999999999999997443
No 270
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=24.63 E-value=27 Score=40.26 Aligned_cols=70 Identities=17% Similarity=0.180 Sum_probs=53.5
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEE-CCCeEEEEeccccCCccc------------cCcccccccCCEEEEEEEEEeccCC
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDF-GAFTDGLVHVSRLSDNFV------------KDVGSIVSVGQEVKVRLIEANAETG 210 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdL-gggV~GLVPiSELS~~~v------------~d~~e~fkVGd~VkVkVl~VD~ekg 210 (681)
.......+.+.|..|...|+-|.| .+|...|||..-|-..+- -+-...|++||.|+|++.+|..+++
T Consensus 558 k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etR 637 (645)
T COG4776 558 KAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETR 637 (645)
T ss_pred ccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhh
Confidence 444567799999999999999998 677899999776654321 1234569999999999999877766
Q ss_pred ceE
Q 005707 211 RIS 213 (681)
Q Consensus 211 rI~ 213 (681)
.|.
T Consensus 638 sii 640 (645)
T COG4776 638 SII 640 (645)
T ss_pred hhh
Confidence 554
No 271
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=24.46 E-value=1.6e+02 Score=31.96 Aligned_cols=49 Identities=24% Similarity=0.226 Sum_probs=40.6
Q ss_pred CCCCCcEEEEEEEEEecCeeEEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEE
Q 005707 144 DLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205 (681)
Q Consensus 144 ~LkvGdIVeGkV~sV~d~GaFVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~V 205 (681)
....|.+-+|.|.+....|.+|++|...-+.++ ..+.+|..|.++|...
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~-------------~~~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLS-------------SPAPPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceecc-------------CCCCCCceEEEEEEec
Confidence 577899999999999999999999985444443 2278999999999985
No 272
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=24.23 E-value=93 Score=27.43 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=26.2
Q ss_pred CCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 306 GSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 306 ~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
.+.+.+||.|.+.|+.++.+++.+.+++.
T Consensus 9 ~Esi~IgddI~itVl~i~gnqVkiGi~AP 37 (73)
T COG1551 9 GESIMIGDDIEITVLSIKGNQVKIGINAP 37 (73)
T ss_pred CceEEecCCeEEEEEEEcCCeEEEeecCC
Confidence 57789999999999999999999999664
No 273
>PLN00208 translation initiation factor (eIF); Provisional
Probab=24.05 E-value=2.2e+02 Score=28.22 Aligned_cols=65 Identities=14% Similarity=0.100 Sum_probs=0.0
Q ss_pred CCCCcEEEEEEEEEecCeeE-EEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEeccCCceEE
Q 005707 145 LIPGATFTGKVRSIQPFGAF-IDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRISL 214 (681)
Q Consensus 145 LkvGdIVeGkV~sV~d~GaF-VdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD~ekgrI~L 214 (681)
+..-..+-|+|+.+...|.| |.+..+..-++|+ ...++. .-.+..||.|.|.+-..+..+++|..
T Consensus 28 ~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~I----pGKmRK-rIWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 28 FKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHI----RGKMRK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred cCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEE----ecccee-eEEecCCCEEEEEccCCCCCEEEEEE
No 274
>PF12337 DUF3637: Protein of unknown function (DUF3637) ; InterPro: IPR022098 This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with PF00073 from PFAM, PF08935 from PFAM.
Probab=22.57 E-value=1.3e+02 Score=25.44 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=34.1
Q ss_pred ccccceeeecccccccccceeEEeccCCceeEEeCcccC
Q 005707 26 NCLTRYNSTRKSTKQTISSQRFLLPLPSSVRFFSQFQSG 64 (681)
Q Consensus 26 ~~~~~~~~~r~~~~~~~s~~~l~~dl~glrGfIP~sq~~ 64 (681)
.|+.-|.|-|+--.|..|+.++.+..+.-..|-|+....
T Consensus 2 aclkifslk~k~kshsyspr~ielkynsdfafkprpla~ 40 (67)
T PF12337_consen 2 ACLKIFSLKRKDKSHSYSPREIELKYNSDFAFKPRPLAP 40 (67)
T ss_pred cceeeeeecccccCcCcCCcceEEEecccccccCCcCch
Confidence 488899999999999999999999988888888887554
No 275
>PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=22.48 E-value=36 Score=20.34 Aligned_cols=10 Identities=30% Similarity=1.318 Sum_probs=8.1
Q ss_pred ccchhhhhhc
Q 005707 658 FNSCFYNFCL 667 (681)
Q Consensus 658 ~~~~~~~~~~ 667 (681)
...||+.||.
T Consensus 3 ~~~CFWKYCv 12 (12)
T PF02083_consen 3 KSECFWKYCV 12 (12)
T ss_pred ccchhhhhcC
Confidence 4579999994
No 276
>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=22.13 E-value=1.6e+02 Score=24.09 Aligned_cols=43 Identities=28% Similarity=0.424 Sum_probs=26.5
Q ss_pred EEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEE
Q 005707 268 GTVKNLTRSGAFISLPE-GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLR 321 (681)
Q Consensus 268 G~VknVt~~GaFVeIg~-GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ 321 (681)
|++....+.-.||...+ +-+-|||..+|.. -.-||+|.|+|+.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~-----------A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNG-----------AMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTT-----------S-TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCC-----------CCCCCEEEEEEec
Confidence 44444433334777775 8899999766543 2459999999998
No 277
>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=21.83 E-value=1.3e+02 Score=26.32 Aligned_cols=30 Identities=30% Similarity=0.546 Sum_probs=26.7
Q ss_pred CCCcccCCCEEEEEEEEEeCCeEEEEEecc
Q 005707 305 GGSSLQVGQEVSVRVLRISRGQVTLTMKKE 334 (681)
Q Consensus 305 p~~~fkVGqkVkVrVL~IDkgKI~LSLK~~ 334 (681)
+.+.+..|+.+.++|+.+..+++.|.+.+.
T Consensus 8 ~gE~I~Igd~I~I~Vl~i~g~~VrlGI~AP 37 (69)
T TIGR00202 8 VNESIQIGDDIEVKVLSVKGDQVKLGIEAP 37 (69)
T ss_pred CCCEEEeCCCEEEEEEEEcCCeEEEEEECC
Confidence 467789999999999999999999999764
No 278
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=21.31 E-value=5.5e+02 Score=22.86 Aligned_cols=53 Identities=13% Similarity=0.146 Sum_probs=39.4
Q ss_pred EEEEEEEEEecceEE-EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEeC
Q 005707 265 DLEGTVKNLTRSGAF-ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRISR 324 (681)
Q Consensus 265 IV~G~VknVt~~GaF-VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~IDk 324 (681)
.+.|+|+.....+.| |.+.+|..-+++++--.. ..-+++.||.|.|.....++
T Consensus 6 q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~R-------k~iwI~~GD~VlVe~~~~~~ 59 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCADGKERLARIPGKMR-------KKVWIRRGDIVLVDPWDFQD 59 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhc-------ccEEEcCCCEEEEEecCCCC
Confidence 467999999888877 578889999888753221 14578999999988766554
No 279
>PF14654 Epiglycanin_C: Mucin, catalytic, TM and cytoplasmic tail region
Probab=20.98 E-value=33 Score=31.79 Aligned_cols=13 Identities=46% Similarity=0.899 Sum_probs=11.3
Q ss_pred hhhccceeeEeeec
Q 005707 664 NFCLRNLYFSVQNV 677 (681)
Q Consensus 664 ~~~~~~~~~~~~~~ 677 (681)
-||+|| |||..|.
T Consensus 39 fFcvR~-~lslrn~ 51 (106)
T PF14654_consen 39 FFCVRN-SLSLRNT 51 (106)
T ss_pred HHHhhh-ccccccc
Confidence 489999 9999886
No 280
>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=20.76 E-value=2.2e+02 Score=23.27 Aligned_cols=42 Identities=17% Similarity=0.085 Sum_probs=24.9
Q ss_pred EEEEEecCeeEEEEC-CCeEEEEeccccCCccccCcccccccCCEEEEEEEE
Q 005707 154 KVRSIQPFGAFIDFG-AFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIE 204 (681)
Q Consensus 154 kV~sV~d~GaFVdLg-ggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~ 204 (681)
++....+.-.||... .+-+-|||..++... ..||.|.|+|+.
T Consensus 2 ~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~ 44 (58)
T PF08206_consen 2 TLKIHPKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITP 44 (58)
T ss_dssp EEEE-SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEE
T ss_pred EEEEEcCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEec
Confidence 344443222355554 468999998877543 379999999998
No 281
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=20.71 E-value=4.1e+02 Score=24.57 Aligned_cols=54 Identities=11% Similarity=0.197 Sum_probs=39.5
Q ss_pred CcEEEEEEEEEecceEE-EEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707 263 GQDLEGTVKNLTRSGAF-ISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 263 GdIV~G~VknVt~~GaF-VeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID 323 (681)
-..+.|+|+.....+.| |.+.+|..-+++++--.. ..-++..||.|.|......
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~R-------k~iwI~~GD~VlVsp~d~~ 72 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLK-------KRIWIREGDVVIVKPWEFQ 72 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhc-------ccEEecCCCEEEEEEccCC
Confidence 34588999999888776 477889999988753221 1457899999998655554
No 282
>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=20.56 E-value=1.9e+02 Score=25.79 Aligned_cols=37 Identities=22% Similarity=0.200 Sum_probs=26.2
Q ss_pred cCCCCCCcE------EEEEEEEEecCeeEEEECCCeEEEEecc
Q 005707 142 NEDLIPGAT------FTGKVRSIQPFGAFIDFGAFTDGLVHVS 178 (681)
Q Consensus 142 ~~~LkvGdI------VeGkV~sV~d~GaFVdLgggV~GLVPiS 178 (681)
.++|++|+. +-|+|.++.+.-+-+++..++.--+.++
T Consensus 35 ~~~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~i~~~r~ 77 (84)
T TIGR00739 35 IESLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTEITFSKN 77 (84)
T ss_pred HHhCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhH
Confidence 568999998 5688888888777777765555544443
No 283
>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=20.39 E-value=2.8e+02 Score=21.65 Aligned_cols=47 Identities=34% Similarity=0.523 Sum_probs=28.5
Q ss_pred EEEEEEec-ceEEEEeCCC-eEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE
Q 005707 268 GTVKNLTR-SGAFISLPEG-EEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322 (681)
Q Consensus 268 G~VknVt~-~GaFVeIg~G-IeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I 322 (681)
|+|.-..+ +| ||...+. -+-++|.+.+.. . ...+..||.|.|++..-
T Consensus 2 G~i~~~~~g~g-fv~~~~~~~~i~v~~~~~~~-~------~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFG-FIRPDDGGKDVFVHPSQIQG-G------LKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCee-EEecCCCCccEEEEhHHhhc-C------CCcCCCCCEEEEEEEEc
Confidence 45554443 45 5554433 578888664332 1 23467799999998764
No 284
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.32 E-value=3.8e+02 Score=25.93 Aligned_cols=59 Identities=20% Similarity=0.246 Sum_probs=0.0
Q ss_pred cCcEEEEEEEEEecce---------EEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEE--eCCeEEE
Q 005707 262 KGQDLEGTVKNLTRSG---------AFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI--SRGQVTL 329 (681)
Q Consensus 262 vGdIV~G~VknVt~~G---------aFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~I--DkgKI~L 329 (681)
.|.++.-+|..+.+.| +.|+|+++-.++.++.. .+. +.+++|++|++.+... +.+.+..
T Consensus 63 ~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~--~~p-------~~v~iGm~V~~v~~~~~~~~~~~~~ 132 (140)
T COG1545 63 EGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD--VDP-------DDVEIGMKVEAVFRKREEDGGRGYI 132 (140)
T ss_pred CeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe--cCc-------ccccCCCEEEEEEEEccccCCceEE
No 285
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=20.19 E-value=3.3e+02 Score=24.16 Aligned_cols=50 Identities=20% Similarity=0.289 Sum_probs=37.1
Q ss_pred cCCCCCCcEEEEEEEEEecCee-EEEECCCeEEEEeccccCCccccCcccccccCCEEEEEEEEEe
Q 005707 142 NEDLIPGATFTGKVRSIQPFGA-FIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEAN 206 (681)
Q Consensus 142 ~~~LkvGdIVeGkV~sV~d~Ga-FVdLgggV~GLVPiSELS~~~v~d~~e~fkVGd~VkVkVl~VD 206 (681)
..-++.|++++-.|..+.+.|= ...+.| ...|+|- ..+|+.|+++|..+-
T Consensus 10 ~~PVeeGe~y~V~I~d~g~~GDGiarveG-fvVFVp~--------------a~~Gd~V~vkI~~v~ 60 (73)
T COG3269 10 TPPVEEGETYEVEIEDVGDQGDGIARVEG-FVVFVPG--------------AEVGDEVKVKITKVK 60 (73)
T ss_pred CCCcccCCEEEEEEEEeccCCCceEEEEE-EEEEeCC--------------CCCCCeeeEEEEEee
Confidence 3468899999999999998764 222223 5666662 468999999999873
No 286
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=20.06 E-value=1.9e+02 Score=31.47 Aligned_cols=52 Identities=25% Similarity=0.336 Sum_probs=42.4
Q ss_pred ccCCccCcEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccccCCCCcccCCCEEEEEEEEEe
Q 005707 257 TTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRIS 323 (681)
Q Consensus 257 ~sklkvGdIV~G~VknVt~~GaFVeIg~GIeGLLpiSELSd~~ie~~~p~~~fkVGqkVkVrVL~ID 323 (681)
...-..|.+-+|.|.+....|.+|++|.+-.+.++ ..+.+|..|+++|.+..
T Consensus 100 ~~~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~---------------~~~~~~~RvTvri~~~~ 151 (272)
T COG2106 100 STSPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLS---------------SPAPPGARVTVRIISRS 151 (272)
T ss_pred cCCccceeecceEEEEecCCceEEEecCCcceecc---------------CCCCCCceEEEEEEecc
Confidence 44567899999999999999999999865555544 23789999999998874
Done!