Query 015066
Match_columns 414
No_of_seqs 389 out of 2307
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 02:45:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015066.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015066hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07400 30S ribosomal protein 100.0 2.9E-56 6.3E-61 439.7 34.9 295 73-368 5-300 (318)
2 COG0539 RpsA Ribosomal protein 100.0 1.3E-47 2.8E-52 393.4 26.8 254 92-349 14-277 (541)
3 PRK07899 rpsA 30S ribosomal pr 100.0 8.1E-46 1.8E-50 382.0 31.3 260 82-343 18-287 (486)
4 COG0539 RpsA Ribosomal protein 100.0 1.7E-45 3.8E-50 377.7 25.2 257 85-346 91-360 (541)
5 PRK06299 rpsA 30S ribosomal pr 100.0 2.8E-42 6.1E-47 366.4 32.2 264 76-343 5-280 (565)
6 PRK06676 rpsA 30S ribosomal pr 100.0 1.5E-41 3.2E-46 345.7 31.3 259 83-343 2-271 (390)
7 PRK13806 rpsA 30S ribosomal pr 100.0 4E-41 8.7E-46 350.8 26.1 247 88-336 191-452 (491)
8 PRK00087 4-hydroxy-3-methylbut 100.0 4.1E-40 8.9E-45 353.7 33.0 290 47-343 255-556 (647)
9 PRK07899 rpsA 30S ribosomal pr 100.0 2E-39 4.3E-44 334.7 34.4 249 86-339 109-369 (486)
10 PRK12269 bifunctional cytidyla 100.0 2.7E-40 5.8E-45 359.9 28.8 250 91-343 485-746 (863)
11 PRK12269 bifunctional cytidyla 100.0 6.3E-40 1.4E-44 356.9 26.8 258 84-344 383-660 (863)
12 PRK13806 rpsA 30S ribosomal pr 100.0 2.4E-39 5.2E-44 337.4 29.0 255 83-344 14-287 (491)
13 PRK06676 rpsA 30S ribosomal pr 100.0 1.2E-38 2.7E-43 324.2 29.2 253 88-344 94-358 (390)
14 TIGR00717 rpsA ribosomal prote 100.0 1E-38 2.2E-43 335.8 28.5 253 85-343 2-266 (516)
15 PRK06299 rpsA 30S ribosomal pr 100.0 9E-38 1.9E-42 332.0 30.5 251 90-343 192-454 (565)
16 TIGR00717 rpsA ribosomal prote 100.0 5.9E-37 1.3E-41 322.5 29.8 252 89-343 177-440 (516)
17 PRK00087 4-hydroxy-3-methylbut 100.0 2.5E-35 5.5E-40 316.6 29.2 252 87-342 377-641 (647)
18 PRK07400 30S ribosomal protein 99.9 5.5E-22 1.2E-26 196.2 19.2 157 176-336 20-186 (318)
19 KOG1070 rRNA processing protei 99.8 5.3E-20 1.2E-24 200.6 15.6 246 96-343 1064-1333(1710)
20 COG1098 VacB Predicted RNA bin 99.8 1.2E-19 2.5E-24 151.1 5.4 80 261-341 2-82 (129)
21 KOG1070 rRNA processing protei 99.8 4.8E-18 1E-22 185.6 17.1 221 115-336 434-672 (1710)
22 COG2996 Predicted RNA-bindinin 99.8 1.9E-16 4.1E-21 148.7 22.7 209 96-336 2-219 (287)
23 PTZ00248 eukaryotic translatio 99.7 4.8E-17 1E-21 158.9 8.6 87 260-346 12-102 (319)
24 cd05705 S1_Rrp5_repeat_hs14 S1 99.7 3.6E-16 7.8E-21 122.2 8.4 70 262-331 1-74 (74)
25 PRK08582 hypothetical protein; 99.7 1.1E-15 2.3E-20 133.7 11.9 85 261-346 2-87 (139)
26 cd05694 S1_Rrp5_repeat_hs2_sc2 99.6 5E-15 1.1E-19 115.7 10.2 71 261-337 1-73 (74)
27 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 5.6E-15 1.2E-19 115.1 9.2 70 262-332 1-72 (73)
28 PTZ00248 eukaryotic translatio 99.6 2.1E-15 4.4E-20 147.5 8.2 124 96-221 13-147 (319)
29 cd05703 S1_Rrp5_repeat_hs12_sc 99.6 5.9E-15 1.3E-19 115.0 9.0 69 265-333 1-72 (73)
30 cd05704 S1_Rrp5_repeat_hs13 S1 99.6 4.6E-15 1E-19 115.3 8.0 70 262-333 1-72 (72)
31 cd04461 S1_Rrp5_repeat_hs8_sc7 99.6 6.5E-15 1.4E-19 117.5 8.8 75 258-332 8-83 (83)
32 PF00575 S1: S1 RNA binding do 99.6 8.6E-15 1.9E-19 113.9 9.2 73 261-333 1-74 (74)
33 PRK07252 hypothetical protein; 99.6 3.1E-14 6.7E-19 121.4 12.8 77 263-339 2-79 (120)
34 cd05698 S1_Rrp5_repeat_hs6_sc5 99.6 1.1E-14 2.3E-19 112.1 8.5 69 265-333 1-70 (70)
35 COG1093 SUI2 Translation initi 99.6 3.7E-15 7.9E-20 139.5 5.5 104 262-365 9-115 (269)
36 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.6 2E-14 4.4E-19 111.4 8.8 68 265-332 1-71 (71)
37 cd04452 S1_IF2_alpha S1_IF2_al 99.5 3.2E-14 7E-19 111.1 9.7 73 262-334 1-76 (76)
38 cd05684 S1_DHX8_helicase S1_DH 99.5 3.9E-14 8.4E-19 111.9 10.1 74 265-340 1-79 (79)
39 cd05706 S1_Rrp5_repeat_sc10 S1 99.5 4.3E-14 9.3E-19 109.8 9.8 72 262-333 1-73 (73)
40 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.5 3E-14 6.6E-19 109.5 8.8 68 265-332 1-69 (69)
41 PHA02945 interferon resistance 99.5 4.1E-14 8.9E-19 111.4 9.1 74 262-338 9-87 (88)
42 PLN00207 polyribonucleotide nu 99.5 2.4E-14 5.2E-19 155.7 10.2 85 260-345 749-835 (891)
43 PRK05807 hypothetical protein; 99.5 6.2E-14 1.3E-18 122.2 10.5 75 261-336 2-76 (136)
44 cd05707 S1_Rrp5_repeat_sc11 S1 99.5 5.4E-14 1.2E-18 107.8 7.9 67 265-331 1-68 (68)
45 cd05690 S1_RPS1_repeat_ec5 S1_ 99.5 6.8E-14 1.5E-18 107.2 8.0 67 265-331 1-69 (69)
46 cd05691 S1_RPS1_repeat_ec6 S1_ 99.5 1.3E-13 2.9E-18 106.6 9.6 72 265-336 1-73 (73)
47 cd05708 S1_Rrp5_repeat_sc12 S1 99.5 1.6E-13 3.5E-18 107.2 9.8 73 263-335 1-75 (77)
48 PLN00207 polyribonucleotide nu 99.5 2.9E-14 6.2E-19 155.1 7.1 161 11-185 669-837 (891)
49 PRK08059 general stress protei 99.5 2.5E-13 5.5E-18 116.5 10.2 80 260-339 3-83 (123)
50 cd05689 S1_RPS1_repeat_ec4 S1_ 99.4 3.7E-13 8.1E-18 104.2 8.7 70 262-331 1-72 (72)
51 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 5.6E-13 1.2E-17 102.6 9.1 69 265-333 1-70 (70)
52 PRK03987 translation initiatio 99.4 5E-13 1.1E-17 128.6 10.0 102 262-363 6-110 (262)
53 cd05692 S1_RPS1_repeat_hs4 S1_ 99.4 9.3E-13 2E-17 100.2 8.7 68 265-333 1-69 (69)
54 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.4 1.1E-12 2.3E-17 100.2 8.4 65 265-331 1-66 (66)
55 cd05693 S1_Rrp5_repeat_hs1_sc1 99.4 4.5E-13 9.7E-18 110.8 6.7 73 262-334 1-96 (100)
56 cd04465 S1_RPS1_repeat_ec2_hs2 99.4 2E-12 4.4E-17 98.8 9.0 67 265-333 1-67 (67)
57 PF00575 S1: S1 RNA binding do 99.4 3.3E-12 7.1E-17 99.3 10.3 73 97-170 2-74 (74)
58 cd05688 S1_RPS1_repeat_ec3 S1_ 99.4 1.8E-12 4E-17 98.5 8.6 68 264-331 1-68 (68)
59 cd05685 S1_Tex S1_Tex: The C-t 99.4 1.4E-12 3E-17 99.0 7.7 67 265-331 1-68 (68)
60 COG1098 VacB Predicted RNA bin 99.4 7.2E-13 1.6E-17 110.7 5.7 77 96-174 2-78 (129)
61 cd05705 S1_Rrp5_repeat_hs14 S1 99.4 3E-12 6.5E-17 100.0 8.7 71 97-168 1-74 (74)
62 cd04472 S1_PNPase S1_PNPase: P 99.3 5.8E-12 1.3E-16 95.9 8.3 67 265-332 1-68 (68)
63 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.3 5E-12 1.1E-16 101.4 8.0 73 262-335 4-81 (86)
64 cd04453 S1_RNase_E S1_RNase_E: 99.3 7.7E-12 1.7E-16 101.0 8.4 74 261-334 4-83 (88)
65 TIGR02696 pppGpp_PNP guanosine 99.3 8.9E-12 1.9E-16 133.3 10.6 92 238-331 611-718 (719)
66 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 1.4E-11 3E-16 98.2 8.5 73 96-169 11-83 (83)
67 cd05703 S1_Rrp5_repeat_hs12_sc 99.3 2.1E-11 4.6E-16 94.9 8.9 70 100-170 1-72 (73)
68 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 3.6E-11 7.8E-16 93.9 10.0 71 96-173 1-72 (74)
69 smart00316 S1 Ribosomal protei 99.3 2.5E-11 5.3E-16 92.4 9.0 71 263-333 1-72 (72)
70 cd04471 S1_RNase_R S1_RNase_R: 99.3 2.8E-11 6.1E-16 95.9 9.6 69 264-332 1-82 (83)
71 cd04465 S1_RPS1_repeat_ec2_hs2 99.3 2.4E-11 5.1E-16 92.8 8.6 65 188-252 1-67 (67)
72 cd05698 S1_Rrp5_repeat_hs6_sc5 99.3 2.6E-11 5.6E-16 93.2 8.7 70 100-170 1-70 (70)
73 PRK11824 polynucleotide phosph 99.2 2.8E-11 6E-16 131.5 10.8 75 260-335 617-692 (693)
74 cd05687 S1_RPS1_repeat_ec1_hs1 99.2 5.3E-11 1.1E-15 91.5 9.1 70 100-170 1-70 (70)
75 TIGR02696 pppGpp_PNP guanosine 99.2 2E-11 4.3E-16 130.6 8.8 137 19-168 570-718 (719)
76 PRK11824 polynucleotide phosph 99.2 3E-11 6.5E-16 131.2 10.2 147 12-172 539-692 (693)
77 COG2183 Tex Transcriptional ac 99.2 1.7E-11 3.7E-16 130.4 7.8 80 260-339 654-734 (780)
78 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 7.2E-11 1.6E-15 90.6 8.8 69 100-169 1-69 (69)
79 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 1.3E-10 2.9E-15 90.0 10.3 73 97-170 1-73 (73)
80 COG1185 Pnp Polyribonucleotide 99.2 5.4E-11 1.2E-15 124.8 9.3 97 238-336 585-691 (692)
81 cd04454 S1_Rrp4_like S1_Rrp4_l 99.2 9.6E-11 2.1E-15 93.1 8.4 72 262-334 4-76 (82)
82 PRK07252 hypothetical protein; 99.2 1.4E-10 3E-15 99.0 9.6 82 97-179 1-82 (120)
83 cd05704 S1_Rrp5_repeat_hs13 S1 99.2 1.4E-10 3.1E-15 90.0 8.6 71 97-170 1-72 (72)
84 cd05702 S1_Rrp5_repeat_hs11_sc 99.2 1.1E-10 2.3E-15 90.1 7.7 62 265-326 1-65 (70)
85 cd04473 S1_RecJ_like S1_RecJ_l 99.2 2.5E-10 5.4E-15 89.8 9.5 64 260-332 12-76 (77)
86 COG2183 Tex Transcriptional ac 99.2 9E-11 1.9E-15 125.0 9.2 112 58-174 621-732 (780)
87 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 1.9E-10 4.2E-15 89.0 8.8 69 100-169 1-71 (71)
88 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 1.6E-10 3.6E-15 88.4 8.0 68 100-168 1-68 (68)
89 cd05691 S1_RPS1_repeat_ec6 S1_ 99.1 2.9E-10 6.4E-15 87.8 9.4 72 100-172 1-72 (73)
90 PRK09521 exosome complex RNA-b 99.1 1.5E-10 3.2E-15 106.7 9.0 93 237-335 40-143 (189)
91 cd04460 S1_RpoE S1_RpoE: RpoE, 99.1 1.8E-10 4E-15 94.9 8.6 79 266-344 1-95 (99)
92 PRK08582 hypothetical protein; 99.1 5.7E-10 1.2E-14 97.7 10.4 82 96-180 2-83 (139)
93 cd04452 S1_IF2_alpha S1_IF2_al 99.1 7.1E-10 1.5E-14 86.4 9.8 73 98-171 2-76 (76)
94 cd00164 S1_like S1_like: Ribos 99.1 2.8E-10 6.2E-15 84.8 7.2 64 268-331 1-65 (65)
95 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.1 4.6E-10 1E-14 85.6 8.3 66 100-168 1-66 (66)
96 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 9.5E-10 2.1E-14 85.7 9.7 74 98-172 1-75 (77)
97 COG2996 Predicted RNA-bindinin 99.0 7.9E-09 1.7E-13 97.8 15.9 148 96-257 70-221 (287)
98 cd05686 S1_pNO40 S1_pNO40: pNO 99.0 1.7E-09 3.7E-14 84.1 9.4 70 98-169 2-72 (73)
99 cd05692 S1_RPS1_repeat_hs4 S1_ 99.0 1.4E-09 3.1E-14 82.4 8.8 69 100-170 1-69 (69)
100 cd05693 S1_Rrp5_repeat_hs1_sc1 99.0 7.9E-10 1.7E-14 91.4 7.7 76 97-173 1-98 (100)
101 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 1.5E-09 3.3E-14 86.2 8.9 75 96-172 3-77 (82)
102 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.0 1.2E-09 2.6E-14 87.5 8.3 75 96-172 3-81 (86)
103 TIGR03591 polynuc_phos polyrib 99.0 5.2E-10 1.1E-14 121.4 7.4 141 13-166 537-683 (684)
104 TIGR03591 polynuc_phos polyrib 99.0 1.2E-09 2.6E-14 118.5 9.9 70 260-330 614-684 (684)
105 smart00316 S1 Ribosomal protei 99.0 2.9E-09 6.2E-14 80.8 9.2 72 98-170 1-72 (72)
106 PRK09202 nusA transcription el 99.0 1.5E-09 3.2E-14 112.5 9.9 116 211-334 72-200 (470)
107 KOG1067 Predicted RNA-binding 99.0 7.7E-10 1.7E-14 112.9 7.5 81 260-341 664-745 (760)
108 PRK05807 hypothetical protein; 99.0 3E-09 6.6E-14 92.8 10.3 75 96-173 2-76 (136)
109 PRK08059 general stress protei 99.0 3.3E-09 7.2E-14 91.0 10.0 78 96-174 4-81 (123)
110 COG1185 Pnp Polyribonucleotide 99.0 6.4E-10 1.4E-14 116.8 5.7 144 16-172 541-690 (692)
111 cd05690 S1_RPS1_repeat_ec5 S1_ 99.0 2.9E-09 6.4E-14 81.3 7.9 68 100-168 1-69 (69)
112 PRK09202 nusA transcription el 98.9 2.2E-09 4.7E-14 111.2 9.1 122 123-254 71-201 (470)
113 cd05685 S1_Tex S1_Tex: The C-t 98.9 3.7E-09 8E-14 80.0 7.8 68 100-168 1-68 (68)
114 cd05688 S1_RPS1_repeat_ec3 S1_ 98.9 5.5E-09 1.2E-13 79.2 8.3 68 99-168 1-68 (68)
115 PHA02945 interferon resistance 98.9 8.8E-09 1.9E-13 81.4 9.2 73 97-173 9-85 (88)
116 cd04455 S1_NusA S1_NusA: N-uti 98.9 8.8E-09 1.9E-13 78.7 8.9 63 263-331 2-66 (67)
117 cd04472 S1_PNPase S1_PNPase: P 98.9 9.1E-09 2E-13 78.1 8.3 68 100-169 1-68 (68)
118 PRK03987 translation initiatio 98.9 9.5E-09 2.1E-13 99.1 9.9 88 97-185 6-95 (262)
119 cd05689 S1_RPS1_repeat_ec4 S1_ 98.9 1.4E-08 3E-13 78.4 8.8 71 97-168 1-72 (72)
120 cd05684 S1_DHX8_helicase S1_DH 98.9 1.8E-08 4E-13 79.3 9.4 72 100-174 1-76 (79)
121 KOG1067 Predicted RNA-binding 98.8 1.6E-09 3.5E-14 110.6 3.9 151 11-175 581-742 (760)
122 TIGR00448 rpoE DNA-directed RN 98.8 1.8E-08 3.8E-13 92.1 10.2 82 262-343 79-176 (179)
123 cd04455 S1_NusA S1_NusA: N-uti 98.8 1.7E-08 3.8E-13 77.1 8.6 64 98-169 2-67 (67)
124 PRK04163 exosome complex RNA-b 98.8 9.5E-09 2.1E-13 97.8 8.6 75 260-335 59-138 (235)
125 cd04453 S1_RNase_E S1_RNase_E: 98.8 2.5E-08 5.3E-13 80.5 8.9 74 96-170 4-82 (88)
126 COG1093 SUI2 Translation initi 98.8 1.1E-08 2.3E-13 96.4 7.1 77 97-174 9-87 (269)
127 cd05702 S1_Rrp5_repeat_hs11_sc 98.7 6.6E-08 1.4E-12 74.4 7.9 63 100-163 1-65 (70)
128 TIGR02063 RNase_R ribonuclease 98.7 5.7E-08 1.2E-12 106.5 10.1 72 261-332 624-708 (709)
129 cd00164 S1_like S1_like: Ribos 98.7 6.2E-08 1.3E-12 72.0 6.8 65 103-168 1-65 (65)
130 KOG2916 Translation initiation 98.6 8.9E-09 1.9E-13 96.5 1.4 104 261-364 13-119 (304)
131 TIGR01953 NusA transcription t 98.6 1.4E-07 3E-12 94.3 8.8 106 145-254 84-199 (341)
132 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.6 1.5E-07 3.4E-12 76.5 7.3 73 262-335 4-87 (92)
133 COG1095 RPB7 DNA-directed RNA 98.6 1.6E-07 3.4E-12 84.6 8.0 76 262-337 79-170 (183)
134 PHA02858 EIF2a-like PKR inhibi 98.6 1.5E-07 3.2E-12 73.7 6.5 70 261-332 13-85 (86)
135 PRK08563 DNA-directed RNA poly 98.6 2.7E-07 5.9E-12 84.9 9.4 75 262-336 79-169 (187)
136 cd04471 S1_RNase_R S1_RNase_R: 98.6 4.8E-07 1E-11 71.4 9.1 70 99-169 1-82 (83)
137 PRK11642 exoribonuclease R; Pr 98.5 3E-07 6.6E-12 101.5 10.6 73 263-335 642-727 (813)
138 cd04473 S1_RecJ_like S1_RecJ_l 98.5 7.6E-07 1.6E-11 69.9 9.9 64 96-169 13-76 (77)
139 TIGR00358 3_prime_RNase VacB a 98.5 3.6E-07 7.8E-12 99.2 10.1 70 263-332 571-653 (654)
140 PRK12327 nusA transcription el 98.4 5.5E-07 1.2E-11 90.6 8.5 103 224-333 84-199 (362)
141 PRK09521 exosome complex RNA-b 98.4 4.6E-07 1E-11 83.5 7.4 78 90-171 55-142 (189)
142 TIGR01953 NusA transcription t 98.4 9.3E-07 2E-11 88.4 9.8 104 224-334 81-198 (341)
143 PRK04163 exosome complex RNA-b 98.3 2.5E-06 5.4E-11 81.3 9.4 75 95-171 59-137 (235)
144 PRK12327 nusA transcription el 98.3 9.1E-06 2E-10 81.8 13.1 78 87-174 124-203 (362)
145 cd04460 S1_RpoE S1_RpoE: RpoE, 98.3 3.9E-06 8.4E-11 69.1 7.9 66 189-254 1-86 (99)
146 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.0 1.8E-05 3.8E-10 61.0 6.8 69 100-170 1-72 (72)
147 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.0 4.2E-05 9.1E-10 61.7 8.5 64 264-327 1-75 (88)
148 TIGR02063 RNase_R ribonuclease 98.0 4.8E-05 1E-09 83.7 11.4 73 96-169 624-708 (709)
149 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.0 3.5E-05 7.6E-10 62.7 7.7 74 96-171 3-86 (92)
150 PRK05054 exoribonuclease II; P 97.9 3.5E-05 7.6E-10 83.6 9.4 68 265-332 562-643 (644)
151 TIGR00448 rpoE DNA-directed RN 97.9 7E-05 1.5E-09 68.4 9.6 77 96-173 78-169 (179)
152 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.9 5.4E-05 1.2E-09 58.3 7.3 63 188-252 1-72 (72)
153 PRK12328 nusA transcription el 97.9 0.00018 3.9E-09 72.3 12.7 76 89-174 130-209 (374)
154 COG1096 Predicted RNA-binding 97.8 8.2E-05 1.8E-09 67.3 8.5 87 244-334 45-142 (188)
155 TIGR00757 RNaseEG ribonuclease 97.8 4.6E-05 1E-09 78.3 7.5 62 260-321 21-97 (414)
156 PF13509 S1_2: S1 domain; PDB: 97.8 0.00011 2.3E-09 55.1 7.5 61 99-170 1-61 (61)
157 COG1095 RPB7 DNA-directed RNA 97.8 7.1E-05 1.5E-09 67.6 7.7 85 95-180 77-177 (183)
158 PHA02858 EIF2a-like PKR inhibi 97.7 0.00013 2.9E-09 57.3 7.0 70 97-169 14-85 (86)
159 PF10447 EXOSC1: Exosome compo 97.7 9.1E-05 2E-09 58.8 5.9 60 262-321 2-82 (82)
160 TIGR00358 3_prime_RNase VacB a 97.7 0.00028 6.2E-09 76.9 11.2 73 96-169 569-653 (654)
161 PRK08563 DNA-directed RNA poly 97.6 0.0004 8.8E-09 63.8 9.5 77 95-173 77-169 (187)
162 PRK11642 exoribonuclease R; Pr 97.6 0.00045 9.7E-09 76.8 11.3 72 98-170 642-725 (813)
163 PTZ00162 DNA-directed RNA poly 97.6 0.00039 8.4E-09 63.4 8.7 74 262-335 79-166 (176)
164 COG0557 VacB Exoribonuclease R 97.4 0.00038 8.2E-09 76.6 8.5 73 261-333 619-704 (706)
165 TIGR02062 RNase_B exoribonucle 97.4 0.00034 7.3E-09 76.0 8.0 67 265-331 558-638 (639)
166 COG1097 RRP4 RNA-binding prote 97.4 0.00053 1.1E-08 64.6 7.9 76 260-336 60-140 (239)
167 PRK12329 nusA transcription el 97.4 0.0015 3.3E-08 66.9 11.4 72 96-174 149-228 (449)
168 COG1107 Archaea-specific RecJ- 97.4 0.00015 3.3E-09 75.4 3.9 72 259-336 117-189 (715)
169 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.3 0.0012 2.6E-08 52.9 8.2 72 262-335 4-76 (86)
170 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.3 0.002 4.3E-08 52.0 8.9 62 99-161 1-72 (88)
171 TIGR00757 RNaseEG ribonuclease 97.3 0.0006 1.3E-08 70.1 7.4 62 96-158 22-97 (414)
172 KOG1856 Transcription elongati 97.3 0.00079 1.7E-08 74.8 8.4 117 58-175 943-1063(1299)
173 PRK12328 nusA transcription el 97.2 0.0018 4E-08 65.2 10.1 67 186-254 137-207 (374)
174 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.2 0.0025 5.5E-08 51.1 8.9 73 96-171 3-75 (86)
175 PF13509 S1_2: S1 domain; PDB: 97.1 0.0023 5E-08 47.9 7.1 59 188-252 2-61 (61)
176 KOG1856 Transcription elongati 97.1 0.00046 9.9E-09 76.6 4.6 77 260-336 981-1061(1299)
177 KOG2916 Translation initiation 97.1 0.0006 1.3E-08 64.6 4.3 77 97-174 14-92 (304)
178 PTZ00162 DNA-directed RNA poly 97.1 0.0023 4.9E-08 58.4 7.9 68 187-254 81-166 (176)
179 COG1097 RRP4 RNA-binding prote 96.8 0.0065 1.4E-07 57.3 9.2 74 95-170 60-137 (239)
180 COG1107 Archaea-specific RecJ- 96.8 0.0092 2E-07 62.5 10.4 149 95-251 118-282 (715)
181 PRK10811 rne ribonuclease E; R 96.6 0.0042 9.1E-08 68.7 7.2 65 262-326 36-112 (1068)
182 PRK05054 exoribonuclease II; P 96.5 0.014 3.1E-07 63.5 10.1 63 188-250 562-642 (644)
183 PRK11712 ribonuclease G; Provi 96.4 0.0075 1.6E-07 63.3 7.1 63 260-322 34-111 (489)
184 PRK12329 nusA transcription el 96.3 0.025 5.5E-07 58.1 10.2 67 186-254 151-226 (449)
185 PF10447 EXOSC1: Exosome compo 96.2 0.02 4.3E-07 45.5 6.9 60 98-158 3-82 (82)
186 PF10246 MRP-S35: Mitochondria 96.2 0.029 6.3E-07 46.0 7.9 67 84-158 5-74 (104)
187 COG1096 Predicted RNA-binding 95.9 0.034 7.4E-07 50.6 7.9 72 96-171 61-142 (188)
188 PRK10811 rne ribonuclease E; R 95.8 0.022 4.9E-07 63.2 7.4 60 98-158 37-107 (1068)
189 PRK11712 ribonuclease G; Provi 95.8 0.021 4.5E-07 60.0 6.9 62 96-158 35-110 (489)
190 KOG3409 Exosomal 3'-5' exoribo 95.2 0.13 2.8E-06 46.2 8.6 72 262-334 66-148 (193)
191 PF08292 RNA_pol_Rbc25: RNA po 95.0 0.13 2.8E-06 44.0 7.9 62 99-160 3-76 (122)
192 COG0557 VacB Exoribonuclease R 94.9 0.1 2.2E-06 57.6 8.9 84 86-169 609-703 (706)
193 TIGR02062 RNase_B exoribonucle 94.6 0.2 4.4E-06 54.6 10.2 71 98-168 554-638 (639)
194 KOG3298 DNA-directed RNA polym 94.0 0.33 7.2E-06 43.1 8.2 64 264-327 81-155 (170)
195 COG1530 CafA Ribonucleases G a 93.7 0.095 2.1E-06 55.3 5.3 73 260-333 33-113 (487)
196 PRK12442 translation initiatio 93.2 0.53 1.1E-05 37.6 7.4 63 267-334 8-73 (87)
197 KOG3298 DNA-directed RNA polym 93.0 0.58 1.2E-05 41.6 8.2 63 96-159 78-150 (170)
198 KOG3409 Exosomal 3'-5' exoribo 92.9 0.48 1E-05 42.6 7.6 73 97-170 66-147 (193)
199 TIGR00008 infA translation ini 92.6 0.58 1.3E-05 35.8 6.7 58 267-329 6-66 (68)
200 PF08292 RNA_pol_Rbc25: RNA po 92.3 0.71 1.5E-05 39.5 7.6 56 187-242 3-76 (122)
201 KOG4078 Putative mitochondrial 91.6 1.3 2.8E-05 38.5 8.4 69 83-159 63-134 (173)
202 COG1530 CafA Ribonucleases G a 89.4 0.55 1.2E-05 49.6 5.2 73 96-169 34-112 (487)
203 PF10246 MRP-S35: Mitochondria 88.8 2 4.3E-05 35.4 6.9 53 263-322 22-75 (104)
204 PRK12442 translation initiatio 88.4 2.2 4.8E-05 34.1 6.7 64 189-252 7-72 (87)
205 TIGR00008 infA translation ini 86.6 4 8.6E-05 31.2 7.0 60 189-248 5-66 (68)
206 cd05700 S1_Rrp5_repeat_hs9 S1_ 86.0 2.4 5.1E-05 31.5 5.2 64 265-332 1-65 (65)
207 PF00313 CSD: 'Cold-shock' DNA 84.0 14 0.00031 27.4 9.1 50 103-157 1-53 (66)
208 COG0361 InfA Translation initi 82.6 8.8 0.00019 29.9 7.4 64 266-333 7-72 (75)
209 KOG1004 Exosomal 3'-5' exoribo 82.4 5.7 0.00012 37.0 7.4 63 95-159 61-123 (230)
210 PF00313 CSD: 'Cold-shock' DNA 81.0 19 0.00041 26.7 8.8 48 268-320 1-53 (66)
211 PRK09937 stationary phase/star 77.4 19 0.00041 27.9 7.8 61 269-335 3-67 (74)
212 PRK15464 cold shock-like prote 76.5 8.9 0.00019 29.4 5.7 49 191-239 5-57 (70)
213 PRK04012 translation initiatio 75.5 11 0.00023 31.2 6.3 63 265-332 20-84 (100)
214 PRK10943 cold shock-like prote 74.9 26 0.00057 26.6 8.0 51 102-157 3-56 (69)
215 PRK15464 cold shock-like prote 74.6 23 0.0005 27.1 7.6 50 103-157 5-57 (70)
216 PRK10943 cold shock-like prote 74.1 12 0.00026 28.6 5.9 50 190-239 3-56 (69)
217 COG4148 ModC ABC-type molybdat 73.8 49 0.0011 32.7 11.3 114 186-322 230-349 (352)
218 PRK09507 cspE cold shock prote 73.7 26 0.00056 26.7 7.7 51 102-157 3-56 (69)
219 PF09883 DUF2110: Uncharacteri 72.8 5.3 0.00011 37.4 4.3 83 95-180 68-157 (225)
220 cd05793 S1_IF1A S1_IF1A: Trans 72.8 14 0.00031 28.9 6.2 60 268-332 2-63 (77)
221 PRK15463 cold shock-like prote 71.4 16 0.00034 28.0 6.0 50 103-157 5-57 (70)
222 PRK09937 stationary phase/star 71.2 30 0.00064 26.8 7.6 60 104-170 3-65 (74)
223 PF03459 TOBE: TOBE domain; I 70.7 15 0.00032 26.9 5.7 47 101-155 5-57 (64)
224 PRK10354 RNA chaperone/anti-te 70.4 35 0.00077 25.9 7.8 50 103-157 5-57 (70)
225 COG4044 Uncharacterized protei 69.9 13 0.00027 34.7 6.0 84 95-178 71-167 (247)
226 PRK15463 cold shock-like prote 69.3 15 0.00032 28.2 5.5 49 191-239 5-57 (70)
227 PRK09507 cspE cold shock prote 68.8 19 0.00042 27.4 6.0 50 190-239 3-56 (69)
228 PRK09890 cold shock protein Cs 68.6 46 0.00099 25.4 8.1 50 103-157 5-57 (70)
229 cd04322 LysRS_N LysRS_N: N-ter 68.2 30 0.00066 28.4 7.7 69 267-335 3-77 (108)
230 KOG3297 DNA-directed RNA polym 67.0 12 0.00026 34.2 5.1 62 97-158 79-156 (202)
231 cd05700 S1_Rrp5_repeat_hs9 S1_ 66.3 29 0.00063 25.8 6.1 64 100-169 1-65 (65)
232 KOG1004 Exosomal 3'-5' exoribo 66.1 22 0.00047 33.3 6.8 60 262-323 63-124 (230)
233 cd04458 CSP_CDS Cold-Shock Pro 64.5 38 0.00083 24.9 6.9 49 269-321 2-54 (65)
234 PRK14998 cold shock-like prote 63.7 50 0.0011 25.5 7.5 57 104-167 3-62 (73)
235 COG4044 Uncharacterized protei 62.4 9.8 0.00021 35.4 3.8 76 260-335 71-161 (247)
236 TIGR02381 cspD cold shock doma 62.4 45 0.00098 25.2 7.0 49 104-157 3-54 (68)
237 PF08206 OB_RNB: Ribonuclease 62.0 27 0.00058 25.5 5.5 42 193-239 1-44 (58)
238 COG0361 InfA Translation initi 59.7 56 0.0012 25.5 7.0 61 190-250 8-70 (75)
239 PRK14998 cold shock-like prote 59.2 29 0.00062 26.8 5.4 49 192-240 3-55 (73)
240 KOG4078 Putative mitochondrial 59.0 24 0.00053 30.7 5.4 54 262-322 80-134 (173)
241 cd05701 S1_Rrp5_repeat_hs10 S1 58.3 17 0.00038 27.4 3.8 62 101-164 2-65 (69)
242 KOG3013 Exosomal 3'-5' exoribo 58.2 16 0.00035 35.2 4.5 39 95-133 81-119 (301)
243 PRK10676 DNA-binding transcrip 57.2 1.3E+02 0.0029 29.0 10.9 102 82-206 109-217 (263)
244 PF01938 TRAM: TRAM domain; I 55.2 42 0.00092 24.4 5.6 55 227-283 2-59 (61)
245 TIGR00638 Mop molybdenum-pteri 53.9 22 0.00047 26.3 3.9 53 266-320 7-61 (69)
246 PRK09890 cold shock protein Cs 53.2 54 0.0012 25.0 6.0 49 191-239 5-57 (70)
247 COG4776 Rnb Exoribonuclease II 52.2 5.1 0.00011 41.6 0.2 146 6-163 473-637 (645)
248 PRK10354 RNA chaperone/anti-te 51.6 55 0.0012 24.9 5.9 49 191-239 5-57 (70)
249 smart00652 eIF1a eukaryotic tr 51.3 67 0.0015 25.4 6.5 62 266-332 5-68 (83)
250 cd04456 S1_IF1A_like S1_IF1A_l 49.7 71 0.0015 25.0 6.3 60 268-332 2-64 (78)
251 COG1545 Predicted nucleic-acid 49.2 1.1E+02 0.0023 26.8 8.0 58 264-328 63-130 (140)
252 TIGR00638 Mop molybdenum-pteri 48.7 53 0.0011 24.1 5.4 48 101-156 7-60 (69)
253 PF03459 TOBE: TOBE domain; I 48.7 68 0.0015 23.2 5.9 47 266-319 5-58 (64)
254 cd03524 RPA2_OBF_family RPA2_O 47.8 85 0.0018 22.3 6.4 66 268-335 2-73 (75)
255 KOG3297 DNA-directed RNA polym 47.2 50 0.0011 30.2 5.7 55 187-241 81-157 (202)
256 cd04458 CSP_CDS Cold-Shock Pro 46.9 1.1E+02 0.0024 22.3 7.8 50 104-158 2-54 (65)
257 TIGR02381 cspD cold shock doma 46.6 45 0.00097 25.2 4.6 48 192-239 3-54 (68)
258 PF07076 DUF1344: Protein of u 45.0 1.1E+02 0.0025 22.8 6.3 55 267-330 4-58 (61)
259 COG4148 ModC ABC-type molybdat 44.2 2.5E+02 0.0055 28.0 10.3 79 98-203 230-308 (352)
260 COG1190 LysU Lysyl-tRNA synthe 43.7 2.1E+02 0.0045 30.4 10.4 86 266-351 64-164 (502)
261 TIGR00523 eIF-1A eukaryotic/ar 43.5 1E+02 0.0022 25.3 6.6 52 265-321 18-71 (99)
262 COG1278 CspC Cold shock protei 43.2 1E+02 0.0022 23.5 6.0 49 104-157 3-54 (67)
263 PF01176 eIF-1a: Translation i 41.8 34 0.00075 25.6 3.3 57 267-328 4-62 (65)
264 PRK09838 periplasmic copper-bi 41.5 1.6E+02 0.0035 24.9 7.6 68 101-171 43-113 (115)
265 PF08206 OB_RNB: Ribonuclease 41.2 72 0.0016 23.2 4.9 43 105-157 1-44 (58)
266 PF01330 RuvA_N: RuvA N termin 40.8 1.1E+02 0.0025 22.3 6.0 43 190-237 4-48 (61)
267 CHL00010 infA translation init 39.0 1.7E+02 0.0036 22.8 6.9 60 190-251 8-71 (78)
268 PRK04012 translation initiatio 38.9 1.6E+02 0.0034 24.3 7.0 64 189-253 21-86 (100)
269 PRK00276 infA translation init 38.4 1.8E+02 0.0038 22.2 7.4 61 189-249 7-69 (72)
270 TIGR00084 ruvA Holliday juncti 37.9 2.3E+02 0.0051 26.0 8.9 54 102-165 4-58 (191)
271 PRK10676 DNA-binding transcrip 37.4 1.6E+02 0.0035 28.4 8.1 117 190-321 129-255 (263)
272 COG4776 Rnb Exoribonuclease II 36.9 13 0.00027 38.8 0.3 63 186-248 560-640 (645)
273 cd04489 ExoVII_LU_OBF ExoVII_L 36.7 1.8E+02 0.0039 21.7 7.6 63 268-335 4-74 (78)
274 cd00210 PTS_IIA_glc PTS_IIA, P 36.7 63 0.0014 27.7 4.6 57 266-322 40-102 (124)
275 COG3269 Predicted RNA-binding 35.7 1.8E+02 0.0039 22.6 6.4 48 185-242 13-61 (73)
276 PRK01712 carbon storage regula 35.6 1.2E+02 0.0025 23.0 5.2 30 304-335 8-37 (64)
277 COG1278 CspC Cold shock protei 35.3 96 0.0021 23.7 4.8 48 192-239 3-54 (67)
278 PF13742 tRNA_anti_2: OB-fold 35.2 1.5E+02 0.0033 24.0 6.4 69 264-337 22-99 (99)
279 PRK14603 ruvA Holliday junctio 34.8 2.7E+02 0.0059 25.7 8.8 59 102-170 4-63 (197)
280 PTZ00329 eukaryotic translatio 34.2 1.3E+02 0.0028 26.8 6.2 63 264-332 31-95 (155)
281 PF11604 CusF_Ec: Copper bindi 32.9 2.2E+02 0.0047 21.6 7.0 63 105-170 1-67 (70)
282 TIGR00830 PTBA PTS system, glu 32.7 88 0.0019 26.7 4.7 57 266-322 40-102 (121)
283 PF07238 PilZ: PilZ domain; I 32.7 1.5E+02 0.0032 22.8 6.0 67 262-335 19-86 (102)
284 PF00358 PTS_EIIA_1: phosphoen 32.2 59 0.0013 28.2 3.7 56 268-323 46-107 (132)
285 COG2106 Uncharacterized conser 32.0 99 0.0021 30.1 5.5 49 96-158 102-150 (272)
286 KOG3013 Exosomal 3'-5' exoribo 31.5 39 0.00084 32.6 2.6 75 260-335 81-166 (301)
287 PLN00208 translation initiatio 31.3 1.6E+02 0.0034 26.0 6.2 61 264-330 31-93 (145)
288 COG3269 Predicted RNA-binding 31.3 2.4E+02 0.0051 21.9 6.4 49 261-323 12-61 (73)
289 cd05701 S1_Rrp5_repeat_hs10 S1 31.0 68 0.0015 24.3 3.3 56 267-323 3-61 (69)
290 PRK00484 lysS lysyl-tRNA synth 30.8 1.9E+02 0.004 30.8 7.9 68 266-334 57-130 (491)
291 PRK14600 ruvA Holliday junctio 30.8 3.6E+02 0.0077 24.7 8.8 46 102-157 4-50 (186)
292 cd05793 S1_IF1A S1_IF1A: Trans 30.2 2.2E+02 0.0049 22.1 6.3 61 191-252 2-64 (77)
293 PRK00276 infA translation init 29.6 2.5E+02 0.0055 21.3 7.7 60 267-330 8-69 (72)
294 PRK13605 endoribonuclease SymE 29.6 83 0.0018 26.5 3.9 42 138-184 45-88 (113)
295 PRK14605 ruvA Holliday junctio 29.6 3.9E+02 0.0085 24.5 8.9 59 102-169 4-63 (194)
296 PRK14604 ruvA Holliday junctio 29.1 3.9E+02 0.0085 24.6 8.8 56 102-166 4-60 (195)
297 PF01336 tRNA_anti-codon: OB-f 28.6 96 0.0021 22.7 4.0 67 267-335 2-72 (75)
298 PF02599 CsrA: Global regulato 28.2 61 0.0013 23.6 2.6 31 304-336 8-38 (54)
299 PF01330 RuvA_N: RuvA N termin 28.2 2.4E+02 0.0052 20.5 6.9 31 102-132 4-35 (61)
300 PF12857 TOBE_3: TOBE-like dom 28.1 1E+02 0.0022 22.3 3.9 48 266-317 5-56 (58)
301 PRK00286 xseA exodeoxyribonucl 27.9 3.2E+02 0.007 28.2 9.0 91 265-370 25-123 (438)
302 CHL00010 infA translation init 27.4 3E+02 0.0064 21.4 7.9 64 268-335 9-74 (78)
303 PRK13901 ruvA Holliday junctio 26.7 4.6E+02 0.01 24.3 8.8 53 102-164 4-57 (196)
304 PRK14601 ruvA Holliday junctio 26.4 4.4E+02 0.0095 24.1 8.5 53 102-164 4-58 (183)
305 PF11604 CusF_Ec: Copper bindi 25.9 1.6E+02 0.0035 22.3 4.8 42 236-277 2-58 (70)
306 PRK02983 lysS lysyl-tRNA synth 25.8 6.7E+02 0.015 29.6 11.8 67 267-333 655-727 (1094)
307 PF11813 DUF3334: Protein of u 25.3 53 0.0011 30.7 2.2 18 277-294 49-67 (229)
308 TIGR00499 lysS_bact lysyl-tRNA 25.0 2.7E+02 0.0059 29.6 7.9 68 266-333 56-129 (496)
309 cd04320 AspRS_cyto_N AspRS_cyt 24.9 1.8E+02 0.004 23.3 5.3 49 267-316 3-60 (102)
310 PRK14605 ruvA Holliday junctio 24.3 1.9E+02 0.0042 26.6 5.8 52 190-245 4-57 (194)
311 COG0195 NusA Transcription elo 24.0 2E+02 0.0043 26.6 5.8 45 123-174 2-47 (190)
312 TIGR00084 ruvA Holliday juncti 23.8 1.9E+02 0.0041 26.6 5.7 51 190-245 4-56 (191)
313 cd04319 PhAsnRS_like_N PhAsnRS 23.5 2.1E+02 0.0044 23.1 5.3 48 267-316 3-56 (103)
314 TIGR00458 aspS_arch aspartyl-t 23.1 2.6E+02 0.0057 29.0 7.2 69 266-335 15-91 (428)
315 PRK14604 ruvA Holliday junctio 22.8 2E+02 0.0042 26.6 5.6 51 190-244 4-56 (195)
316 COG2106 Uncharacterized conser 22.4 1.9E+02 0.0041 28.3 5.5 50 260-322 101-151 (272)
317 PF07076 DUF1344: Protein of u 22.3 3.4E+02 0.0074 20.3 7.2 45 102-155 4-48 (61)
318 PRK05585 yajC preprotein trans 22.0 3.8E+02 0.0082 22.2 6.6 33 96-128 52-90 (106)
319 cd04486 YhcR_OBF_like YhcR_OBF 21.9 1.6E+02 0.0035 22.8 4.1 54 268-332 2-68 (78)
320 COG1545 Predicted nucleic-acid 21.8 4.2E+02 0.0092 23.0 7.2 59 97-163 61-128 (140)
321 PF01176 eIF-1a: Translation i 21.8 2.4E+02 0.0052 20.9 5.0 56 190-248 4-63 (65)
322 PRK14606 ruvA Holliday junctio 21.5 5.1E+02 0.011 23.7 8.0 54 102-165 4-59 (188)
323 PF10844 DUF2577: Protein of u 20.7 4.6E+02 0.01 21.2 7.9 32 98-133 15-46 (100)
324 PF14604 SH3_9: Variant SH3 do 20.6 1.6E+02 0.0036 20.4 3.6 34 96-131 14-47 (49)
325 PRK00568 carbon storage regula 20.5 1.4E+02 0.003 23.4 3.4 30 304-335 8-37 (76)
326 PRK12445 lysyl-tRNA synthetase 20.5 3.8E+02 0.0082 28.6 7.9 69 266-334 68-142 (505)
327 TIGR00074 hypC_hupF hydrogenas 20.4 3.4E+02 0.0075 21.1 5.6 40 268-316 5-44 (76)
328 PRK14600 ruvA Holliday junctio 20.3 2.4E+02 0.0053 25.8 5.6 45 190-239 4-50 (186)
No 1
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.9e-56 Score=439.74 Aligned_cols=295 Identities=49% Similarity=0.877 Sum_probs=278.7
Q ss_pred cCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEE
Q 015066 73 TAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEE 152 (414)
Q Consensus 73 ~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~ 152 (414)
+.++.++.|++++|+++|++|++.++.|++|+|+|+++.++|+||+||++.+||||.+|+++.+..++.+. +++|+.++
T Consensus 5 ~~~~~~~~~~~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~-~~~G~~v~ 83 (318)
T PRK07400 5 NTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETRE 83 (318)
T ss_pred cCcccccCCCHHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHc-cCCCCEEE
Confidence 45667889999999999999887899999999999999999999999999999999999999888888887 89999999
Q ss_pred EEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCCccccccCCe
Q 015066 153 FVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKD 232 (414)
Q Consensus 153 v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~ 232 (414)
|+|++++++++++.||+|+......|+.+.+++..|.+++|+|++++++|+||+++|++||||.||++|....+.++|+.
T Consensus 84 ~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~~~~vG~~ 163 (318)
T PRK07400 84 FFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEE 163 (318)
T ss_pred EEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCccccCCCE
Confidence 99999999999999999998877899999999999999999999999999999999999999999999875555679999
Q ss_pred EEEEEEEeecccceEEeehhhhhhh-HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066 233 LPLKFVEVDEEQSRLVLSNRKAMAD-SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (414)
Q Consensus 233 V~vkVl~vD~e~~ri~LS~K~~l~~-~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G 311 (414)
++|+|+++|++++++.||+|+++.+ ...++++|++|.|+|++|++||+||+++|++||+|+++++|.++.++.+.|++|
T Consensus 164 i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vG 243 (318)
T PRK07400 164 LPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVN 243 (318)
T ss_pred EEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCC
Confidence 9999999999999999999987654 567899999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccCCchhhhhhHHHHHHHHHHHHHHHH
Q 015066 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAE 368 (414)
Q Consensus 312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (414)
|.|+|+|+++|.++++|.||+|+++++||+++++++.+|++|++|++++++++.++.
T Consensus 244 d~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (318)
T PRK07400 244 DEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLLAQA 300 (318)
T ss_pred CEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Confidence 999999999999999999999999999999999999999999999999999998763
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-47 Score=393.43 Aligned_cols=254 Identities=38% Similarity=0.627 Sum_probs=237.3
Q ss_pred hhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066 92 KYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (414)
Q Consensus 92 ~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~ 171 (414)
...+.+++|++|+|+|+++.+++++|++|++++|++|.+|++...... . +++|+.+++.|..+.+..+.++||+++
T Consensus 14 ~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~---~-~~~gd~v~v~v~~~e~~~g~~~lS~~k 89 (541)
T COG0539 14 KSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVED---V-VQVGDEVEVLVLRVEDGEGELVLSRRK 89 (541)
T ss_pred cchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccccc---e-ecCCCEEEEEEEEEecCCceEEeeHHH
Confidence 345689999999999999999999999999999999999998765433 2 889999999999999888999999999
Q ss_pred hhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEEeecccceEEe
Q 015066 172 IQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVL 249 (414)
Q Consensus 172 ~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~vD~e~~ri~L 249 (414)
+...++|..+++.+..|++++|+|+..+++|++|+++|++||+|.|+++.. .+...++|++++++|+++|.+++++++
T Consensus 90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~ 169 (541)
T COG0539 90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVL 169 (541)
T ss_pred HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECCEEEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEE
Confidence 999999999999999999999999999999999999999999999999977 677788999999999999999999999
Q ss_pred ehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066 250 SNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 250 S~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i 321 (414)
|+|..+.+ ..+++++|++|.|+|++|++||+||+|+|++||+|+++|||.|+.+|+++|++||+|+|+|+++
T Consensus 170 SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~ 249 (541)
T COG0539 170 SRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL 249 (541)
T ss_pred EhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEE
Confidence 99988753 2479999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCCeEEEEEeeCCCCCCcccCCchhh
Q 015066 322 DRERGRVSLSTKKLEPTPGDMIRNPKLV 349 (414)
Q Consensus 322 d~e~~ri~LS~K~~~~~p~~~~~~~~~~ 349 (414)
|++++||+||||++.++||+.+.+...+
T Consensus 250 D~e~~RVsLSlK~l~~dPw~~i~~~~~~ 277 (541)
T COG0539 250 DEERGRVSLSLKQLEEDPWEGIEKKYPV 277 (541)
T ss_pred ccCCCeEEEEehhcccCcHHHHhhhcCC
Confidence 9999999999999999999988775544
No 3
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=8.1e-46 Score=382.05 Aligned_cols=260 Identities=32% Similarity=0.538 Sum_probs=240.7
Q ss_pred CHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC
Q 015066 82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA 161 (414)
Q Consensus 82 ~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~ 161 (414)
|.++|.++++++...++.|++|+|+|++++++|++|+||++.+|+||.+|+++....++++. +++|++++|+|+++++.
T Consensus 18 ~~e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~-~~vGd~Ie~~V~~~~~~ 96 (486)
T PRK07899 18 SAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEV-VEVGDEVEALVLQKEDK 96 (486)
T ss_pred CHHHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhc-CCCCCEEEEEEEEEECC
Confidence 66788888877766799999999999999999999999999999999999999877778776 89999999999999999
Q ss_pred CCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEE
Q 015066 162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE 239 (414)
Q Consensus 162 ~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~ 239 (414)
++++.||+|++.....|..++++++.|++++|+|++++++|++|++ |++||||.|++++. .++..++|++|+|+|++
T Consensus 97 ~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~~~~~~~vGq~V~vkVle 175 (486)
T PRK07899 97 EGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIE 175 (486)
T ss_pred CCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhcccccCChhhcCCCEEEEEEEE
Confidence 9999999999988889999999998899999999999999999999 79999999999976 35566899999999999
Q ss_pred eecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066 240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (414)
Q Consensus 240 vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G 311 (414)
+|++++++.||+|..+.+ ....+++|+++.|+|+++++||+||+|+|++||||+|+++|.++.++.+.|++|
T Consensus 176 id~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvG 255 (486)
T PRK07899 176 LDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVG 255 (486)
T ss_pred EECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCC
Confidence 999999999999975432 236899999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
|.|+|+|+++|++++||.||+|++.++||+.+
T Consensus 256 d~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~ 287 (486)
T PRK07899 256 QEVTVEVLDVDMDRERVSLSLKATQEDPWQQF 287 (486)
T ss_pred CEEEEEEEEEECCCCEEEEEEeeccccchhhh
Confidence 99999999999999999999999999999754
No 4
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-45 Score=377.71 Aligned_cols=257 Identities=30% Similarity=0.447 Sum_probs=233.1
Q ss_pred HHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066 85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (414)
Q Consensus 85 ~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~ 164 (414)
+.+..|++....++.|.+|+|+|+...++|+.|++++ .+||+|.|+++..++++.. ..+|.+++++|+++|..+++
T Consensus 91 ~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~v~d~~---~~~Gk~~~~kiie~d~~~n~ 166 (541)
T COG0539 91 ERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRPVRDLD---PLIGKELEFKILELDKKRNN 166 (541)
T ss_pred HHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhccccccccc---ccCCceEEEEEEEEccccCc
Confidence 5678899988899999999999999999999999986 9999999999988776655 35899999999999999999
Q ss_pred EEEEeeehhhhHH----HHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--Cccccc--cCCeEEEE
Q 015066 165 LVLSLRMIQYELA----WERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK 236 (414)
Q Consensus 165 i~LS~k~~~~~~~----~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~--vGq~V~vk 236 (414)
+++|+|....... .+.+.+ .+.|++++|+|++++++|+||+++|++||+|.+||+|. .+|+++ +||+|+|+
T Consensus 167 vv~SrR~~~e~~~~~~r~e~~~~-l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~Vkvk 245 (541)
T COG0539 167 VVLSRRAVLEEERSEQREELLNK-LEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVK 245 (541)
T ss_pred EEEEhHHHhhHHHHHHHHHHHhc-CCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEE
Confidence 9999999876322 223433 46778999999999999999999999999999999997 456665 79999999
Q ss_pred EEEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCC
Q 015066 237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG 311 (414)
Q Consensus 237 Vl~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G 311 (414)
|+++|++++|+.||+|++..++| ..+++|+.+.|+|+++++|||||+++ |++||+|+|||||.+...|++++++|
T Consensus 246 Vi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~G 325 (541)
T COG0539 246 VISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVG 325 (541)
T ss_pred EEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccC
Confidence 99999999999999999987766 68899999999999999999999998 99999999999999988899999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccCCc
Q 015066 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNP 346 (414)
Q Consensus 312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~~~ 346 (414)
|+|.|+|+++|++++||+||+|++..+||+....+
T Consensus 326 q~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~ 360 (541)
T COG0539 326 QEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK 360 (541)
T ss_pred CEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh
Confidence 99999999999999999999999999999866554
No 5
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.8e-42 Score=366.41 Aligned_cols=264 Identities=31% Similarity=0.487 Sum_probs=239.8
Q ss_pred CCCCCCCHHHHHHHHHhhc--ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEE
Q 015066 76 MEGVSFTLEEFHSALEKYD--FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEF 153 (414)
Q Consensus 76 ~~~~~~~~~~f~~~l~~~~--~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v 153 (414)
+++..-+.++|+++++++. +.++.|++|+|+|++++++|++|++|++.+||||.+|++... ... .+++|++++|
T Consensus 5 ~~~~~~~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~---~~~-~~~vG~~i~~ 80 (565)
T PRK06299 5 AQNQNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ---GEL-EVKVGDEVEV 80 (565)
T ss_pred ccccccchHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc---ccc-cCCCCCEEEE
Confidence 3444456778999998876 568999999999999999999999999999999999998432 122 2899999999
Q ss_pred EEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccccCC
Q 015066 154 VIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEELLGK 231 (414)
Q Consensus 154 ~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~vGq 231 (414)
+|+.+++.++++.||+++......|+.+.++++.|++++|+|++++++|++|+++|++||||.+|+++.. ++..++|+
T Consensus 81 ~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~~~~~~~vG~ 160 (565)
T PRK06299 81 YVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGK 160 (565)
T ss_pred EEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCCCChHHhCCC
Confidence 9999999899999999999988999999999999999999999999999999999999999999999863 44457999
Q ss_pred eEEEEEEEeecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccC
Q 015066 232 DLPLKFVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD 303 (414)
Q Consensus 232 ~V~vkVl~vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~ 303 (414)
+++|+|+++|++++++.||+|+++.+ ...++++|+++.|+|+++.+||+||+++|++||+|+++++|.++.+
T Consensus 161 ~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~~ 240 (565)
T PRK06299 161 ELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNH 240 (565)
T ss_pred EEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccCC
Confidence 99999999999999999999987642 2468999999999999999999999999999999999999999999
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
+.+.|++||+|+|+|+++|++++++.||+|.+.++||+.+
T Consensus 241 ~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~ 280 (565)
T PRK06299 241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAI 280 (565)
T ss_pred HhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHH
Confidence 9999999999999999999999999999999999999754
No 6
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.5e-41 Score=345.68 Aligned_cols=259 Identities=35% Similarity=0.597 Sum_probs=237.9
Q ss_pred HHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC
Q 015066 83 LEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA 161 (414)
Q Consensus 83 ~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~ 161 (414)
+++|++.++... ++++|++|+|+|.+++++|++|++ +++.+|+||.+|+++....++.+. +++|+.++|+|++++.+
T Consensus 2 ~~~~~~~~~~~~-~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~-~~vGd~v~~~V~~v~~~ 79 (390)
T PRK06676 2 MEEFEESLNSVK-EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDV-VKVGDELEVYVLKVEDG 79 (390)
T ss_pred hHHHHHHhhhhh-cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccc-cCCCCEEEEEEEEEECC
Confidence 467888887544 899999999999999999999999 878999999999998777777766 89999999999999988
Q ss_pred CCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEE
Q 015066 162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE 239 (414)
Q Consensus 162 ~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~ 239 (414)
++++.||+++......|+.+.+.+..|++++|+|+++.++|+||+++|++||||.+++++. .+++.++|++++|+|++
T Consensus 80 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~ 159 (390)
T PRK06676 80 EGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIE 159 (390)
T ss_pred CCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccCCChHHcCCCEEEEEEEE
Confidence 8999999999888889999999989999999999999999999999999999999999976 34566799999999999
Q ss_pred eecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066 240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (414)
Q Consensus 240 vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G 311 (414)
+|++++++.||+|.+... ...++++|++|.|+|+++.++|+||+++|++|++|++++++.++.++.+.|++|
T Consensus 160 ~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vG 239 (390)
T PRK06676 160 LDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVG 239 (390)
T ss_pred EECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCC
Confidence 999999999999986432 236789999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
|.|+|+|+++|+++++|.||+|++.++||+.+
T Consensus 240 d~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 271 (390)
T PRK06676 240 QEVEVKVLSIDWETERISLSLKDTLPGPWEGV 271 (390)
T ss_pred CEEEEEEEEEeCCCCEEEEEEeecccCccccc
Confidence 99999999999999999999999999999754
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=4e-41 Score=350.76 Aligned_cols=247 Identities=26% Similarity=0.394 Sum_probs=223.4
Q ss_pred HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC----C
Q 015066 88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD----D 163 (414)
Q Consensus 88 ~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~----~ 163 (414)
+.|+.+...+++|++++|+|+++.++|+||+++++.+||+|.+|+++.+..++.+. |++|+.++|+|+++|.++ +
T Consensus 191 ~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~-~~vGd~i~vkVl~id~~~~~~~~ 269 (491)
T PRK13806 191 EALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA-VSVGDTVRVKVLGIERAKKGKGL 269 (491)
T ss_pred HHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh-cCCCCEEEEEEEEEecccCCcce
Confidence 45555555789999999999999999999999878999999999999888888877 899999999999999776 4
Q ss_pred eEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC---Ccccc--ccCCeEEEEE
Q 015066 164 SLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE--LLGKDLPLKF 237 (414)
Q Consensus 164 ~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~---~~~~~--~vGq~V~vkV 237 (414)
++.||+|++.. .+|..+.+.+..|++++|+|+++.++|+||+++ |++||+|.|+++|. .++.. .+||.|+|+|
T Consensus 270 ri~lS~K~~~~-~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkV 348 (491)
T PRK13806 270 RISLSIKQAGG-DPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKI 348 (491)
T ss_pred EEEEEehhhhc-ccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEE
Confidence 79999998854 689998888888999999999999999999997 99999999999984 22333 2799999999
Q ss_pred EEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCC
Q 015066 238 VEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGD 312 (414)
Q Consensus 238 l~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~ 312 (414)
+++|++++++.||+|++..+++ ..+++|++|+|+|+++++||+||++. |++||||+|+++|.+..++.+.|++||
T Consensus 349 l~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd 428 (491)
T PRK13806 349 KDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGD 428 (491)
T ss_pred EEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCC
Confidence 9999999999999998866554 57889999999999999999999997 999999999999999999999999999
Q ss_pred EEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 313 TLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 313 ~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
+|+|+|+.+|++++||+||+|++.
T Consensus 429 ~v~~~V~~id~e~~ri~Ls~~~~~ 452 (491)
T PRK13806 429 SVTLVVEEIDTAKRKISLAPAGAA 452 (491)
T ss_pred EEEEEEEEEeCCCCEEEEEeehhh
Confidence 999999999999999999999773
No 8
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=4.1e-40 Score=353.68 Aligned_cols=290 Identities=31% Similarity=0.509 Sum_probs=255.6
Q ss_pred EEEeCCcchhHHHHHHHHHHHHhhcccC-CCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeE
Q 015066 47 VAISNAETREREELNQLFEEAYERCRTA-PMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSA 125 (414)
Q Consensus 47 ~~~~~~~~~~~~~l~~iiee~~~~~~~~-~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g 125 (414)
+.|..|-..+ +.+|++++..++.. .+. ..+.+++.+.|+.....+++|++|+|+|.+++++|++|+++++.+|
T Consensus 255 vgitagaStP----~~~i~~v~~~l~~~~~~~--~~~~~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G 328 (647)
T PRK00087 255 IGVTAGASTP----DWIIEEVIKKMSELDNME--EVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEG 328 (647)
T ss_pred EEEEeccCCC----HHHHHHHHHHHHHhcccc--ccCHHHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEE
Confidence 5555555334 45666666666542 111 2345667777888778999999999999999999999999999999
Q ss_pred EEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEE
Q 015066 126 YLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVA 205 (414)
Q Consensus 126 ~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V 205 (414)
++|.+|+++....++.+. +++|+.++|+|++++++++++.||++.......|+.+.+.++.|++++|+|++++++|+||
T Consensus 329 ~lp~~els~~~~~~~~~~-~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V 407 (647)
T PRK00087 329 VIPLRELTLDEISSLKES-VKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLV 407 (647)
T ss_pred EEEHHHhcccccCChhhc-cCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEE
Confidence 999999998887777776 8999999999999998999999999999888899999999999999999999999999999
Q ss_pred EECCEEEEEeccccCCCC--ccccccCCeEEEEEEEeecccce-EEeehhhhhh--------hHHhhccccEEEEEEEEE
Q 015066 206 EVEGLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSR-LVLSNRKAMA--------DSQAQLGIGSVVIGTVQS 274 (414)
Q Consensus 206 ~i~gi~GfIp~sels~~~--~~~~~vGq~V~vkVl~vD~e~~r-i~LS~K~~l~--------~~~~~l~~G~iv~g~V~~ 274 (414)
+++|++||||.+++++.. ++..++|+.+.|+|+++|+++++ +.+|+|..+. ..++++++|++|.|+|++
T Consensus 408 ~lggi~gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~ 487 (647)
T PRK00087 408 DYGGVRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKR 487 (647)
T ss_pred EECCEEEEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEE
Confidence 999999999999999763 55567999999999999999998 9999998753 234678999999999999
Q ss_pred EeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 275 LKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 275 i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
+.++|+||+++|++|++|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||+.+
T Consensus 488 v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~ 556 (647)
T PRK00087 488 LTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENV 556 (647)
T ss_pred EeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999754
No 9
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2e-39 Score=334.66 Aligned_cols=249 Identities=27% Similarity=0.407 Sum_probs=221.4
Q ss_pred HHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 86 f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
+...|+.+...++.|++|+|+|+++.++|++|++| .+||||.+++++.+..++.+ ++|+.++|+|+++|.+++++
T Consensus 109 ~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~i 183 (486)
T PRK07899 109 YERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNV 183 (486)
T ss_pred ccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEE
Confidence 35678887766679999999999999999999994 79999999998876666553 58999999999999999999
Q ss_pred EEEeeehhh---hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--cCCeEEEEEE
Q 015066 166 VLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--LGKDLPLKFV 238 (414)
Q Consensus 166 ~LS~k~~~~---~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl 238 (414)
.||+|..+. ...|+.+...+..|++++|+|++++++|+||+++|++||||.|+++|.. ++..+ +||.|+|+|+
T Consensus 184 vLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl 263 (486)
T PRK07899 184 VLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVL 263 (486)
T ss_pred EEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEE
Confidence 999997543 3567777667788899999999999999999999999999999999863 44443 7999999999
Q ss_pred EeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCE
Q 015066 239 EVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDT 313 (414)
Q Consensus 239 ~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~ 313 (414)
++|+++++|.||+|+...+++ ..+++|++|.|+|+++.+||+||++. |++||+|++++++.++.++.+.|++||+
T Consensus 264 ~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~ 343 (486)
T PRK07899 264 DVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDE 343 (486)
T ss_pred EEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCE
Confidence 999999999999998876554 45778999999999999999999997 8999999999999999999999999999
Q ss_pred EEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066 314 LKVMILSHDRERGRVSLSTKKLEPTP 339 (414)
Q Consensus 314 V~vkVl~id~e~~ri~LS~K~~~~~p 339 (414)
|+|+|+++|++++||.||+|++.++-
T Consensus 344 V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 344 VFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred EEEEEEEEECCCCEEEEEEEEcccCC
Confidence 99999999999999999999987553
No 10
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.7e-40 Score=359.87 Aligned_cols=250 Identities=23% Similarity=0.370 Sum_probs=225.3
Q ss_pred HhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 91 EKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 91 ~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+++..++++|++|+|+|.++.++|+||+++ +.+||+|.+++++.+..++.+. +++|++++|+|+++|++++++.||+|
T Consensus 485 ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~-~kvGq~v~vkVi~iD~e~~rI~LSlK 562 (863)
T PRK12269 485 EEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREF-VKKGQTIELKVIRLDQAEKRINLSLK 562 (863)
T ss_pred HHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHh-ccCCCEEEEEEEEEecCCCeEEEEEe
Confidence 333346889999999999999999999996 5999999999999988888877 88999999999999999999999999
Q ss_pred ehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC---Cccccc--cCCeEEEEEEEeeccc
Q 015066 171 MIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDLPLKFVEVDEEQ 244 (414)
Q Consensus 171 ~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~---~~~~~~--vGq~V~vkVl~vD~e~ 244 (414)
.... .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.|+++|. .++.+. +||+|+|+|+.+|+++
T Consensus 563 ~l~~-~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~ 641 (863)
T PRK12269 563 HFQP-DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQA 641 (863)
T ss_pred cccc-chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEeccc
Confidence 8754 689998888889999999999999999999997 99999999999983 244443 7999999999999999
Q ss_pred ceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc-cCcccccCCCCEEEEEE
Q 015066 245 SRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDTLKVMI 318 (414)
Q Consensus 245 ~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vkV 318 (414)
+++.||+|++..++| ..+++|++++|+|+++++||+||+++ |++||||.|+++|.+. .++...|++||.|+|+|
T Consensus 642 ~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkV 721 (863)
T PRK12269 642 GRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMV 721 (863)
T ss_pred CceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEE
Confidence 999999999866544 57889999999999999999999997 9999999999999765 44566899999999999
Q ss_pred EEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 319 LSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 319 l~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
+++|++++||.||+|++.++||+.+
T Consensus 722 l~ID~e~rrI~LS~K~l~~dpw~~~ 746 (863)
T PRK12269 722 IECDPQARRIRLGVKQLSDNPWQVF 746 (863)
T ss_pred EEEeccCCEEEEEecccccChHHHH
Confidence 9999999999999999999999754
No 11
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=6.3e-40 Score=356.94 Aligned_cols=258 Identities=27% Similarity=0.413 Sum_probs=228.1
Q ss_pred HHHHHHHHhhcccCCCCCEEEEEEEEEe--CCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeC-
Q 015066 84 EEFHSALEKYDFNSELGTKVKGTVFCTD--NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE- 160 (414)
Q Consensus 84 ~~f~~~l~~~~~~l~~G~iV~G~V~~v~--~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~- 160 (414)
.+....|++....++.|++|+|+|++++ ++|++|+++.+.+||||.+|+......++. ..+|+.++|.|+.++.
T Consensus 383 ~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~---~~vG~~ie~~V~~~~~~ 459 (863)
T PRK12269 383 ADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE---SLIGLTSKFYIERISQS 459 (863)
T ss_pred hhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchH---HhCCCeEEEEEEEEecc
Confidence 3566789888888999999999999984 579999998889999999999766554443 3589999999999864
Q ss_pred ----CCCeEEEEeeehhhhHHHHHhhhccc---CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--c
Q 015066 161 ----ADDSLVLSLRMIQYELAWERCRQLQS---EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--L 229 (414)
Q Consensus 161 ----~~~~i~LS~k~~~~~~~~~~l~~~~~---~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--v 229 (414)
++++++||+|+...+..|+.+.+++. .|++++|+|++++++|+||+++|++||||.|+++|.. ++.+. +
T Consensus 460 ~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~kv 539 (863)
T PRK12269 460 KQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKK 539 (863)
T ss_pred cccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEchhccccccCCHHHhccC
Confidence 34689999999988888888776553 5789999999999999999999999999999999863 44443 7
Q ss_pred CCeEEEEEEEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc-ccccC
Q 015066 230 GKDLPLKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVAD 303 (414)
Q Consensus 230 Gq~V~vkVl~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~-~~~~~ 303 (414)
||+++|+|+++|++++++.||+|+...+.+ +.+++|++|+|+|+++.+||+||+++ |++||+|+|+++| .++.+
T Consensus 540 Gq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~ 619 (863)
T PRK12269 540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSK 619 (863)
T ss_pred CCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCC
Confidence 999999999999999999999998865543 57899999999999999999999997 9999999999999 57899
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccC
Q 015066 304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIR 344 (414)
Q Consensus 304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~ 344 (414)
|.+.|++||+|+|+|+++|++++|++||+|++.+|||+.+.
T Consensus 620 p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~ 660 (863)
T PRK12269 620 PSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIE 660 (863)
T ss_pred HHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHH
Confidence 99999999999999999999999999999999999998663
No 12
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2.4e-39 Score=337.45 Aligned_cols=255 Identities=30% Similarity=0.460 Sum_probs=226.0
Q ss_pred HHHHHHHHHhhcc----cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066 83 LEEFHSALEKYDF----NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 83 ~~~f~~~l~~~~~----~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
.++|+++++++.+ .++.|++|+|+|++++++|++|++|.+.+||||.+|+.... .+..+++|++++|+|+++
T Consensus 14 ~~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~----~~~~~~~G~~i~~~Vi~~ 89 (491)
T PRK13806 14 SESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD----GELTVAVGDEVELYVVSV 89 (491)
T ss_pred hHHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc----ccccccCCCEEEEEEEEE
Confidence 3579999987753 38999999999999999999999999999999999986432 122378999999999998
Q ss_pred eCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEE
Q 015066 159 NEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLK 236 (414)
Q Consensus 159 d~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vk 236 (414)
++ +.+.||++.. ....|+.+.+++..|++++|+|++++++|++|+++|++||||.||+++. .++..++|++++|+
T Consensus 90 ~~--~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~ 166 (491)
T PRK13806 90 NG--QEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFL 166 (491)
T ss_pred cC--CEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEECCEEEEEEHHHhccccCCChHHcCCCeEEEE
Confidence 74 5799997643 4578999999999999999999999999999999999999999999975 45666799999999
Q ss_pred EEEeecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccc
Q 015066 237 FVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV 307 (414)
Q Consensus 237 Vl~vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~ 307 (414)
|+.+|++++++.||+|+.+.. ....+++|++|+|+|+++.+||+||+++ |+.||||+|+++|.++.++.+.
T Consensus 167 V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~ 246 (491)
T PRK13806 167 ITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA 246 (491)
T ss_pred EEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh
Confidence 999999999999999987532 2357999999999999999999999997 8999999999999999999999
Q ss_pred cCCCCEEEEEEEEEeCCC----CeEEEEEeeCCCCCCcccC
Q 015066 308 LQPGDTLKVMILSHDRER----GRVSLSTKKLEPTPGDMIR 344 (414)
Q Consensus 308 ~~~G~~V~vkVl~id~e~----~ri~LS~K~~~~~p~~~~~ 344 (414)
|++||.|+|+|+++|+++ +||.||+|++.++||+.+.
T Consensus 247 ~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~ 287 (491)
T PRK13806 247 VSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVG 287 (491)
T ss_pred cCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhh
Confidence 999999999999999876 4899999999999997653
No 13
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.2e-38 Score=324.21 Aligned_cols=253 Identities=29% Similarity=0.447 Sum_probs=224.7
Q ss_pred HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066 88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL 167 (414)
Q Consensus 88 ~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~L 167 (414)
..|+++...++.|++++|+|+++.++|++|++++ .+||+|.+|+++.+..++.+ .+|+.++|+|+++|.+++++.|
T Consensus 94 ~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~---~vG~~v~~~Vl~~d~~~~~i~l 169 (390)
T PRK06676 94 KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSD---FKGKTLEVKIIELDPEKNRVIL 169 (390)
T ss_pred hhHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHH---cCCCEEEEEEEEEECCCCEEEE
Confidence 4577666677999999999999999999999964 69999999999877766654 3899999999999999999999
Q ss_pred Eeeehhhh---HHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--cCCeEEEEEEEe
Q 015066 168 SLRMIQYE---LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVEV 240 (414)
Q Consensus 168 S~k~~~~~---~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl~v 240 (414)
|+|..... ..|..+...+..|++++|+|+++.++|+||.+++++||||.+++++.. ++... +|+.|+|+|+++
T Consensus 170 S~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~v 249 (390)
T PRK06676 170 SRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSI 249 (390)
T ss_pred EeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEE
Confidence 99986542 467766666678899999999999999999999999999999999863 33332 799999999999
Q ss_pred ecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEE
Q 015066 241 DEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK 315 (414)
Q Consensus 241 D~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~ 315 (414)
|++++++.||+|+...+++ +++++|+++.|+|+++.+||+||++. |+.||+|+|++++.++.++.+.|++||.|+
T Consensus 250 d~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~ 329 (390)
T PRK06676 250 DWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVK 329 (390)
T ss_pred eCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEE
Confidence 9999999999998765443 57899999999999999999999997 899999999999999999999999999999
Q ss_pred EEEEEEeCCCCeEEEEEeeCCCCCCcccC
Q 015066 316 VMILSHDRERGRVSLSTKKLEPTPGDMIR 344 (414)
Q Consensus 316 vkVl~id~e~~ri~LS~K~~~~~p~~~~~ 344 (414)
|+|+++|++++++.||+|++.++||+...
T Consensus 330 v~V~~id~e~~~i~ls~k~~~~~~~~~~~ 358 (390)
T PRK06676 330 VKVLEVNEEEKRISLSIKALEEAPAEEED 358 (390)
T ss_pred EEEEEEECCCCEEEEEEEecccChhhhhh
Confidence 99999999999999999999999997653
No 14
>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=1e-38 Score=335.85 Aligned_cols=253 Identities=32% Similarity=0.533 Sum_probs=230.0
Q ss_pred HHHHHHHhh--cccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC
Q 015066 85 EFHSALEKY--DFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD 162 (414)
Q Consensus 85 ~f~~~l~~~--~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~ 162 (414)
+|+++++++ ...+++|++|+|+|++++++|++|++|++.+|+||.+|++... +. +++|++++++|++++++.
T Consensus 2 ~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~~-----~~-~~vGd~i~~~V~~~~~~~ 75 (516)
T TIGR00717 2 SFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAP-----LE-IQVGDEVEVYLDRVEDRF 75 (516)
T ss_pred hHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCCc-----cC-CCCCCEEEEEEEEEeCCC
Confidence 688888765 3468999999999999999999999999999999999997532 23 789999999999998888
Q ss_pred CeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEEe
Q 015066 163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEV 240 (414)
Q Consensus 163 ~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~v 240 (414)
+++.||+++......|..+++++..|++++|+|++++++|++|+++|++||||.+|++.. .+...++|++++|+|+++
T Consensus 76 g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~ 155 (516)
T TIGR00717 76 GETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKL 155 (516)
T ss_pred CcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEEEEECCEEEEEeHHHhcCcccCchhhhCCCEEEEEEEEE
Confidence 999999998887789999999999999999999999999999999999999999999865 244557999999999999
Q ss_pred ecccceEEeehhhhhhhH--------HhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCC
Q 015066 241 DEEQSRLVLSNRKAMADS--------QAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGD 312 (414)
Q Consensus 241 D~e~~ri~LS~K~~l~~~--------~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~ 312 (414)
|+.++++.+|+|+++.+. ...+++|++++|+|+++.++|+||+++|++|++|.++++|.++.++.+.|++||
T Consensus 156 ~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g~~g~lp~~e~s~~~~~~~~~~~~vG~ 235 (516)
T TIGR00717 156 DQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQ 235 (516)
T ss_pred ECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCCCCCCHHHhccCCC
Confidence 999999999999875432 368999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 313 TLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 313 ~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
.|.|+|+++|++++++.||+|.+.++||+.+
T Consensus 236 ~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~ 266 (516)
T TIGR00717 236 EVKVKVIKFDKEKGRISLSLKQLGEDPWEAI 266 (516)
T ss_pred EEEEEEEEEECCCCcEEEEEEecchhHHHHH
Confidence 9999999999999999999999988888643
No 15
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=9e-38 Score=331.98 Aligned_cols=251 Identities=27% Similarity=0.455 Sum_probs=226.9
Q ss_pred HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
|..+..++++|++++|+|+++.++|+||+++ +.+|++|.+|+++.+..++.+. +++|+.++|+|+++|++++++.||+
T Consensus 192 ~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~-~kvG~~v~v~V~~~d~~~~~i~lS~ 269 (565)
T PRK06299 192 REELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEV-VNVGDEVKVKVLKFDKEKKRVSLGL 269 (565)
T ss_pred HHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhc-CCCCCEEEEEEEEEeCCCCeEEEEE
Confidence 3333446889999999999999999999998 6999999999999888888877 8999999999999999999999999
Q ss_pred eehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC---cccc--ccCCeEEEEEEEeecc
Q 015066 170 RMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAEE--LLGKDLPLKFVEVDEE 243 (414)
Q Consensus 170 k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~---~~~~--~vGq~V~vkVl~vD~e 243 (414)
|.... .+|+.+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|.. ++.. .+|+.|+|+|+++|++
T Consensus 270 k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~ 348 (565)
T PRK06299 270 KQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEE 348 (565)
T ss_pred Eeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCC
Confidence 98776 689998877888999999999999999999997 999999999999752 3333 2799999999999999
Q ss_pred cceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc-cCcccccCCCCEEEEE
Q 015066 244 QSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDTLKVM 317 (414)
Q Consensus 244 ~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vk 317 (414)
++++.||+|++..+++ ..+++|++|.|+|+++.++|+||+++ +++|++|++++++.+. .++.+.|++||.|+|+
T Consensus 349 ~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~ 428 (565)
T PRK06299 349 KRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAV 428 (565)
T ss_pred CCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEE
Confidence 9999999998755433 57889999999999999999999998 8999999999999876 8899999999999999
Q ss_pred EEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 318 ILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 318 Vl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
|+++|+++++|.||+|++..+||...
T Consensus 429 Il~vd~~~~~i~ls~k~~~~~p~~~~ 454 (565)
T PRK06299 429 VLKVDVEKERISLGIKQLEEDPFEEF 454 (565)
T ss_pred EEEEeCCCCEEEEEEehhhcCchhHH
Confidence 99999999999999999999999643
No 16
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=5.9e-37 Score=322.47 Aligned_cols=252 Identities=27% Similarity=0.453 Sum_probs=224.3
Q ss_pred HHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 89 ~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
.++.....+++|++++|+|.++.++|+||++++ .+||+|.+|+++....++.+. +++|+.++|+|+++|++++++.||
T Consensus 177 ~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~~~~~~~~~-~~vG~~v~v~Vl~~d~~~~~i~lS 254 (516)
T TIGR00717 177 AREELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEY-VKVGQEVKVKVIKFDKEKGRISLS 254 (516)
T ss_pred HHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCCCCHHHh-ccCCCEEEEEEEEEECCCCcEEEE
Confidence 344444578999999999999999999999975 999999999999888888776 899999999999999999999999
Q ss_pred eeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC---cccc--ccCCeEEEEEEEeec
Q 015066 169 LRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAEE--LLGKDLPLKFVEVDE 242 (414)
Q Consensus 169 ~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~---~~~~--~vGq~V~vkVl~vD~ 242 (414)
+|.... .+|+.+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|.. ++.. .+||.++|+|+++|+
T Consensus 255 ~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~ 333 (516)
T TIGR00717 255 LKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDP 333 (516)
T ss_pred EEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcC
Confidence 998765 689988877788999999999999999999997 999999999999752 3332 389999999999999
Q ss_pred ccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-ccCcccccCCCCEEEE
Q 015066 243 EQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKV 316 (414)
Q Consensus 243 e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-~~~~~~~~~~G~~V~v 316 (414)
+++++.||+|++..+++ +.+++|+++.|+|+++.+||+||+++ |++||+|+++++|.+ ..++...|++||.|.|
T Consensus 334 ~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~ 413 (516)
T TIGR00717 334 ERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEA 413 (516)
T ss_pred CCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEE
Confidence 99999999998755443 46889999999999999999999998 899999999999975 4567788999999999
Q ss_pred EEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 317 MILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 317 kVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
+|+++|+++++|.||+|++.++||+..
T Consensus 414 ~Vl~vd~~~~~i~ls~K~~~~~p~~~~ 440 (516)
T TIGR00717 414 VVLAVDKEKKRISLGVKQLTENPWEKF 440 (516)
T ss_pred EEEEEeCcCCEEEEeeccccCCchhhh
Confidence 999999999999999999999998644
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=2.5e-35 Score=316.65 Aligned_cols=252 Identities=32% Similarity=0.496 Sum_probs=221.4
Q ss_pred HHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe-E
Q 015066 87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS-L 165 (414)
Q Consensus 87 ~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~-i 165 (414)
...|+++...+++|++++|+|+++.++|++|++++ .+||+|.+|+++.+..++.+ .+|+.++|+|+++|+++++ +
T Consensus 377 ~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~~~l 452 (647)
T PRK00087 377 EKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRRKKV 452 (647)
T ss_pred hhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCCcEE
Confidence 45677776678999999999999999999999997 99999999999877666653 3899999999999998888 9
Q ss_pred EEEeeehhh---hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--cccc-c-cCCeEEEEEE
Q 015066 166 VLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFV 238 (414)
Q Consensus 166 ~LS~k~~~~---~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~-~-vGq~V~vkVl 238 (414)
.+|+|.... ...|....+.+..|++++|+|+++.++|+||+++|++||+|.++++|.. ++.. + +|+.++++|+
T Consensus 453 ~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~ 532 (647)
T PRK00087 453 VLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYIL 532 (647)
T ss_pred EEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEE
Confidence 999988753 2334444444567899999999999999999999999999999999863 2322 2 7999999999
Q ss_pred EeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCE
Q 015066 239 EVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDT 313 (414)
Q Consensus 239 ~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~ 313 (414)
++|++++++.||+|+.+.+++ .++++|+++.|+|+++.+||+||+++ |+.||+|++++++.++.++.+.|++||.
T Consensus 533 ~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~ 612 (647)
T PRK00087 533 DIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEE 612 (647)
T ss_pred EEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCE
Confidence 999999999999998865543 56889999999999999999999997 8999999999999999999999999999
Q ss_pred EEEEEEEEeCCCCeEEEEEeeCCCCCCcc
Q 015066 314 LKVMILSHDRERGRVSLSTKKLEPTPGDM 342 (414)
Q Consensus 314 V~vkVl~id~e~~ri~LS~K~~~~~p~~~ 342 (414)
|+|+|+++|++++++.||+|++.++|++.
T Consensus 613 V~vkV~~id~e~~rI~lslk~~~~~~~~~ 641 (647)
T PRK00087 613 VKAKILEVDPEEKRIRLSIKEVEEEPGDI 641 (647)
T ss_pred EEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence 99999999999999999999999999653
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.89 E-value=5.5e-22 Score=196.15 Aligned_cols=157 Identities=21% Similarity=0.288 Sum_probs=132.7
Q ss_pred HHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC--ccccc--cCCeEEEEEEEeecccceEEee
Q 015066 176 LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVEVDEEQSRLVLS 250 (414)
Q Consensus 176 ~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl~vD~e~~ri~LS 250 (414)
..|+.+...+..|++++|+|+++.++|++|++| +.+||||.+++++.. ++.+. +|++++|+|+++|.+++++.||
T Consensus 20 ~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS 99 (318)
T PRK07400 20 ALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLS 99 (318)
T ss_pred HHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEe
Confidence 345444444678899999999999999999998 699999999999864 34443 6999999999999999999999
Q ss_pred hhhhhh-hHH----hhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC
Q 015066 251 NRKAMA-DSQ----AQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER 325 (414)
Q Consensus 251 ~K~~l~-~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~ 325 (414)
+|++.. +.| +..+.|++|.|+|+++.++|+||+++|+.||||+|+++|.+.. +. .+|+.+.|+|+.+|+++
T Consensus 100 ~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~---~~-~vG~~i~~kVl~id~~~ 175 (318)
T PRK07400 100 IRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPK---EE-LVGEELPLKFLEVDEER 175 (318)
T ss_pred hhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCc---cc-cCCCEEEEEEEEEEccc
Confidence 998642 333 2445699999999999999999999999999999999986432 33 49999999999999999
Q ss_pred CeEEEEEeeCC
Q 015066 326 GRVSLSTKKLE 336 (414)
Q Consensus 326 ~ri~LS~K~~~ 336 (414)
++|.||+|...
T Consensus 176 ~~i~lS~K~~~ 186 (318)
T PRK07400 176 NRLVLSHRRAL 186 (318)
T ss_pred CEEEEEhhHhh
Confidence 99999999653
No 19
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.83 E-value=5.3e-20 Score=200.61 Aligned_cols=246 Identities=23% Similarity=0.296 Sum_probs=206.2
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEc-CccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh-
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ- 173 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp-~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~- 173 (414)
...+|++.-|+|..+..+++.++++.+..|-.. ..++++.+..+|.+. |..++.+.+.++.++..++.+.||++...
T Consensus 1064 ~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~-f~~~~~v~~~~L~vs~~n~~leLslr~sr~ 1142 (1710)
T KOG1070|consen 1064 NPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEH-FTKIQIVYVCVLSVSALNKGLELSLRESRT 1142 (1710)
T ss_pred CCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHh-cccccEEEEEEEEEecccccceeecccccc
Confidence 445999999999999999999999999988444 447888777777776 88899999999999987777999999433
Q ss_pred ------h-hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC--ccc-cc-cCCeEEEEEEEee
Q 015066 174 ------Y-ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAE-EL-LGKDLPLKFVEVD 241 (414)
Q Consensus 174 ------~-~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~--~~~-~~-vGq~V~vkVl~vD 241 (414)
. .......+++ ..|+++.|.|..+.+.|+|+.++ ++.||+|.|++++.+ ..+ .+ +|+.+..+|+.+|
T Consensus 1143 ~~t~~~~kd~~iks~eDl-k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve 1221 (1710)
T KOG1070|consen 1143 KITPVDSKDGSIKSIEDL-KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVE 1221 (1710)
T ss_pred cCccccccCCcccchhhc-ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEee
Confidence 1 1222334444 56789999999999999999998 999999999998653 222 22 7999999999999
Q ss_pred cccceEEeehhhhhh-------hHHhhccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCC
Q 015066 242 EEQSRLVLSNRKAMA-------DSQAQLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPG 311 (414)
Q Consensus 242 ~e~~ri~LS~K~~l~-------~~~~~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G 311 (414)
+..+|+.||++..-. ....++++|+.+.|+|..+.+||.||++. ++.|++|++++++.+..+....+..|
T Consensus 1222 ~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~ 1301 (1710)
T KOG1070|consen 1222 EDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAG 1301 (1710)
T ss_pred ccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhcccceecc
Confidence 999999999998632 12368999999999999999999999998 37999999999999999999999999
Q ss_pred CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~ 343 (414)
+.|++.++.++.+++||+|.+|..--.-.++.
T Consensus 1302 ~~V~a~~lk~~~ek~rIsl~~k~s~~~~~dd~ 1333 (1710)
T KOG1070|consen 1302 DRVKACVLKEDSEKKRISLGLKSSYLSSEDDA 1333 (1710)
T ss_pred ceeeeEeeeccchhhhhhhhhhhhccCChhhh
Confidence 99999999999999999999998754433333
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=1.2e-19 Score=151.05 Aligned_cols=80 Identities=39% Similarity=0.730 Sum_probs=76.4
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p 339 (414)
.+++|++++|+|++|++|||||+|+ |-.|||||||+++.++.++.+.+++||.|+|+|+++|. +++|+||+|.++..|
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 4789999999999999999999998 79999999999999999999999999999999999997 999999999999877
Q ss_pred Cc
Q 015066 340 GD 341 (414)
Q Consensus 340 ~~ 341 (414)
-.
T Consensus 81 e~ 82 (129)
T COG1098 81 EK 82 (129)
T ss_pred cc
Confidence 64
No 21
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.77 E-value=4.8e-18 Score=185.56 Aligned_cols=221 Identities=20% Similarity=0.293 Sum_probs=187.0
Q ss_pred EEEEeCCCe-eEEEcCccccccccCCccc---cCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeE
Q 015066 115 ALVDITAKS-SAYLPTQEACIHKIKHVEE---AGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVV 190 (414)
Q Consensus 115 ~~Vdig~k~-~g~lp~sEls~~~~~~~~e---~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~i 190 (414)
++++..... .+|+...++++.++..... -.+.+|.++.+++..+-+.+..+.+|.++......+.++.+ .+-|+.
T Consensus 434 v~~~sK~pvis~y~~~~~~t~~~l~~v~q~~v~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~ 512 (1710)
T KOG1070|consen 434 VLCVSKLPVISMYADAVKLTHGMLSKVPQGMVPIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQL 512 (1710)
T ss_pred eeEeecCcceEEEeeccccCcchhhccccCCCCceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccce
Confidence 667665544 7888888877766654422 12678999999999999999999999987665555555666 477899
Q ss_pred EEEEEEEEecCcEEEEE--CCEEEEEeccccCCCC----ccccccCCeEEEEEEEeecccceEEeehhhhhhhH------
Q 015066 191 VKGKVVGANKGGVVAEV--EGLRGFVPFSQISSKS----TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS------ 258 (414)
Q Consensus 191 v~G~V~~v~~~G~~V~i--~gi~GfIp~sels~~~----~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~------ 258 (414)
|.|+|.++++.|+.|.+ +++.|++|.+|+++.. .....+|..+++||+.++.+.+++.|++|.++.+.
T Consensus 513 V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~ 592 (1710)
T KOG1070|consen 513 VPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPS 592 (1710)
T ss_pred eeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCcc
Confidence 99999999999999987 3699999999999752 22234788888899999999999999999987543
Q ss_pred -HhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 259 -QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 259 -~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
..+..+|+++.|+|.++.++||||+|. |++|+.|.+++++.++.++++.|.+||+|.|+|.++|.+++|+.+++|+..
T Consensus 593 d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~ 672 (1710)
T KOG1070|consen 593 DFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS 672 (1710)
T ss_pred chhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence 367789999999999999999999997 799999999999999999999999999999999999999999999999764
No 22
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.76 E-value=1.9e-16 Score=148.69 Aligned_cols=209 Identities=19% Similarity=0.173 Sum_probs=169.7
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCe-eEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKS-SAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~-~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
+..+|++.+..|.+..++|+|++=+... .-++|.++... ....+|+.|++.|+- +.+++++++.+....
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~--------~e~evGdev~vFiY~--D~~~rl~aTt~~p~~ 71 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEE--------DELEVGDEVTVFIYV--DSEDRLIATTREPKA 71 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcC--------CccccCcEEEEEEEE--CCCCceeheeecceE
Confidence 4679999999999999999999987654 66777775532 226789999999966 568899999886654
Q ss_pred hHHHHHhhhcccCCeEEEEEEEEEe-cCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066 175 ELAWERCRQLQSEDVVVKGKVVGAN-KGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 175 ~~~~~~l~~~~~~g~iv~G~V~~v~-~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K 252 (414)
..|+.-+++|+.++ +-|+|+++| .-+.|+|.+++....+.+..+|+.+-|. +.+|.. +|+.-.++
T Consensus 72 -----------tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~-l~~Dkk-~Ri~g~~a 138 (287)
T COG2996 72 -----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVY-LYVDKK-GRIWGTLA 138 (287)
T ss_pred -----------eecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccCCCCCCEEEEE-EEEccC-CcEEEEec
Confidence 45678899999998 789999999 8999999999997766666689999997 688965 58777665
Q ss_pred hh--hhhHHhhcc---ccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 015066 253 KA--MADSQAQLG---IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326 (414)
Q Consensus 253 ~~--l~~~~~~l~---~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ 326 (414)
.. +.+...... .|+.+.|+|+++..-|.||-++ +.-|+||.||.-. ..+.|+.++++|+.+.+ ++
T Consensus 139 ~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~--------~prlG~~l~~rVi~~re-Dg 209 (287)
T COG2996 139 IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFA--------EPRLGERLTARVIGVRE-DG 209 (287)
T ss_pred chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcc--------cccCCceEEEEEEEEcc-CC
Confidence 33 222222222 3899999999999999999998 7999999998633 45799999999999975 99
Q ss_pred eEEEEEeeCC
Q 015066 327 RVSLSTKKLE 336 (414)
Q Consensus 327 ri~LS~K~~~ 336 (414)
+|.||++.+-
T Consensus 210 ~lnLSl~p~~ 219 (287)
T COG2996 210 KLNLSLRPRA 219 (287)
T ss_pred eeeccccccc
Confidence 9999999764
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.69 E-value=4.8e-17 Score=158.86 Aligned_cols=87 Identities=23% Similarity=0.452 Sum_probs=81.0
Q ss_pred hhcc-ccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 260 AQLG-IGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 260 ~~l~-~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.++ +|++|.|+|++|.+||+||+|. |++||||+|+|||.|+.++++.+++||.|.|+|+++|+++++|.||+|++
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 3555 8999999999999999999994 89999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccCCc
Q 015066 336 EPTPGDMIRNP 346 (414)
Q Consensus 336 ~~~p~~~~~~~ 346 (414)
.++||..+...
T Consensus 92 ~~~pw~~~~e~ 102 (319)
T PTZ00248 92 SPEDIEACEEK 102 (319)
T ss_pred ccchHHHHHHh
Confidence 99999765443
No 24
>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=99.66 E-value=3.6e-16 Score=122.18 Aligned_cols=70 Identities=27% Similarity=0.393 Sum_probs=65.7
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADI---ATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~---~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
+++|++|.|+|+++++||+||+++ +++|++|+++++|.++.++ .+.|++||.|+|+|+++|+++++|.||
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 578999999999999999999998 8999999999999987775 589999999999999999999999986
No 25
>PRK08582 hypothetical protein; Provisional
Probab=99.65 E-value=1.1e-15 Score=133.71 Aligned_cols=85 Identities=32% Similarity=0.629 Sum_probs=78.3
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p 339 (414)
.+++|++|.|+|++|++||+||+|+ +++||||+|++++.++.++.+.|++||.|+|+|+++|. +++|.||+|++.++|
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 3789999999999999999999998 79999999999999999999999999999999999997 599999999999999
Q ss_pred CcccCCc
Q 015066 340 GDMIRNP 346 (414)
Q Consensus 340 ~~~~~~~ 346 (414)
|..-+.|
T Consensus 81 ~~~~~~~ 87 (139)
T PRK08582 81 KRQHDRP 87 (139)
T ss_pred hhhcccc
Confidence 9754433
No 26
>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=99.61 E-value=5e-15 Score=115.71 Aligned_cols=71 Identities=28% Similarity=0.361 Sum_probs=66.6
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP 337 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~ 337 (414)
++++|+++.|+|++|.+||+||+++ |++||+|.+++++. +.|++||.+.|+|+++|++++++.||+|++.+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 4789999999999999999999997 89999999999986 68999999999999999999999999998764
No 27
>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=99.59 E-value=5.6e-15 Score=115.06 Aligned_cols=70 Identities=31% Similarity=0.529 Sum_probs=65.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEECC--EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~g--v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
++.|+++.|+|+++.+||+||++.| .+||+|+|++++.++.++.+.|++||+|+|+|+++|.++ ++.||+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 3589999999999999999999986 699999999999999999999999999999999999876 999987
No 28
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.59 E-value=2.1e-15 Score=147.49 Aligned_cols=124 Identities=17% Similarity=0.150 Sum_probs=112.2
Q ss_pred cCC-CCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066 96 NSE-LGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (414)
Q Consensus 96 ~l~-~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~ 172 (414)
.+. +|++|.|+|+++.++|+||+|. ++.+||||.+|+++.+..++.+. +++|+++.|+|+++|++++++.||+|+.
T Consensus 13 ~~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 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKL-IRVGRHEVVVVLRVDKEKGYIDLSKKRV 91 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHh-cCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence 455 7999999999999999999995 47999999999999999999998 9999999999999999999999999998
Q ss_pred hhhHHHHHhhhcccCCeEEEEEEEEE-ecCcEEEE-------ECCEEEEEeccccCC
Q 015066 173 QYELAWERCRQLQSEDVVVKGKVVGA-NKGGVVAE-------VEGLRGFVPFSQISS 221 (414)
Q Consensus 173 ~~~~~~~~l~~~~~~g~iv~G~V~~v-~~~G~~V~-------i~gi~GfIp~sels~ 221 (414)
... +|..+.+.+..|.+++|+|..+ .++|+++. ...+++|.|..++..
T Consensus 92 ~~~-pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~ 147 (319)
T PTZ00248 92 SPE-DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALK 147 (319)
T ss_pred ccc-hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHH
Confidence 886 9999999999999999999999 55899986 247888888877653
No 29
>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=99.59 E-value=5.9e-15 Score=115.04 Aligned_cols=69 Identities=22% Similarity=0.359 Sum_probs=65.9
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~--~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
|++|.|+|+++.++|+||.++ +++|+||++++++.+ ..++.+.|++||.|+|+|+++|+++++|.||+|
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 789999999999999999997 899999999999864 889999999999999999999999999999997
No 30
>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=99.58 E-value=4.6e-15 Score=115.30 Aligned_cols=70 Identities=27% Similarity=0.495 Sum_probs=66.0
Q ss_pred ccccEEEEEEEEEEee-ceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 262 LGIGSVVIGTVQSLKP-YGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~-~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
+++|++|.|+|+++.+ ||+||++. |.+|++|+|+++++++.++.+.|++||.|+|+|+++| ++++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~--~~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKK--DGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEec--CCEEEEEeC
Confidence 4789999999999986 89999998 8999999999999999999999999999999999998 499999986
No 31
>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=99.58 E-value=6.5e-15 Score=117.51 Aligned_cols=75 Identities=33% Similarity=0.501 Sum_probs=71.4
Q ss_pred HHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 258 ~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
...++++|++|.|+|+++.+||+||+++ |++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.|||
T Consensus 8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 4567999999999999999999999997 89999999999999999999999999999999999999999999996
No 32
>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=99.58 E-value=8.6e-15 Score=113.87 Aligned_cols=73 Identities=40% Similarity=0.783 Sum_probs=70.1
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
++++|+++.|+|+++.++|+||+++ |++|+||++++++.+..++...|++||+|.|+|+++|++++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 3789999999999999999999999 999999999999999999999999999999999999999999999986
No 33
>PRK07252 hypothetical protein; Provisional
Probab=99.57 E-value=3.1e-14 Score=121.40 Aligned_cols=77 Identities=35% Similarity=0.670 Sum_probs=73.2
Q ss_pred cccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p 339 (414)
++|++|.|+|++|.++|+||+++ ++.||+|+++++++++.++.+.|++||.|+|+|+++|++++++.||+|.++++.
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 57999999999999999999997 799999999999999999999999999999999999999999999999998744
No 34
>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=99.57 E-value=1.1e-14 Score=112.14 Aligned_cols=69 Identities=32% Similarity=0.481 Sum_probs=66.4
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
|++|.|+|+++.++|+||+|+ +++||+|+++++++++.++.+.|++||.++|+|+++|++++++.||+|
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 789999999999999999998 799999999999999999999999999999999999999999999986
No 35
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=3.7e-15 Score=139.47 Aligned_cols=104 Identities=23% Similarity=0.456 Sum_probs=86.9
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 338 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~ 338 (414)
+.+|++|-|+|++|.+||+||.|. |++|++|+||++..|+.++++++++||++-|+||++|+.++.|.||||.+.++
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~ 88 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHH
Confidence 568999999999999999999995 79999999999999999999999999999999999999999999999999875
Q ss_pred CCcccCCchhhhhhHHHHHHHHHHHHH
Q 015066 339 PGDMIRNPKLVFEKAEEMAQTFRQRIA 365 (414)
Q Consensus 339 p~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (414)
--......+....+|+...+..++++.
T Consensus 89 q~~~k~~~wk~~qka~klle~aaekl~ 115 (269)
T COG1093 89 QRRKKIQEWKKEQKADKLLELAAEKLG 115 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 333333333344555655555555543
No 36
>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=99.55 E-value=2e-14 Score=111.36 Aligned_cols=68 Identities=29% Similarity=0.454 Sum_probs=64.9
Q ss_pred cEEEE-EEEEEE-eeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 265 GSVVI-GTVQSL-KPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 265 G~iv~-g~V~~i-~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
|++|. |+|+++ .+||+||++. |++||+|+|++++.+..++.+.|++||.++|+|+++|++++++.||+
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 6999999997 89999999999999999999999999999999999999999999996
No 37
>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=99.55 E-value=3.2e-14 Score=111.13 Aligned_cols=73 Identities=29% Similarity=0.531 Sum_probs=69.0
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
++.|++|.|+|+++.++|+||++. |++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|+
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 468999999999999999999995 5999999999999999999999999999999999999999999999984
No 38
>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=99.54 E-value=3.9e-14 Score=111.88 Aligned_cols=74 Identities=32% Similarity=0.627 Sum_probs=69.3
Q ss_pred cEEEEEEEEEEeeceEEEEEC----CEEEEEeecccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQISHDRV-ADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~----gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p 339 (414)
|+++.|+|+++.+||+||+++ +.+||+|++++++.+. .++.+.|++||.|+|+|+++| ++++.||+|++++++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~~~ 78 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQDT 78 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecccCC
Confidence 689999999999999999998 6899999999999986 899999999999999999999 899999999998875
Q ss_pred C
Q 015066 340 G 340 (414)
Q Consensus 340 ~ 340 (414)
+
T Consensus 79 ~ 79 (79)
T cd05684 79 G 79 (79)
T ss_pred C
Confidence 3
No 39
>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=99.54 E-value=4.3e-14 Score=109.75 Aligned_cols=72 Identities=18% Similarity=0.371 Sum_probs=68.3
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
+++|++|.|+|+++.++|+||+++ +++|++|++++++++..++.+.|++||.|+|+|+++|++++++.||+|
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 468999999999999999999998 899999999999988888889999999999999999999999999985
No 40
>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=99.54 E-value=3e-14 Score=109.49 Aligned_cols=68 Identities=32% Similarity=0.573 Sum_probs=65.3
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
|++|.|+|+++.++|+||+++ +++|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
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 789999999999999999997 89999999999999989999999999999999999999999999985
No 41
>PHA02945 interferon resistance protein; Provisional
Probab=99.53 E-value=4.1e-14 Score=111.41 Aligned_cols=74 Identities=23% Similarity=0.329 Sum_probs=69.0
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeeccc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQI--SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sel--s~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
+.+|+++.|+|+. .+||+||.|. |.+||+|+|++ +..++.+ ++.+ .||+|.|||+.+|+.++.|.||+|++.
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V~ 85 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC 85 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence 5789999999999 9999999995 79999999955 9999999 9999 999999999999999999999999986
Q ss_pred CC
Q 015066 337 PT 338 (414)
Q Consensus 337 ~~ 338 (414)
++
T Consensus 86 ~~ 87 (88)
T PHA02945 86 RH 87 (88)
T ss_pred cC
Confidence 53
No 42
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.53 E-value=2.4e-14 Score=155.71 Aligned_cols=85 Identities=27% Similarity=0.545 Sum_probs=79.0
Q ss_pred hhccccEEEE-EEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066 260 AQLGIGSVVI-GTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP 337 (414)
Q Consensus 260 ~~l~~G~iv~-g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~ 337 (414)
...++|++|. |+|++|.+||+||+|. |++||||+|+|+|+++.++.+.|++||.|+|+|+++|+ ++||.||+|++.+
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 4678999996 6999999999999998 89999999999999999999999999999999999997 7999999999999
Q ss_pred CCCcccCC
Q 015066 338 TPGDMIRN 345 (414)
Q Consensus 338 ~p~~~~~~ 345 (414)
+||+....
T Consensus 828 ~Pw~~~~~ 835 (891)
T PLN00207 828 EANSEKSS 835 (891)
T ss_pred Cchhhhhh
Confidence 99985533
No 43
>PRK05807 hypothetical protein; Provisional
Probab=99.52 E-value=6.2e-14 Score=122.22 Aligned_cols=75 Identities=37% Similarity=0.651 Sum_probs=71.8
Q ss_pred hccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
.+++|++|.|+|++|.+||+||+|++..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 367899999999999999999999989999999999999999999999999999999999997 799999999987
No 44
>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=99.51 E-value=5.4e-14 Score=107.77 Aligned_cols=67 Identities=30% Similarity=0.566 Sum_probs=64.5
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
|++|.|+|+++.++|+||+|. +++|++|++++++++..++.+.|++||.|+|+|+++|+++++|.||
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 789999999999999999998 7999999999999999999999999999999999999999999886
No 45
>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=99.50 E-value=6.8e-14 Score=107.23 Aligned_cols=67 Identities=37% Similarity=0.743 Sum_probs=63.0
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~-~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
|++|.|+|+++++||+||+|+ +++||+|+++++| .+..++.+.|++||.|+|+|+++|.++++|.||
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 789999999999999999998 8999999999996 577888999999999999999999999999885
No 46
>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=99.50 E-value=1.3e-13 Score=106.60 Aligned_cols=72 Identities=36% Similarity=0.634 Sum_probs=68.6
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
|++|.|+|+++.++|+||+++ +++|++|++++++.++.++.+.|++||.++|+|+++|++++++.||+|.++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~ 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 789999999999999999997 899999999999999999999999999999999999999999999999764
No 47
>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=99.49 E-value=1.6e-13 Score=107.19 Aligned_cols=73 Identities=40% Similarity=0.681 Sum_probs=69.1
Q ss_pred cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
++|++|.|+|+++.++|+||++. +++|++|++++++++..++.+.|++||.|+|+|+++|++++++.||+|..
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 46999999999999999999997 59999999999999988999999999999999999999999999999974
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.49 E-value=2.9e-14 Score=155.11 Aligned_cols=161 Identities=19% Similarity=0.223 Sum_probs=133.0
Q ss_pred CccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCC-CC---CCHHHH
Q 015066 11 LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEG-VS---FTLEEF 86 (414)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~-~~---~~~~~f 86 (414)
-+|.|-|...||+||| .|+.++..|.++..+|++++ ..+++|++|.-.++.+..+++ +. .+.+..
T Consensus 669 ~~~i~~pr~~~s~~aP-------~i~~~~i~~~ki~~vIG~GG----ktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i 737 (891)
T PLN00207 669 SKCSPPPSKRLSKYAP-------LIHIMKVKPEKVNMIIGSGG----KKVKSIIEETGVEAIDTQDDGTVKITAKDLSSL 737 (891)
T ss_pred HHHHhhhhhhhcccCC-------eeEEEEcCHHHHHHHhcCCc----hhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHH
Confidence 3688899999999999 89999999999999999999 889999999988844433333 22 233333
Q ss_pred HH---HHHhhcccCCCCCEEE-EEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC
Q 015066 87 HS---ALEKYDFNSELGTKVK-GTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD 162 (414)
Q Consensus 87 ~~---~l~~~~~~l~~G~iV~-G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~ 162 (414)
+. +++.+....++|+++. |+|+++.++|+||++..+.+|++|.+++++.+..++++. +++||.|+|+|+++|+ +
T Consensus 738 ~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv-~kvGD~V~VkVi~ID~-~ 815 (891)
T PLN00207 738 EKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA-FKVGDRIDVKLIEVND-K 815 (891)
T ss_pred HHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHh-cCCCCEEEEEEEEECC-C
Confidence 33 3455555789999996 699999999999999888999999999999888888887 9999999999999996 7
Q ss_pred CeEEEEeeehhhhHHHHHhhhcc
Q 015066 163 DSLVLSLRMIQYELAWERCRQLQ 185 (414)
Q Consensus 163 ~~i~LS~k~~~~~~~~~~l~~~~ 185 (414)
+++.||+|.... .+|+......
T Consensus 816 grI~LSlK~l~~-~Pw~~~~~~~ 837 (891)
T PLN00207 816 GQLRLSRRALLP-EANSEKSSQK 837 (891)
T ss_pred CcEEEEEecccc-Cchhhhhhhh
Confidence 899999998755 5898876543
No 49
>PRK08059 general stress protein 13; Validated
Probab=99.47 E-value=2.5e-13 Score=116.52 Aligned_cols=80 Identities=45% Similarity=0.787 Sum_probs=76.2
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 338 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~ 338 (414)
.++++|++|.|+|+++.++|+||+++ +++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|.+..+
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~ 82 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA 82 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence 45889999999999999999999998 79999999999999998999999999999999999999999999999999888
Q ss_pred C
Q 015066 339 P 339 (414)
Q Consensus 339 p 339 (414)
|
T Consensus 83 ~ 83 (123)
T PRK08059 83 P 83 (123)
T ss_pred c
Confidence 7
No 50
>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=99.45 E-value=3.7e-13 Score=104.18 Aligned_cols=70 Identities=36% Similarity=0.682 Sum_probs=63.9
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
+++|+++.|+|+++++||+||+|. +++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.|+
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 468999999999999999999997 89999999999875 55577788999999999999999999999875
No 51
>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=99.44 E-value=5.6e-13 Score=102.60 Aligned_cols=69 Identities=32% Similarity=0.552 Sum_probs=66.3
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
|++|.|+|.++.++|+||+++ +.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
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 789999999999999999998 799999999999999999999999999999999999988899999986
No 52
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.43 E-value=5e-13 Score=128.60 Aligned_cols=102 Identities=23% Similarity=0.421 Sum_probs=82.7
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 338 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~ 338 (414)
+++|++|.|+|++|.++|+||+|. |++|++|+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|.+.++
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~ 85 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEH 85 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecccc
Confidence 678999999999999999999996 79999999999999999999999999999999999999999999999999764
Q ss_pred CCcccCCchhhhhhHHHHHHHHHHH
Q 015066 339 PGDMIRNPKLVFEKAEEMAQTFRQR 363 (414)
Q Consensus 339 p~~~~~~~~~~~~~~~~~~~~~~~~ 363 (414)
.-......+....+++...+..+++
T Consensus 86 e~~~~~~~~~~~~~~~~il~~~a~~ 110 (262)
T PRK03987 86 QRREKIQEWKNEQKADKWLELAAEK 110 (262)
T ss_pred hHHHHHHHHHHHhhHhhHHHHHHHH
Confidence 3221112222333445555444444
No 53
>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=99.41 E-value=9.3e-13 Score=100.17 Aligned_cols=68 Identities=62% Similarity=1.024 Sum_probs=65.1
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
|+++.|+|+++.++|+||+++ +.+|++|.++++++++.++.+.|++||.|+|+|+++|+ ++++.||+|
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 789999999999999999998 89999999999999999999999999999999999998 899999986
No 54
>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=99.40 E-value=1.1e-12 Score=100.25 Aligned_cols=65 Identities=20% Similarity=0.339 Sum_probs=59.8
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
|++++|+|+++.++|+||+|. +++|++|.++++..+.. .+.|++||+|+|+|+.+|+++++|.||
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 789999999999999999996 79999999999866544 778999999999999999999999886
No 55
>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=99.40 E-value=4.5e-13 Score=110.77 Aligned_cols=73 Identities=23% Similarity=0.501 Sum_probs=66.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-------------------ccCcccccCCCCEEEEEEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-------------------VADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-------------------~~~~~~~~~~G~~V~vkVl~i 321 (414)
|++|++|.|+|+++.++|+||.|. |+.|++|++++++.+ ..++.+.|++||.|+|+|+++
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 578999999999999999999998 899999999999864 335788999999999999999
Q ss_pred eCC---CCeEEEEEee
Q 015066 322 DRE---RGRVSLSTKK 334 (414)
Q Consensus 322 d~e---~~ri~LS~K~ 334 (414)
|++ +++|.||+|.
T Consensus 81 d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 81 DKSKSGKKRIELSLEP 96 (100)
T ss_pred cCCcCCCcEEEEEecH
Confidence 997 7899999985
No 56
>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=99.39 E-value=2e-12 Score=98.77 Aligned_cols=67 Identities=34% Similarity=0.522 Sum_probs=62.3
Q ss_pred cEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 265 GSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
|++|.|+|+++.++|+||+++|++||+|.+++++.+..++.+ .+||.++|+|+++|+++++|.||.|
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 789999999999999999999999999999999988777766 4899999999999999999999976
No 57
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.39 E-value=3.3e-12 Score=99.25 Aligned_cols=73 Identities=22% Similarity=0.338 Sum_probs=68.3
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
++.|++++|+|.+++++|+||+++++.+||||.+++++.....+.+. +.+|+.++|+|+++|.+++++.||+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEV-YKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGT-CETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccc-cCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 57999999999999999999999988999999999998877777776 99999999999999999999999986
No 58
>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=99.38 E-value=1.8e-12 Score=98.52 Aligned_cols=68 Identities=47% Similarity=0.827 Sum_probs=64.9
Q ss_pred ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
+|+++.|+|+++.++|+||++++++|++|.+++++.++.++.+.|++||.|+|+|+++|++++++.||
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 48999999999999999999999999999999999888889999999999999999999999999886
No 59
>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=99.38 E-value=1.4e-12 Score=99.00 Aligned_cols=67 Identities=42% Similarity=0.746 Sum_probs=63.8
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
|++|.|+|++++++|+||+++ +.+|++|.+++++.++.++.+.|++||.++|+|+++|++++++.||
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 689999999999999999998 7999999999999988899999999999999999999999999886
No 60
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.37 E-value=7.2e-13 Score=110.68 Aligned_cols=77 Identities=18% Similarity=0.349 Sum_probs=73.4
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.+++|++++|+|+.++++||||.+.++..|++|+||+.+.+++++.+. +.+|++|.|+|+++|+ +|++.||+|.++.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~-L~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDH-LKVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHH-hcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence 578999999999999999999999999999999999999999999998 9999999999999996 9999999998765
No 61
>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=99.36 E-value=3e-12 Score=100.01 Aligned_cols=71 Identities=13% Similarity=0.134 Sum_probs=64.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCcc---ccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE---EAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~---e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
+++|++|.|+|.++.++|+||+++.+.+|++|.+++++.+..+++ +. |++|+.++|+|+++|++++++.||
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 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKY-LPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcc-cCCCCEEEEEEEEEECCCCEEecC
Confidence 478999999999999999999999899999999999998866653 45 899999999999999999998886
No 62
>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=99.33 E-value=5.8e-12 Score=95.85 Aligned_cols=67 Identities=43% Similarity=0.793 Sum_probs=63.6
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
|+++.|+|+++.++|+||+++ +.+|++|++++++.++.++.+.|++||.|+|+|+++|+ ++++.||+
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 689999999999999999998 79999999999999988899999999999999999998 89999985
No 63
>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=99.32 E-value=5e-12 Score=101.36 Aligned_cols=73 Identities=29% Similarity=0.418 Sum_probs=66.6
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH----DRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~----~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+++|++|.|+|+++.++|+||+++ +++|++|++++++ .+..++.+.|++||.++|+|+++|++ +++.||+|..
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 578999999999999999999998 8999999999986 45567788899999999999999876 9999999875
No 64
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.31 E-value=7.7e-12 Score=100.99 Aligned_cols=74 Identities=31% Similarity=0.525 Sum_probs=66.5
Q ss_pred hccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCc---ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 261 QLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~---~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
.+++|++|.|+|++|.+| |+||+++ |.+||+|+|+++| .++.++.+.+++||.|.|+|+......+--.||.+-
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~ 83 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNI 83 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEE
Confidence 567999999999999997 9999998 8999999999999 678899999999999999999988777766777653
No 65
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.30 E-value=8.9e-12 Score=133.27 Aligned_cols=92 Identities=29% Similarity=0.547 Sum_probs=75.4
Q ss_pred EEeecccceEEeehhhh--hhh-------HHh--hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccC----cccc
Q 015066 238 VEVDEEQSRLVLSNRKA--MAD-------SQA--QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----HDRV 301 (414)
Q Consensus 238 l~vD~e~~ri~LS~K~~--l~~-------~~~--~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels----~~~~ 301 (414)
++++. ++.+.++-... ... ... .+++|++|.|+|++|++||+||+|. |++||||+|+|+ +.++
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv 689 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRV 689 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCc
Confidence 45664 57776655332 111 112 4789999999999999999999997 899999999996 4689
Q ss_pred cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 302 ADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 302 ~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
.++.++|++||.|+|||+++|. ++||+|+
T Consensus 690 ~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 690 ENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred CCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 9999999999999999999995 7899986
No 66
>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=99.28 E-value=1.4e-11 Score=98.22 Aligned_cols=73 Identities=16% Similarity=0.166 Sum_probs=68.4
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
++++|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. |.+||.++|+|+++|.+++++.||+
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~-~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFG-FKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHh-cCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 689999999999999999999999988999999999998888777776 9999999999999999999999985
No 67
>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=99.27 E-value=2.1e-11 Score=94.93 Aligned_cols=70 Identities=20% Similarity=0.254 Sum_probs=64.2
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc--cCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~--~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
|++|+|+|.++.++|+||.++.+.+|+||.+++++.. ..++.+. |++|+.++|+|+++|++++++.||++
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKK-FPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHh-CCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 8999999999999999999998899999999998753 5666666 99999999999999999999999986
No 68
>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=99.27 E-value=3.6e-11 Score=93.90 Aligned_cols=71 Identities=18% Similarity=0.250 Sum_probs=63.8
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~ 173 (414)
+++.|++|.|+|.+++++|+||+++ ++.+||+|.+|+++. +. +++|+.+.|+|+++|++++++.||+++..
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------SK-LKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cc-cCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 4789999999999999999999997 579999999999854 22 78999999999999999999999998754
No 69
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.27 E-value=2.5e-11 Score=92.37 Aligned_cols=71 Identities=49% Similarity=0.869 Sum_probs=66.8
Q ss_pred cccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
++|+++.|+|.++.++|+||+++ ++.|++|.+++.+.+..++.+.|++||.++|+|++++++++++.||++
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 36999999999999999999999 899999999999988778888999999999999999998899999985
No 70
>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=99.27 E-value=2.8e-11 Score=95.92 Aligned_cols=69 Identities=25% Similarity=0.564 Sum_probs=61.8
Q ss_pred ccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
+|+++.|+|++++++|+||+++ |++|++|.++++++++. +....|++||.|+|+|+++|.+++++.|
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 3889999999999999999998 69999999999876432 4557899999999999999999999999
Q ss_pred EE
Q 015066 331 ST 332 (414)
Q Consensus 331 S~ 332 (414)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 86
No 71
>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=99.27 E-value=2.4e-11 Score=92.82 Aligned_cols=65 Identities=40% Similarity=0.776 Sum_probs=58.8
Q ss_pred CeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccccCCeEEEEEEEeecccceEEeehh
Q 015066 188 DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 188 g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~vGq~V~vkVl~vD~e~~ri~LS~K 252 (414)
|++++|+|+++.++|++|+++|++||||.+|+++.. ++...+|+.++|+|+++|.+++++.||+|
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 578999999999999999999999999999999653 44556999999999999999999999975
No 72
>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=99.26 E-value=2.6e-11 Score=93.20 Aligned_cols=70 Identities=24% Similarity=0.356 Sum_probs=64.8
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
|++++|+|.++.++|+||+++++.+||+|.++++..+..++.+. +++|+.++|+|+++|++.+++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEH-FRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHc-ccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 88999999999999999999988999999999998777777766 89999999999999999999999985
No 73
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.24 E-value=2.8e-11 Score=131.47 Aligned_cols=75 Identities=39% Similarity=0.719 Sum_probs=71.8
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
.++++|++|.|+|++|.+||+||++. |.+||+|+|+++++++.++.+.|++||.|+|+|+++|.+ +++.||+|.+
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 46889999999999999999999998 899999999999999999999999999999999999986 9999999986
No 74
>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=99.23 E-value=5.3e-11 Score=91.53 Aligned_cols=70 Identities=33% Similarity=0.444 Sum_probs=65.3
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
|++|+|+|.++.++|++|+++.+.+|++|.+|++..+..++.+. +++|+.++|+|+++++.++++.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~-~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDE-VKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHc-CCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 89999999999999999999988999999999998887777777 89999999999999988899999985
No 75
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.23 E-value=2e-11 Score=130.61 Aligned_cols=137 Identities=18% Similarity=0.160 Sum_probs=111.9
Q ss_pred CccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCC---CHHHHHHH---HHh
Q 015066 19 TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFHSA---LEK 92 (414)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~---~~~~f~~~---l~~ 92 (414)
..+|+||| -|..++..|.+..-.|++++ ..+++|+++.-..++-.++..+.. +.+..+.+ ++.
T Consensus 570 ~~~s~~aP-------~~~~~~I~~~ki~~vIG~gG----k~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~ 638 (719)
T TIGR02696 570 DEMSPYAP-------RIITVKIPVDKIGEVIGPKG----KMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINA 638 (719)
T ss_pred cccccCCC-------eeEEEEeChHHhhheeCCCc----HhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHH
Confidence 57999999 77889999999999999999 788999999877777655555532 33333333 333
Q ss_pred hcc--cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccc----ccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066 93 YDF--NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC----IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (414)
Q Consensus 93 ~~~--~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls----~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~ 166 (414)
+.. .+++|++++|+|+++.++|+||++..+.+||+|.+|++ +.+..++.+. +++||+|+|+|+++|+ ++++.
T Consensus 639 i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv-~kvGd~V~VKVl~ID~-~gKI~ 716 (719)
T TIGR02696 639 IANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LSVGQKIQVEIADIDD-RGKLS 716 (719)
T ss_pred hhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHc-CCCCCEEEEEEEEECC-CCCee
Confidence 333 47899999999999999999999988899999999996 3567788887 9999999999999994 78888
Q ss_pred EE
Q 015066 167 LS 168 (414)
Q Consensus 167 LS 168 (414)
|+
T Consensus 717 L~ 718 (719)
T TIGR02696 717 LV 718 (719)
T ss_pred ec
Confidence 75
No 76
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.23 E-value=3e-11 Score=131.18 Aligned_cols=147 Identities=16% Similarity=0.179 Sum_probs=118.6
Q ss_pred ccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCC-C---CCHHHHH
Q 015066 12 RCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGV-S---FTLEEFH 87 (414)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~-~---~~~~~f~ 87 (414)
+|-+-|-..+|+++| -+..++..|.++.-.|+.++ ..+++|+++.-..+ +.++++. . ...+..+
T Consensus 539 ~aI~~~r~~~~~~ap-------~~~~~~I~~~kI~~vIG~gg----~~ik~I~~~~~~~i-di~d~G~v~i~~~~~~~~~ 606 (693)
T PRK11824 539 EAISEPRAELSPYAP-------RIETIKIPPDKIRDVIGPGG----KTIREITEETGAKI-DIEDDGTVKIAATDGEAAE 606 (693)
T ss_pred HHhcCChhhhcccCc-------hheeecCCHHHHHHHhcCCc----hhHHHHHHHHCCcc-ccCCCceEEEEcccHHHHH
Confidence 345555666999998 67778889999999999999 88999999986644 4343333 1 2222222
Q ss_pred ---HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066 88 ---SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (414)
Q Consensus 88 ---~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~ 164 (414)
+.++.+...+++|+++.|+|+++.++|+||++..+.+|++|.+++++.+..++.+. +++||.++++|+++|+. ++
T Consensus 607 ~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v-~kvGD~V~VkV~~iD~~-gr 684 (693)
T PRK11824 607 AAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDV-LKEGDEVKVKVLEIDKR-GR 684 (693)
T ss_pred HHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccce-eCCCCEEEEEEEEECCC-Cc
Confidence 33444446789999999999999999999999988999999999999888888877 89999999999999976 99
Q ss_pred EEEEeeeh
Q 015066 165 LVLSLRMI 172 (414)
Q Consensus 165 i~LS~k~~ 172 (414)
+.||+|..
T Consensus 685 I~LS~k~~ 692 (693)
T PRK11824 685 IRLSRKAV 692 (693)
T ss_pred EEEEEEec
Confidence 99999864
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.22 E-value=1.7e-11 Score=130.39 Aligned_cols=80 Identities=38% Similarity=0.596 Sum_probs=76.4
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 338 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~ 338 (414)
.+|++|+++.|+|+++.+||+||+|+ ..+||||+|++++.++.+|.+++++||.|+|+|+++|..++||.|||+..+..
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~ 733 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEE 733 (780)
T ss_pred hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence 58999999999999999999999999 89999999999999999999999999999999999999999999999987654
Q ss_pred C
Q 015066 339 P 339 (414)
Q Consensus 339 p 339 (414)
+
T Consensus 734 ~ 734 (780)
T COG2183 734 G 734 (780)
T ss_pred c
Confidence 3
No 78
>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=7.2e-11 Score=90.61 Aligned_cols=69 Identities=28% Similarity=0.430 Sum_probs=63.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
|++++|+|+++.++|+||+++.+.+||+|.+++++.+..++.+. +++|+.++|+|+++|.+++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKK-FKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHc-CCCCCEEEEEEEEEECCCCEEEEEC
Confidence 78999999999999999999888999999999998777666665 8999999999999999999999985
No 79
>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=99.21 E-value=1.3e-10 Score=90.03 Aligned_cols=73 Identities=16% Similarity=0.142 Sum_probs=66.4
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+++|+++.|+|.++.++|+||+++.+.+|++|.+++++.+..++.+. |++||.++++|+++|..++++.||++
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 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYK-FKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccc-cCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 46899999999999999999999989999999999998776666565 89999999999999998999999975
No 80
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.19 E-value=5.4e-11 Score=124.80 Aligned_cols=97 Identities=29% Similarity=0.608 Sum_probs=83.5
Q ss_pred EEeecccceEEeehhhhh---------hhHHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccc
Q 015066 238 VEVDEEQSRLVLSNRKAM---------ADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV 307 (414)
Q Consensus 238 l~vD~e~~ri~LS~K~~l---------~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~ 307 (414)
+.++ +++.+.++..... .....++++|++|.|+|+++.+||+||.|. |-+||||+|++++.|+.+..++
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dv 663 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDV 663 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccce
Confidence 3566 6777776655421 122368999999999999999999999997 8999999999999999999999
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 308 LQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 308 ~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
+++||.|+|||+.+|+ ++|+.||+|.+.
T Consensus 664 lk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~ 691 (692)
T COG1185 664 LKEGDEVKVKVIEIDK-QGRIRLSIKAVL 691 (692)
T ss_pred eecCceEEEEEeeecc-cCCccceehhcc
Confidence 9999999999999995 799999999764
No 81
>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=99.18 E-value=9.6e-11 Score=93.13 Aligned_cols=72 Identities=26% Similarity=0.302 Sum_probs=67.9
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
+++|++|.|+|+++.+.|++|+++ +.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
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 578999999999999999999998 799999999999888888899999999999999999986 899999986
No 82
>PRK07252 hypothetical protein; Provisional
Probab=99.17 E-value=1.4e-10 Score=98.97 Aligned_cols=82 Identities=21% Similarity=0.254 Sum_probs=74.5
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhH
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYEL 176 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~ 176 (414)
+++|+++.|+|+++.++|+||+++++..|++|.+++++.+..++.+. +.+||.++|+|+++|.+.+++.||++....+.
T Consensus 1 ~kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~-~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~ 79 (120)
T PRK07252 1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQL-LKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK 79 (120)
T ss_pred CCCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhc-cCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 36899999999999999999999888999999999998877777666 89999999999999999999999999988876
Q ss_pred HHH
Q 015066 177 AWE 179 (414)
Q Consensus 177 ~~~ 179 (414)
.|.
T Consensus 80 ~~~ 82 (120)
T PRK07252 80 QHF 82 (120)
T ss_pred ccc
Confidence 664
No 83
>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=99.17 E-value=1.4e-10 Score=90.00 Aligned_cols=71 Identities=20% Similarity=0.179 Sum_probs=65.0
Q ss_pred CCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 97 SELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~-~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+++|+++.|+|.++.+ .|+||+++.+.+|++|.+++++.+..++.+. +++||.++|+|++++. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~-~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEG-FKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHh-CCCCCEEEEEEEEecC--CEEEEEeC
Confidence 4689999999999986 8999999999999999999999988888776 8999999999999974 89999985
No 84
>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=99.16 E-value=1.1e-10 Score=90.08 Aligned_cols=62 Identities=19% Similarity=0.386 Sum_probs=57.5
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVMILSHDRERG 326 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~--~~~~~~~~~~G~~V~vkVl~id~e~~ 326 (414)
|++|.|+|+++.++|+||+++ |++|++|++++++.+ ..++.+.|++||.|+|+|+++|.++.
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 789999999999999999998 899999999999874 78899999999999999999997654
No 85
>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=99.15 E-value=2.5e-10 Score=89.80 Aligned_cols=64 Identities=28% Similarity=0.553 Sum_probs=58.9
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
.++++|+.+.|+|+++++||+||++. +.+||+|.+++. +.+++||+++|+|.++ .+++++.||+
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 46889999999999999999999998 799999999963 4699999999999999 8899999986
No 86
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.15 E-value=9e-11 Score=124.99 Aligned_cols=112 Identities=21% Similarity=0.240 Sum_probs=102.2
Q ss_pred HHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc
Q 015066 58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI 137 (414)
Q Consensus 58 ~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~ 137 (414)
..+++|+.|+.++.++++.+ |...-|.+.+.+.. ++++|+++.|+|.++.++|+|||||-+.+|++|.+++++.++
T Consensus 621 ~Tl~dIi~eL~kp~rdpR~~---f~~~~~~~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv 696 (780)
T COG2183 621 PTLEDIILELEKPGRDPRDE---FHTPTLDEGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFV 696 (780)
T ss_pred chHHHHHHHhhcCCCCCccc---ccccchhhhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhc
Confidence 56899999999999999886 66666666666665 899999999999999999999999999999999999999999
Q ss_pred CCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 138 KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 138 ~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
++|.++ +++|+.|+++|+++|...+++.||++....
T Consensus 697 ~~P~~v-v~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~ 732 (780)
T COG2183 697 KDPNEV-VKVGDIVKVKVIEVDTARKRIALSMRLDEE 732 (780)
T ss_pred CChHHh-cccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence 999888 999999999999999999999999997655
No 87
>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=99.15 E-value=1.9e-10 Score=89.00 Aligned_cols=69 Identities=22% Similarity=0.233 Sum_probs=62.7
Q ss_pred CCEEE-EEEEEE-eCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 100 GTKVK-GTVFCT-DNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 100 G~iV~-G~V~~v-~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
|++++ |+|+++ .++|+||++..+.+||+|.+++++....++.+. +++|+.++++|+++|+.++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGP-FKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccc-cCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78899 999999 699999999888999999999988777776665 9999999999999999999999985
No 88
>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=99.15 E-value=1.6e-10 Score=88.35 Aligned_cols=68 Identities=18% Similarity=0.191 Sum_probs=63.3
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
|+++.|+|+++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++++|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKR-FKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhc-cCCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999988999999999998877777776 899999999999999999999876
No 89
>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=99.14 E-value=2.9e-10 Score=87.76 Aligned_cols=72 Identities=22% Similarity=0.318 Sum_probs=66.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~ 172 (414)
|+++.|+|+++.++|+||+++.+.+|++|.++++..+..++.+. |.+|+.++|+|+++|..++++.||++..
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATER-FKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHc-cCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 78999999999999999999888999999999998877777776 8999999999999999889999999864
No 90
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.14 E-value=1.5e-10 Score=106.68 Aligned_cols=93 Identities=24% Similarity=0.348 Sum_probs=78.6
Q ss_pred EEEeecccceEEeehhhhhhhHHhhccccEEEEEEEEEEeeceEEEEEC-----------CEEEEEeecccCcccccCcc
Q 015066 237 FVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIA 305 (414)
Q Consensus 237 Vl~vD~e~~ri~LS~K~~l~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~-----------gv~Glvh~sels~~~~~~~~ 305 (414)
++++|.+++++.+.- +......+++|++|.|+|+++.++|+||+|. ++.|++|.+++++.+..++.
T Consensus 40 ~~~id~~~~~Isv~P---~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~ 116 (189)
T PRK09521 40 KVFIDDINRKISVIP---FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT 116 (189)
T ss_pred EEEEcCCCCEEEEec---CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence 345677777887742 2222356789999999999999999999984 57899999999998888899
Q ss_pred cccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 306 TVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 306 ~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.|++||.|+|+|++++ +++.||+|..
T Consensus 117 ~~~~~GD~V~akV~~i~---~~i~LS~k~~ 143 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT---DPLQLSTKGK 143 (189)
T ss_pred hccCCCCEEEEEEEecC---CcEEEEEecC
Confidence 99999999999999998 7899999963
No 91
>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=99.14 E-value=1.8e-10 Score=94.94 Aligned_cols=79 Identities=30% Similarity=0.514 Sum_probs=69.2
Q ss_pred EEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEE
Q 015066 266 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD-----------IATVLQPGDTLKVMILSHDRER-----GRVS 329 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~-----------~~~~~~~G~~V~vkVl~id~e~-----~ri~ 329 (414)
++|.|+|+++.++|+||++.+++|++|+++++++++.. ....|++||.|+|+|.++|.+. +++.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence 47899999999999999999999999999999876543 3578999999999999999864 5899
Q ss_pred EEEeeCCCCCCcccC
Q 015066 330 LSTKKLEPTPGDMIR 344 (414)
Q Consensus 330 LS~K~~~~~p~~~~~ 344 (414)
||+|+-...||+.+.
T Consensus 81 ls~k~~~~g~~~~~~ 95 (99)
T cd04460 81 LTMRQPGLGKLEWIE 95 (99)
T ss_pred EEEecCCCCcHHHhh
Confidence 999999888887653
No 92
>PRK08582 hypothetical protein; Provisional
Probab=99.10 E-value=5.7e-10 Score=97.65 Aligned_cols=82 Identities=20% Similarity=0.321 Sum_probs=72.9
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE 175 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~ 175 (414)
.+++|++|.|+|+.+.++|+||+|+.+.+|++|.+++++.+..++.+. +.+|+.++|+|++++. ++++.||++++..
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~-l~vGD~VkvkV~~id~-~gkI~LSlk~~~~- 78 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDH-LKVGDEVEVKVLNVED-DGKIGLSIKKAKD- 78 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccc-cCCCCEEEEEEEEECC-CCcEEEEEEeccc-
Confidence 468999999999999999999999999999999999998888777766 8999999999999986 5899999999865
Q ss_pred HHHHH
Q 015066 176 LAWER 180 (414)
Q Consensus 176 ~~~~~ 180 (414)
.+|..
T Consensus 79 ~~~~~ 83 (139)
T PRK08582 79 RPKRQ 83 (139)
T ss_pred Cchhh
Confidence 35643
No 93
>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=99.10 E-value=7.1e-10 Score=86.43 Aligned_cols=73 Identities=22% Similarity=0.236 Sum_probs=66.6
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~ 171 (414)
+.|+++.|+|+++.++|+||++.+ +.+|++|.+++++.+..++.+. +.+||.++++|+++|...+++.||+++
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKL-VKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHe-eCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 579999999999999999999963 4899999999998888887776 899999999999999888999999874
No 94
>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=99.10 E-value=2.8e-10 Score=84.77 Aligned_cols=64 Identities=41% Similarity=0.765 Sum_probs=60.0
Q ss_pred EEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 268 v~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
+.|+|+++.++|+||+++ +.+|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
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 579999999999999998 8999999999999888888899999999999999999999999876
No 95
>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=99.09 E-value=4.6e-10 Score=85.62 Aligned_cols=66 Identities=17% Similarity=0.092 Sum_probs=58.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
|++|+|+|.++.++|++|++.+..+||+|.+|++..... .+. |++|++++|+|+++|++++++.||
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--KST-YKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccC-cCCCCEEEEEEEEEeCCCCEEecC
Confidence 799999999999999999997779999999999754333 333 899999999999999999998886
No 96
>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=99.07 E-value=9.5e-10 Score=85.71 Aligned_cols=74 Identities=19% Similarity=0.304 Sum_probs=66.6
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~ 172 (414)
++|+++.|+|.++.++|+||++.+ +.+|++|.+++++.+..++.+. |++||.++++|++++.+.+++.||+|..
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 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKL-FRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHe-ecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 469999999999999999999984 7999999999998776666665 8999999999999999999999999864
No 97
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.04 E-value=7.9e-09 Score=97.75 Aligned_cols=148 Identities=19% Similarity=0.162 Sum_probs=115.1
Q ss_pred cCCCCCEEEEEEEEEe-CCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 96 NSELGTKVKGTVFCTD-NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~-~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.+.+|+.=.++|+.++ +.|+|||+|-..+.++|.+|+.....-+ +++|+++-|.+.- | .++++..+++.-..
T Consensus 70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~w-----pq~Gd~l~v~l~~-D-kk~Ri~g~~a~~~~ 142 (287)
T COG2996 70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLW-----PQKGDKLLVYLYV-D-KKGRIWGTLAIEKI 142 (287)
T ss_pred eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccC-----CCCCCEEEEEEEE-c-cCCcEEEEecchhH
Confidence 5678999999999999 7899999999899999999986432222 4689999888754 3 56788877754332
Q ss_pred hHHHHHhhhccc--CCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeeh
Q 015066 175 ELAWERCRQLQS--EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN 251 (414)
Q Consensus 175 ~~~~~~l~~~~~--~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~ 251 (414)
-|........ .++.+.|+|.+....|.||-++ ++.||||.|+.-... .+|+.++++|+.+.+ +++|.||.
T Consensus 143 --l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p----rlG~~l~~rVi~~re-Dg~lnLSl 215 (287)
T COG2996 143 --LENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAEP----RLGERLTARVIGVRE-DGKLNLSL 215 (287)
T ss_pred --HHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcccc----cCCceEEEEEEEEcc-CCeeeccc
Confidence 1222222222 2568999999999999999886 999999999976543 389999999999986 89999999
Q ss_pred hhhhhh
Q 015066 252 RKAMAD 257 (414)
Q Consensus 252 K~~l~~ 257 (414)
++...+
T Consensus 216 ~p~~~E 221 (287)
T COG2996 216 RPRAHE 221 (287)
T ss_pred ccccHH
Confidence 986433
No 98
>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=99.03 E-value=1.7e-09 Score=84.10 Aligned_cols=70 Identities=24% Similarity=0.305 Sum_probs=62.5
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
+.|+++.|+|+++.++|+||++.+ +.+|++|.+++++....++.+. +++||+++++|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~-~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEV-VDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhE-ECCCCEEEEEEEEECCCC-cEEEEe
Confidence 589999999999999999999954 3799999999998887777776 899999999999999765 888886
No 99
>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=99.03 E-value=1.4e-09 Score=82.45 Aligned_cols=69 Identities=22% Similarity=0.355 Sum_probs=63.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
|+++.|+|.++.++|+||+++.+.+||+|.++++..+..++.+. +.+|+.++++|++++. ++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDV-LKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHc-cCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 78999999999999999999988999999999998777777665 8999999999999998 899999975
No 100
>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=99.03 E-value=7.9e-10 Score=91.41 Aligned_cols=76 Identities=14% Similarity=0.164 Sum_probs=66.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-------------------CccccCccCCcEEEEEEEE
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-------------------HVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-------------------~~~e~~~~vG~~v~v~Vl~ 157 (414)
+++|++|.|+|.++.+.|++|+++++.+||+|.+++++.+.. ++.+. |++||.+.|+|++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-f~vGd~V~~kVi~ 79 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDL-FSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHh-ccCCCEEEEEEEE
Confidence 478999999999999999999999899999999999876522 24455 8999999999999
Q ss_pred EeCC---CCeEEEEeeehh
Q 015066 158 ENEA---DDSLVLSLRMIQ 173 (414)
Q Consensus 158 id~~---~~~i~LS~k~~~ 173 (414)
+++. ++++.||+|+..
T Consensus 80 ~d~~~~~~~~i~LSlr~~~ 98 (100)
T cd05693 80 LDKSKSGKKRIELSLEPEL 98 (100)
T ss_pred ccCCcCCCcEEEEEecHHH
Confidence 9987 789999998754
No 101
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.02 E-value=1.5e-09 Score=86.22 Aligned_cols=75 Identities=21% Similarity=0.198 Sum_probs=66.9
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~ 172 (414)
..++|++|.|+|+++.+++++|+++.+.+|++|.++++.....+..+. +++|+.+.|+|+++++. +++.||++..
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKS-LQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhc-CCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 458999999999999999999999999999999999987666666665 89999999999999876 8999999763
No 102
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.02 E-value=1.2e-09 Score=87.47 Aligned_cols=75 Identities=21% Similarity=0.166 Sum_probs=64.5
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc----cccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~----~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~ 171 (414)
.+++|++|.|+|+++.++|++|+++.+.+|++|.++++. ....+..+. +++|+.+.|+|++++++ +++.||++.
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~-l~vGd~i~~~V~~~~~~-~~i~LS~~~ 80 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSY-LDEGDLIVAEVQSVDSD-GSVSLHTRS 80 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhh-CCCCCEEEEEEEEECCC-CCEEEEeCc
Confidence 468999999999999999999999999999999999974 233344444 89999999999999865 899999987
Q ss_pred h
Q 015066 172 I 172 (414)
Q Consensus 172 ~ 172 (414)
.
T Consensus 81 ~ 81 (86)
T cd05789 81 L 81 (86)
T ss_pred c
Confidence 5
No 103
>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=99.00 E-value=5.2e-10 Score=121.36 Aligned_cols=141 Identities=15% Similarity=0.157 Sum_probs=113.9
Q ss_pred cCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCC---CHHHHH--
Q 015066 13 CPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFH-- 87 (414)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~---~~~~f~-- 87 (414)
|-+-+...+|+||| -+..++..|.+..-+|++++ +.+++|+++.-..++-..++.+.. ..+...
T Consensus 537 ~l~~~~~~~~~~~p-------~~~~~~I~~~kI~~vIG~gG----k~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a 605 (684)
T TIGR03591 537 VISEPRAELSPYAP-------RIETIKINPDKIRDVIGPGG----KVIREITEETGAKIDIEDDGTVKIAASDGEAAEAA 605 (684)
T ss_pred HHhhhhccccccCC-------eEEEEecCHHHHHhhcCCCc----HHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHH
Confidence 34445667999999 77888999999999999999 788999999877776544444422 222233
Q ss_pred -HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066 88 -SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (414)
Q Consensus 88 -~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~ 166 (414)
+.++.+...+++|+++.|+|+++.++|+||++..+.+||+|.+++++.+..++.+. +++||.+.++|+++|. .+++.
T Consensus 606 ~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~-~kvGD~V~VkVi~id~-~gki~ 683 (684)
T TIGR03591 606 IKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDV-LKEGDEVKVKVLEIDK-QGRIK 683 (684)
T ss_pred HHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhc-cCCCCEEEEEEEEECC-CCCcc
Confidence 33344445679999999999999999999999888999999999999888888887 8999999999999986 56654
No 104
>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=99.00 E-value=1.2e-09 Score=118.54 Aligned_cols=70 Identities=39% Similarity=0.750 Sum_probs=65.8
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
..+++|++|.|+|++|.+||+||++. |.+||+|+|++++.++.++.+.|++||.|+|+|+++|. ++++.|
T Consensus 614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 46789999999999999999999997 89999999999999999999999999999999999997 788765
No 105
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.99 E-value=2.9e-09 Score=80.83 Aligned_cols=72 Identities=28% Similarity=0.422 Sum_probs=64.4
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+.|+++.|+|.++.++|++|+++.+..|++|.+++...+..++.+. +++|+.+.++|++++..++++.+|++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 4699999999999999999999988999999999987765555555 89999999999999988899999975
No 106
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.99 E-value=1.5e-09 Score=112.52 Aligned_cols=116 Identities=13% Similarity=0.262 Sum_probs=90.9
Q ss_pred EEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhh---------HHhhcc--ccEEEEEEEEEEeece
Q 015066 211 RGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD---------SQAQLG--IGSVVIGTVQSLKPYG 279 (414)
Q Consensus 211 ~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~---------~~~~l~--~G~iv~g~V~~i~~~G 279 (414)
.++|+.++.-.. ++...+|+.+.+.|...+. .+....+.|+.+.. ..+.++ .|++|+|+|.++.++|
T Consensus 72 ~~eI~L~eAk~~-~~~~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~g 149 (470)
T PRK09202 72 TKEISLEEARKI-DPDAEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGN 149 (470)
T ss_pred cceeeHHHHhhh-CccccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCC
Confidence 366777665432 4555699999999988873 22333334444321 235676 8999999999999999
Q ss_pred EEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEee
Q 015066 280 AFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLSTKK 334 (414)
Q Consensus 280 ~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS~K~ 334 (414)
+||+++|++|++|.++++ |.+.|++||+|+|+|++++++++ +|.||.+.
T Consensus 150 iiVDLggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 150 IIVDLGRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred EEEEECCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 999999999999999985 67889999999999999999877 89999874
No 107
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.99 E-value=7.7e-10 Score=112.93 Aligned_cols=81 Identities=28% Similarity=0.551 Sum_probs=75.5
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 338 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~ 338 (414)
.++..|.+|+|+|+++.+||+||+|. +..||+|+||++.+++.+|++.+.+||.|.||.+..|+ ++.+.||-|.+.|+
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ralLp~ 742 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRALLPD 742 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhhhcCC
Confidence 47889999999999999999999998 89999999999999999999999999999999999997 77788888889888
Q ss_pred CCc
Q 015066 339 PGD 341 (414)
Q Consensus 339 p~~ 341 (414)
|.-
T Consensus 743 p~~ 745 (760)
T KOG1067|consen 743 PAT 745 (760)
T ss_pred ccc
Confidence 754
No 108
>PRK05807 hypothetical protein; Provisional
Probab=98.99 E-value=3e-09 Score=92.77 Aligned_cols=75 Identities=20% Similarity=0.312 Sum_probs=68.3
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~ 173 (414)
.+++|++|+|+|+.+.++|+||++. +..|++|.+++++.+..++.+. +.+|+.++|+|++++. ++++.||++.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~-~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREH-LKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCcccc-CCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 3678999999999999999999995 5899999999999888887776 8999999999999987 799999999865
No 109
>PRK08059 general stress protein 13; Validated
Probab=98.98 E-value=3.3e-09 Score=91.03 Aligned_cols=78 Identities=19% Similarity=0.300 Sum_probs=71.1
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.+++|+++.|+|+++.++|+||+++.+.+|++|.++++..+..++.+. +.+|+.++|+|+++|.+++++.||++....
T Consensus 4 ~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~-~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDF-LSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred cCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHc-CCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 478999999999999999999999988999999999988777666665 899999999999999999999999998755
No 110
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.96 E-value=6.4e-10 Score=116.83 Aligned_cols=144 Identities=15% Similarity=0.188 Sum_probs=120.3
Q ss_pred CCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCCCHHH------HHHH
Q 015066 16 ISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE------FHSA 89 (414)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~~~~~------f~~~ 89 (414)
-|.+-||+||| =|.-++..+.+..-.|++++ +.+++|+++.-..+...+++.+..+..+ -.+.
T Consensus 541 ~pr~els~~aP-------ri~t~~i~~dKI~dvIG~gG----k~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~ 609 (692)
T COG1185 541 EPRKELSPYAP-------RIETIKIDPDKIRDVIGPGG----KTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKER 609 (692)
T ss_pred hhhhhhhccCC-------ceEEEccCHHHHhhccCCcc----cchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHH
Confidence 34455999999 67788999999999999999 7788999998888876655555333322 1233
Q ss_pred HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
++.....+++|+++.|+|+++.++|+||.+..+.+|++|.++++.....++++. +++||.+.++|+.+| ..|++.||+
T Consensus 610 I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dv-lk~Gd~v~Vkv~~iD-~~Gri~ls~ 687 (692)
T COG1185 610 IEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDV-LKEGDEVKVKVIEID-KQGRIRLSI 687 (692)
T ss_pred HHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccce-eecCceEEEEEeeec-ccCCcccee
Confidence 455567899999999999999999999999999999999999999988888887 899999999999998 578999999
Q ss_pred eeh
Q 015066 170 RMI 172 (414)
Q Consensus 170 k~~ 172 (414)
+..
T Consensus 688 ~~~ 690 (692)
T COG1185 688 KAV 690 (692)
T ss_pred hhc
Confidence 764
No 111
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.95 E-value=2.9e-09 Score=81.33 Aligned_cols=68 Identities=18% Similarity=0.317 Sum_probs=60.3
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc-cccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~-~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
|+++.|+|.++.++|+||++..+.+|++|.+++++ ....++.+. |++||.++++|+++|.+++++.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~-~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEI-YKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhE-ECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999988999999999984 445566555 899999999999999999988775
No 112
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.95 E-value=2.2e-09 Score=111.25 Aligned_cols=122 Identities=14% Similarity=0.109 Sum_probs=90.1
Q ss_pred eeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHH-----HHhhhccc--CCeEEEEEE
Q 015066 123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAW-----ERCRQLQS--EDVVVKGKV 195 (414)
Q Consensus 123 ~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~-----~~l~~~~~--~g~iv~G~V 195 (414)
..+.++.+++... ++ .+.+|+.+++.|...+ -+++.++..+......| +.+.+.+. .|++++|+|
T Consensus 71 ~~~eI~L~eAk~~---~~---~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V 142 (470)
T PRK09202 71 PTKEISLEEARKI---DP---DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVV 142 (470)
T ss_pred CcceeeHHHHhhh---Cc---cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEE
Confidence 3466776666322 22 2689999999998765 44444443332222333 35555565 789999999
Q ss_pred EEEecCcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccc--eEEeehhhh
Q 015066 196 VGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS--RLVLSNRKA 254 (414)
Q Consensus 196 ~~v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~--ri~LS~K~~ 254 (414)
.+++++|++|++||+.||||.+++..... ..+|++++|+|++++++++ +|.||++..
T Consensus 143 ~ri~~~giiVDLggvea~LP~sE~ip~E~--~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 143 KRVERGNIIVDLGRAEAILPRKEQIPREN--FRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred EEEecCCEEEEECCeEEEecHHHcCCCcc--CCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 99999999999999999999999973322 2389999999999999877 899999865
No 113
>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=98.94 E-value=3.7e-09 Score=80.01 Aligned_cols=68 Identities=24% Similarity=0.316 Sum_probs=61.9
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
|+++.|+|.++.++|+||+++.+.+|++|.+++++.+..++.+. +++|+.++|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~-~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDV-VSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHh-cCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999988999999999988776666655 899999999999999888988876
No 114
>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=98.92 E-value=5.5e-09 Score=79.21 Aligned_cols=68 Identities=24% Similarity=0.331 Sum_probs=61.4
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
+|+++.|+|.++.++|+||+++ +.+|++|.+++++.+..++.+. |++|+.++|+|++++.+++++.||
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-GVDGLLHISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHE-ECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999998 5999999999987777666666 899999999999999988998876
No 115
>PHA02945 interferon resistance protein; Provisional
Probab=98.91 E-value=8.8e-09 Score=81.43 Aligned_cols=73 Identities=15% Similarity=0.232 Sum_probs=65.5
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccc--cccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066 97 SELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEA--CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEl--s~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~ 172 (414)
.++|+++-|+|.. .++|+||++. ++.+||||.+|. +..++++ .+. + +|+++-|+|+++|+.+|.+-||+|+.
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~-l-~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDK-L-VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeE-e-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 3789999999999 9999999993 469999999965 9888888 776 6 99999999999999999999999975
Q ss_pred h
Q 015066 173 Q 173 (414)
Q Consensus 173 ~ 173 (414)
.
T Consensus 85 ~ 85 (88)
T PHA02945 85 C 85 (88)
T ss_pred c
Confidence 3
No 116
>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=98.90 E-value=8.8e-09 Score=78.73 Aligned_cols=63 Identities=22% Similarity=0.427 Sum_probs=55.5
Q ss_pred cccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEE
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLS 331 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS 331 (414)
..|++|+|+|.++.++|+||++++.+|++|.++++. .+.|++||.|+|.|++++.++ ..|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 469999999999999999999999999999999863 457899999999999999654 467777
No 117
>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=98.88 E-value=9.1e-09 Score=78.06 Aligned_cols=68 Identities=21% Similarity=0.312 Sum_probs=61.7
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
|+++.|+|.++.++|+||+++.+..||+|.++++..+..++.+. +.+|+.+.++|+++|+ .+++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDV-LKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHc-cCCCCEEEEEEEEECC-CCcEEeeC
Confidence 78999999999999999999988999999999988777666665 8999999999999998 88999885
No 118
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.87 E-value=9.5e-09 Score=99.07 Aligned_cols=88 Identities=20% Similarity=0.279 Sum_probs=77.0
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.++|++|.|+|.++.++|+||++.. +.+||+|.+|++..+..++.+. +++|+.+.|+|+++|..++++.||++....
T Consensus 6 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 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDH-VKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHh-CCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 5789999999999999999999964 6899999999998888887776 899999999999999999999999998877
Q ss_pred hHHHHHhhhcc
Q 015066 175 ELAWERCRQLQ 185 (414)
Q Consensus 175 ~~~~~~l~~~~ 185 (414)
...|+.+.+..
T Consensus 85 ~e~~~~~~~~~ 95 (262)
T PRK03987 85 HQRREKIQEWK 95 (262)
T ss_pred chHHHHHHHHH
Confidence 66666555443
No 119
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.86 E-value=1.4e-08 Score=78.42 Aligned_cols=71 Identities=18% Similarity=0.240 Sum_probs=60.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc-ccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~-~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
+.+|+++.|+|.++.++|+||++..+.+|++|.+++.+. ...++.+. +++||.++|+|+++|.+++++.||
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999999999999999999998889999999999753 22344444 899999999999999888888764
No 120
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.86 E-value=1.8e-08 Score=79.33 Aligned_cols=72 Identities=15% Similarity=0.271 Sum_probs=63.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeC---CCeeEEEcCcccccccc-CCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 100 GTKVKGTVFCTDNRGALVDIT---AKSSAYLPTQEACIHKI-KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig---~k~~g~lp~sEls~~~~-~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
|+++.|+|.++.++|+||+++ .+.+|++|.+++++.+. .++.+. |++|+.++++|+++| .+++.+|++....
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 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDV-VKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhe-eCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 789999999999999999998 35899999999988765 666666 899999999999998 7999999987543
No 121
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.85 E-value=1.6e-09 Score=110.59 Aligned_cols=151 Identities=13% Similarity=0.083 Sum_probs=119.0
Q ss_pred CccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCC---CCCHHHHH
Q 015066 11 LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGV---SFTLEEFH 87 (414)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~---~~~~~~f~ 87 (414)
-||.|.|..++++|.| ++..++++|.+.+..|++++ ..+|.|..|.- .+....++.+ ..+...++
T Consensus 581 ~k~i~~Pr~~~~~y~P-------~~~tlkv~~sk~~~lIGp~G----~~~kki~~EtG-ai~~vDe~t~~i~A~~~~am~ 648 (760)
T KOG1067|consen 581 EKNINSPRGSDKEYSP-------VLETLKVSPSKRATLIGPGG----VLKKKIEVETG-AISQVDEGTFSIFAPTQAAME 648 (760)
T ss_pred HhhcCCcccCccccCc-------eeeEEeecchhhheeecCcc----ceeeeEeeecc-ceeeecCceEEEEecCHHHHH
Confidence 4899999999999999 99999999999999999999 45566666644 3333222222 23333333
Q ss_pred HH---HHhhc-----ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066 88 SA---LEKYD-----FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159 (414)
Q Consensus 88 ~~---l~~~~-----~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id 159 (414)
++ ++.+. .+++.|-+.+++|+++.+.|+||.+.....|++|.+||+..++.++++. +.+||+|+++.++.|
T Consensus 649 ~Ak~~I~~i~~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~-levGq~I~vk~ie~d 727 (760)
T KOG1067|consen 649 EAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDL-LEVGQEIQVKYIERD 727 (760)
T ss_pred HHHHHHHHHhcCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHH-HhhcceeEEEEEeec
Confidence 33 33222 3678899999999999999999999999999999999999999999999 999999999999998
Q ss_pred CCCCeEEEEeeehhhh
Q 015066 160 EADDSLVLSLRMIQYE 175 (414)
Q Consensus 160 ~~~~~i~LS~k~~~~~ 175 (414)
+ .+.+.+|.|+.+..
T Consensus 728 ~-~g~~~ls~ralLp~ 742 (760)
T KOG1067|consen 728 P-RGGIMLSSRALLPD 742 (760)
T ss_pred C-ccceeehhhhhcCC
Confidence 6 45567777766653
No 122
>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=98.84 E-value=1.8e-08 Score=92.14 Aligned_cols=82 Identities=28% Similarity=0.515 Sum_probs=69.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEe-----CCC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHD-----RER 325 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id-----~e~ 325 (414)
..+|+++.|+|++++++|+||+++.++|++|.+++.+++.. +....|+.||.|+++|+++| ++.
T Consensus 79 p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~ 158 (179)
T TIGR00448 79 PELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEG 158 (179)
T ss_pred ccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCc
Confidence 44799999999999999999999889999999999866432 23467999999999999998 667
Q ss_pred CeEEEEEeeCCCCCCccc
Q 015066 326 GRVSLSTKKLEPTPGDMI 343 (414)
Q Consensus 326 ~ri~LS~K~~~~~p~~~~ 343 (414)
.+|.||||+--.-|.+.+
T Consensus 159 ~~I~lt~k~~~LG~~~w~ 176 (179)
T TIGR00448 159 SKIGLTMRQPLLGKLEWI 176 (179)
T ss_pred ceEEEEeccCcCCccccc
Confidence 899999998776666554
No 123
>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=98.84 E-value=1.7e-08 Score=77.09 Aligned_cols=64 Identities=25% Similarity=0.336 Sum_probs=55.0
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEEEEe
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSL 169 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~LS~ 169 (414)
..|++|+|+|.+++++|+||++++ .+||||.+|++. .+. +++|+++++.|+++++.+ +++.||+
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------GES-YRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC------CCc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 479999999999999999999986 999999999862 233 789999999999998654 4788885
No 124
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.84 E-value=9.5e-09 Score=97.83 Aligned_cols=75 Identities=28% Similarity=0.325 Sum_probs=68.0
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~----~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
-.+++||+|.|+|+++.++|+||+++ +..|++|++++++.++ .++.+.|++||.|.|+|++++++ +++.||+|.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~LS~k~ 137 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVLTLKG 137 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEEEEcC
Confidence 34689999999999999999999999 7999999999999887 78899999999999999999864 459999986
Q ss_pred C
Q 015066 335 L 335 (414)
Q Consensus 335 ~ 335 (414)
-
T Consensus 138 ~ 138 (235)
T PRK04163 138 K 138 (235)
T ss_pred C
Confidence 4
No 125
>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=98.81 E-value=2.5e-08 Score=80.54 Aligned_cols=74 Identities=18% Similarity=0.161 Sum_probs=63.3
Q ss_pred cCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEcCccccc---cccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACI---HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~--G~~Vdig~k~~g~lp~sEls~---~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
.++.|+++.|+|+++.++ |+||+++.+.+||||.+|+++ ....++.+. +++|+.+.|+|+......+...||.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~-~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKL-LKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHc-CCCCCEEEEEEEEecCCCCCceEEEE
Confidence 567999999999999996 999999988999999999987 445566665 89999999999998766677777765
No 126
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.79 E-value=1.1e-08 Score=96.37 Aligned_cols=77 Identities=21% Similarity=0.271 Sum_probs=72.1
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.++|++|-|+|.++.++|+||.+ .++.+||+|.||++..+++++.++ +++|+++-|+|+++|+..|.+-||+|+...
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~-vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDY-VKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHH-hhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 57899999999999999999999 456999999999999999999998 999999999999999999999999998754
No 127
>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=98.70 E-value=6.6e-08 Score=74.40 Aligned_cols=63 Identities=19% Similarity=0.127 Sum_probs=55.8
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc--cCCccccCccCCcEEEEEEEEEeCCCC
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~--~~~~~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
|++|.|+|+++.++|++|+++.+.+|++|.+++++.+ ..++.+. |++|+.++++|++++..+.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~-~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSK-FKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHh-CCCCCEEEEEEEEEeCccc
Confidence 8999999999999999999999999999999998764 5566565 8999999999999986543
No 128
>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=98.69 E-value=5.7e-08 Score=106.47 Aligned_cols=72 Identities=25% Similarity=0.548 Sum_probs=63.8
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCe
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGR 327 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~r 327 (414)
.-++|+++.|+|++|++||+||++. |++||+|+++++++++ .+....|++||.|+|+|.++|.++++
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~ 703 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK 703 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 4467999999999999999999997 6999999999986643 33456799999999999999999999
Q ss_pred EEEEE
Q 015066 328 VSLST 332 (414)
Q Consensus 328 i~LS~ 332 (414)
|.|++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99986
No 129
>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=98.67 E-value=6.2e-08 Score=71.96 Aligned_cols=65 Identities=18% Similarity=0.240 Sum_probs=57.5
Q ss_pred EEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066 103 VKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (414)
Q Consensus 103 V~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS 168 (414)
+.|+|.++.++|++|+++.+.+|++|.++++..+..++.+. +.+|+.+.|+|+++|+.++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~-~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV-FKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhE-eCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999988999999999987766555555 899999999999999888888875
No 130
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.64 E-value=8.9e-09 Score=96.50 Aligned_cols=104 Identities=19% Similarity=0.397 Sum_probs=83.3
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP 337 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~ 337 (414)
-+.++++|-+.|.+|.+.|+||.|- +++|++-.||||..|+.+++...++|..=-|.|+.+|+++|.|.||.+.+.+
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 3668999999999999999999984 7999999999999999999999999999999999999999999999999987
Q ss_pred CCCcccCCchhhhhhHHHHHHHHHHHH
Q 015066 338 TPGDMIRNPKLVFEKAEEMAQTFRQRI 364 (414)
Q Consensus 338 ~p~~~~~~~~~~~~~~~~~~~~~~~~~ 364 (414)
+--..+++......-+.......++++
T Consensus 93 ed~~kC~Er~~ksK~v~sIlrhvAe~~ 119 (304)
T KOG2916|consen 93 EDKEKCEERFAKSKLVYSILRHVAEKL 119 (304)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 543333332222222334444444443
No 131
>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=98.60 E-value=1.4e-07 Score=94.29 Aligned_cols=106 Identities=19% Similarity=0.224 Sum_probs=78.4
Q ss_pred ccCCcEEEEEEEEEeCCCCeEEEEe-eehh----hhHHHHHhhhcc--cCCeEEEEEEEEEecCc-EEEEECCEEEEEec
Q 015066 145 IVPGLKEEFVIIGENEADDSLVLSL-RMIQ----YELAWERCRQLQ--SEDVVVKGKVVGANKGG-VVAEVEGLRGFVPF 216 (414)
Q Consensus 145 ~~vG~~v~v~Vl~id~~~~~i~LS~-k~~~----~~~~~~~l~~~~--~~g~iv~G~V~~v~~~G-~~V~i~gi~GfIp~ 216 (414)
+.+|+.+++.+...+ -++..++. |+.. .+..++.+.+.+ ..|++++|+|.+++++| ++|++|++.||||.
T Consensus 84 ~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~ 161 (341)
T TIGR01953 84 VQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPK 161 (341)
T ss_pred cccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecH
Confidence 789999998885432 34444333 3321 233455555555 37899999999999988 69999999999999
Q ss_pred cccCCCCccccccCCeEEEEEEEeeccc--ceEEeehhhh
Q 015066 217 SQISSKSTAEELLGKDLPLKFVEVDEEQ--SRLVLSNRKA 254 (414)
Q Consensus 217 sels~~~~~~~~vGq~V~vkVl~vD~e~--~ri~LS~K~~ 254 (414)
++...... ..+|+++++.|++++.+. ..+.||++..
T Consensus 162 ~E~ip~E~--~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 162 KEQIPGEK--FRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred HHcCCCcC--CCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 99885432 237999999999999654 4699999875
No 132
>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=98.59 E-value=1.5e-07 Score=76.53 Aligned_cols=73 Identities=25% Similarity=0.403 Sum_probs=64.3
Q ss_pred ccccEEEEEEEEEEeeceEEEEE--------C-CEEEEEeecccCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDI--------G-GINGLLHVSQISHDRVA--DIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l--------~-gv~Glvh~sels~~~~~--~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
+++|++|.|+|+++....++|++ . ...|++|++++...... ++.+.|++||.|+|||++++. ...+.|
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 57999999999999999999999 4 48999999999877666 688999999999999999974 467999
Q ss_pred EEeeC
Q 015066 331 STKKL 335 (414)
Q Consensus 331 S~K~~ 335 (414)
|++.-
T Consensus 83 st~~~ 87 (92)
T cd05791 83 STAEN 87 (92)
T ss_pred EecCC
Confidence 99863
No 133
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.59 E-value=1.6e-07 Score=84.58 Aligned_cols=76 Identities=32% Similarity=0.527 Sum_probs=63.9
Q ss_pred ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc----------cC-cccccCCCCEEEEEEEEEeCCC-----
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------AD-IATVLQPGDTLKVMILSHDRER----- 325 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~----------~~-~~~~~~~G~~V~vkVl~id~e~----- 325 (414)
+..|++|.|.|+++..||+||+++-++||+|+|++.++++ .. -...+++||.|.+||+++....
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~ 158 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE 158 (183)
T ss_pred eccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence 4469999999999999999999999999999999988732 12 2337999999999999987655
Q ss_pred CeEEEEEeeCCC
Q 015066 326 GRVSLSTKKLEP 337 (414)
Q Consensus 326 ~ri~LS~K~~~~ 337 (414)
.+|.|+||+.-.
T Consensus 159 ~~I~lTmrq~~L 170 (183)
T COG1095 159 SKIGLTMRQPGL 170 (183)
T ss_pred ceEEEEeccccC
Confidence 589999998643
No 134
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.58 E-value=1.5e-07 Score=73.67 Aligned_cols=70 Identities=19% Similarity=0.338 Sum_probs=65.4
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC--CEEEEEe-ecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLH-VSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh-~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
-+++|+++. .|..+.+.|++|.|- |++|++. .+|++.+|+.++.+.+ +|-.+.|+|+.+|+++|.|.||.
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 367899999 889999999999985 8999999 9999999999999999 99999999999999999999985
No 135
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.57 E-value=2.7e-07 Score=84.85 Aligned_cols=75 Identities=31% Similarity=0.559 Sum_probs=64.4
Q ss_pred ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCC----
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERG---- 326 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~---- 326 (414)
+.+|+++.|+|+++.++|+||+++.++|++|.+++.+++.. +....+++||.|+++|.+++.+.+
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~ 158 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRG 158 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCC
Confidence 55799999999999999999999989999999999876432 345679999999999999997543
Q ss_pred -eEEEEEeeCC
Q 015066 327 -RVSLSTKKLE 336 (414)
Q Consensus 327 -ri~LS~K~~~ 336 (414)
+|.||+|+--
T Consensus 159 ~~I~ls~~~~~ 169 (187)
T PRK08563 159 SKIGLTMRQPG 169 (187)
T ss_pred CEEEEEecCCC
Confidence 8999999754
No 136
>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=98.55 E-value=4.8e-07 Score=71.42 Aligned_cols=70 Identities=10% Similarity=0.145 Sum_probs=58.5
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066 99 LGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSLV 166 (414)
Q Consensus 99 ~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~~i~ 166 (414)
.|+++.|+|+++.++|+||+++. +.+|++|.+++++.+.. ..... +++|+.++++|+++|.+.+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEE
Confidence 48999999999999999999987 69999999999754211 12233 7899999999999998889998
Q ss_pred EEe
Q 015066 167 LSL 169 (414)
Q Consensus 167 LS~ 169 (414)
+++
T Consensus 80 ~~l 82 (83)
T cd04471 80 FEL 82 (83)
T ss_pred EEE
Confidence 875
No 137
>PRK11642 exoribonuclease R; Provisional
Probab=98.55 E-value=3e-07 Score=101.53 Aligned_cols=73 Identities=23% Similarity=0.447 Sum_probs=64.2
Q ss_pred cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERGRVS 329 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~ri~ 329 (414)
++|+++.|+|++|++||+||+|. +++||||++++.++++. +....|++||.|+|+|.++|.++++|.
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~ 721 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID 721 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence 68999999999999999999997 49999999999876322 234679999999999999999999999
Q ss_pred EEEeeC
Q 015066 330 LSTKKL 335 (414)
Q Consensus 330 LS~K~~ 335 (414)
|++-..
T Consensus 722 f~l~~~ 727 (813)
T PRK11642 722 FSLISS 727 (813)
T ss_pred EEEecc
Confidence 998543
No 138
>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=98.54 E-value=7.6e-07 Score=69.91 Aligned_cols=64 Identities=16% Similarity=0.166 Sum_probs=57.6
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
+++.|+.+.|+|.++.++|+||++..+.+|++|.+++. +. +++|+.++++|.++ .+++++.+|.
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~-~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RD-YEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------Cc-CCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 57899999999999999999999998899999999863 22 78999999999999 7889998875
No 139
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.52 E-value=3.6e-07 Score=99.23 Aligned_cols=70 Identities=24% Similarity=0.515 Sum_probs=62.5
Q ss_pred cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGRVS 329 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~ri~ 329 (414)
++|+.++|+|+++++||+||+|. +++||||++++.++++ .+....|++||+|+|+|.++|.++++|.
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 57999999999999999999997 7999999999987641 2344679999999999999999999999
Q ss_pred EEE
Q 015066 330 LST 332 (414)
Q Consensus 330 LS~ 332 (414)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 986
No 140
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.44 E-value=5.5e-07 Score=90.55 Aligned_cols=103 Identities=16% Similarity=0.266 Sum_probs=77.9
Q ss_pred ccccccCCeEEEEEEEeecccceEEeehhhhhhh---------HHhhc--cccEEEEEEEEEEeeceEEEEECCEEEEEe
Q 015066 224 TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD---------SQAQL--GIGSVVIGTVQSLKPYGAFIDIGGINGLLH 292 (414)
Q Consensus 224 ~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~---------~~~~l--~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh 292 (414)
+++..+|+.+...+...+..+..+ .+.|+.+.. .++.| +.|++++|+|.++.++|+||++++++|++|
T Consensus 84 ~~~~~vGD~i~~~I~~~~fgR~aa-q~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP 162 (362)
T PRK12327 84 NPAYELGDVIEIEVTPKDFGRIAA-QTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLP 162 (362)
T ss_pred CccccCCCEEEEecCcCCCChHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEec
Confidence 455568999999876665433222 333433221 23566 899999999999999999999999999999
Q ss_pred ecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 015066 293 VSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLSTK 333 (414)
Q Consensus 293 ~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS~K 333 (414)
.+++. +.+.|++||+++|.|++++.+++ .|.||..
T Consensus 163 ~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 163 PAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred HHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 98874 36779999999999999996654 4666654
No 141
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.44 E-value=4.6e-07 Score=83.50 Aligned_cols=78 Identities=23% Similarity=0.202 Sum_probs=65.7
Q ss_pred HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066 90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159 (414)
Q Consensus 90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~----------k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id 159 (414)
|..+.+.+++|++|.|+|+++.++|++|+|+. ..+|++|.+++++....+..+. |++||.+.|+|++++
T Consensus 55 ~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~-~~~GD~V~akV~~i~ 133 (189)
T PRK09521 55 FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA-FKIGDIVRAKVISYT 133 (189)
T ss_pred CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc-cCCCCEEEEEEEecC
Confidence 33344577899999999999999999999953 4789999999987766666665 899999999999987
Q ss_pred CCCCeEEEEeee
Q 015066 160 EADDSLVLSLRM 171 (414)
Q Consensus 160 ~~~~~i~LS~k~ 171 (414)
+++.||++.
T Consensus 134 ---~~i~LS~k~ 142 (189)
T PRK09521 134 ---DPLQLSTKG 142 (189)
T ss_pred ---CcEEEEEec
Confidence 789999974
No 142
>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=98.44 E-value=9.3e-07 Score=88.36 Aligned_cols=104 Identities=13% Similarity=0.293 Sum_probs=77.8
Q ss_pred ccccccCCeEEEEEEEeecccceEEeehhhhhh----h-----HHhhc--cccEEEEEEEEEEeece-EEEEECCEEEEE
Q 015066 224 TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMA----D-----SQAQL--GIGSVVIGTVQSLKPYG-AFIDIGGINGLL 291 (414)
Q Consensus 224 ~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~----~-----~~~~l--~~G~iv~g~V~~i~~~G-~fV~l~gv~Glv 291 (414)
+++..+|+.+.+.+..-+. .+....+.|+.+. + .++.+ +.|++|+|+|.++.+.| +||++++++|++
T Consensus 81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~L 159 (341)
T TIGR01953 81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGIL 159 (341)
T ss_pred ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEe
Confidence 4555689999988754432 2333344444321 1 12455 59999999999999988 699999999999
Q ss_pred eecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEEee
Q 015066 292 HVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLSTKK 334 (414)
Q Consensus 292 h~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS~K~ 334 (414)
|.++.. +.+.|++||+++|.|++++.+. ..|.||.+.
T Consensus 160 P~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 160 PKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred cHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 999986 3456999999999999999553 579999874
No 143
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.32 E-value=2.5e-06 Score=81.28 Aligned_cols=75 Identities=23% Similarity=0.238 Sum_probs=64.8
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc----CCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~----~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+..++||+|.|+|+++..++++|+|+....|+||.++++..+. .++.+. |.+||.+.|+|+++++ ++.+.||++
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~-~~~GDlV~akV~~i~~-~~~~~LS~k 136 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKY-LDIGDYIIAKVKDVDR-TRDVVLTLK 136 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhh-CCCCCEEEEEEEEECC-CCcEEEEEc
Confidence 4568999999999999999999999988999999999987654 555555 8999999999999985 445999986
Q ss_pred e
Q 015066 171 M 171 (414)
Q Consensus 171 ~ 171 (414)
.
T Consensus 137 ~ 137 (235)
T PRK04163 137 G 137 (235)
T ss_pred C
Confidence 4
No 144
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.30 E-value=9.1e-06 Score=81.83 Aligned_cols=78 Identities=19% Similarity=0.222 Sum_probs=62.6
Q ss_pred HHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC--e
Q 015066 87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--S 164 (414)
Q Consensus 87 ~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~--~ 164 (414)
+..|++| .-+.|++|+|+|.+++++|++|++|+ .+||||.+++.. .+. |++|++++|+|++++...+ +
T Consensus 124 e~v~~ef--~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip------~e~-~~~Gd~Ika~V~~V~~~~kgp~ 193 (362)
T PRK12327 124 EIIYNEF--SEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP------GET-YKHGDRIKVYVVKVEKTTKGPQ 193 (362)
T ss_pred HHHHHHH--HHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC------CCC-CCCCCEEEEEEEEEecCCCCCe
Confidence 3445544 34899999999999999999999986 999999988742 343 8999999999999985543 6
Q ss_pred EEEEeeehhh
Q 015066 165 LVLSLRMIQY 174 (414)
Q Consensus 165 i~LS~k~~~~ 174 (414)
+.||+.....
T Consensus 194 IivSRt~p~~ 203 (362)
T PRK12327 194 IFVSRTHPGL 203 (362)
T ss_pred EEEEeCCHHH
Confidence 8888876554
No 145
>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=98.25 E-value=3.9e-06 Score=69.09 Aligned_cols=66 Identities=24% Similarity=0.341 Sum_probs=55.3
Q ss_pred eEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC---cc-----------cc-ccCCeEEEEEEEeeccc-----ceEE
Q 015066 189 VVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS---TA-----------EE-LLGKDLPLKFVEVDEEQ-----SRLV 248 (414)
Q Consensus 189 ~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~---~~-----------~~-~vGq~V~vkVl~vD~e~-----~ri~ 248 (414)
+++.|+|++++++|+||+++++.||+|.+++++.. +. .. .+|+.++++|.++|.+. .++.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence 37899999999999999998899999999998642 11 11 37999999999999874 4799
Q ss_pred eehhhh
Q 015066 249 LSNRKA 254 (414)
Q Consensus 249 LS~K~~ 254 (414)
||++..
T Consensus 81 ls~k~~ 86 (99)
T cd04460 81 LTMRQP 86 (99)
T ss_pred EEEecC
Confidence 999875
No 146
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.03 E-value=1.8e-05 Score=60.97 Aligned_cols=69 Identities=19% Similarity=0.212 Sum_probs=56.0
Q ss_pred CCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccc-cCccCCcEE-EEEEEEEeCCCCeEEEEee
Q 015066 100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEE-AGIVPGLKE-EFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e-~~~~vG~~v-~v~Vl~id~~~~~i~LS~k 170 (414)
|++|+|+|+..++++++|++.+ +..|++|..++++...++... ..+.+|+++ ++.|+ +...+.+.+|.|
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 7899999999999999999976 899999999999843332221 226799999 89998 667788888865
No 147
>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=97.98 E-value=4.2e-05 Score=61.71 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=52.5
Q ss_pred ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCc-----------ccccCCCCEEEEEEEEEeCCCCe
Q 015066 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI-----------ATVLQPGDTLKVMILSHDRERGR 327 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~-----------~~~~~~G~~V~vkVl~id~e~~r 327 (414)
+|+++.|+|+++.++|+||+++.+++|+|.+.+..+..-++ ...++.|+.|.+||+++..+.+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 75 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATD 75 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCc
Confidence 48999999999999999999999999999999865432222 34588999999999998765443
No 148
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=97.96 E-value=4.8e-05 Score=83.66 Aligned_cols=73 Identities=8% Similarity=0.156 Sum_probs=61.2
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCCCC
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
.-++|++++|+|+++.++|+||.+.+ +.+|++|.+++++.+. ...... +++||+++|+|+++|..++
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~-~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-FRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcE-ECCCCEEEEEEEEEecccC
Confidence 45789999999999999999999986 6999999999975432 111223 8899999999999999999
Q ss_pred eEEEEe
Q 015066 164 SLVLSL 169 (414)
Q Consensus 164 ~i~LS~ 169 (414)
++.+++
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 999885
No 149
>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=97.95 E-value=3.5e-05 Score=62.68 Aligned_cols=74 Identities=19% Similarity=0.147 Sum_probs=61.2
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEe--------CCCeeEEEcCccccccccC--CccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDI--------TAKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdi--------g~k~~g~lp~sEls~~~~~--~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
-.++|++|.|+|+++....+.|+| .....|++|.+++...+.. +..+. |.+||.+.++|++.++ ...+
T Consensus 3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~-f~~GDiV~AkVis~~~-~~~~ 80 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKC-FRPGDIVRAKVISLGD-ASSY 80 (92)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhh-cCCCCEEEEEEEEcCC-CCCc
Confidence 358999999999999999999999 7777899999998755444 34444 8999999999999874 3568
Q ss_pred EEEeee
Q 015066 166 VLSLRM 171 (414)
Q Consensus 166 ~LS~k~ 171 (414)
.||.+.
T Consensus 81 ~Lst~~ 86 (92)
T cd05791 81 YLSTAE 86 (92)
T ss_pred EEEecC
Confidence 899875
No 150
>PRK05054 exoribonuclease II; Provisional
Probab=97.92 E-value=3.5e-05 Score=83.65 Aligned_cols=68 Identities=15% Similarity=0.179 Sum_probs=57.3
Q ss_pred cEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccc--c--c-C-------cccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDR--V--A-D-------IATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~--~--~-~-------~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
|+.+.|.|+++++||+||+|. |++||||++.+.+.+ + . + -...|+.||+|+|+|.++|.++++|.+
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 459999999999999999997 799999999986531 1 0 1 124699999999999999999999988
Q ss_pred EE
Q 015066 331 ST 332 (414)
Q Consensus 331 S~ 332 (414)
++
T Consensus 642 ~~ 643 (644)
T PRK05054 642 RP 643 (644)
T ss_pred EE
Confidence 75
No 151
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=97.90 E-value=7e-05 Score=68.42 Aligned_cols=77 Identities=18% Similarity=0.169 Sum_probs=61.9
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-Ccc---------ccCccCCcEEEEEEEEEe-----C
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-HVE---------EAGIVPGLKEEFVIIGEN-----E 160 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-~~~---------e~~~~vG~~v~v~Vl~id-----~ 160 (414)
....|+++.|+|+++++.|+||+++. .+|+++.+++...+.. +.. ...+..|+.++++|++++ +
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 45689999999999999999999975 9999999998754321 111 123789999999999998 5
Q ss_pred CCCeEEEEeeehh
Q 015066 161 ADDSLVLSLRMIQ 173 (414)
Q Consensus 161 ~~~~i~LS~k~~~ 173 (414)
+..++.+|+|..-
T Consensus 157 ~~~~I~lt~k~~~ 169 (179)
T TIGR00448 157 EGSKIGLTMRQPL 169 (179)
T ss_pred CcceEEEEeccCc
Confidence 5678999998754
No 152
>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=97.89 E-value=5.4e-05 Score=58.30 Aligned_cols=63 Identities=17% Similarity=0.375 Sum_probs=51.9
Q ss_pred CeEEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCc--c---cc-ccCCeE-EEEEEEeecccceEEeehh
Q 015066 188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKST--A---EE-LLGKDL-PLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 188 g~iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~--~---~~-~vGq~V-~vkVl~vD~e~~ri~LS~K 252 (414)
|++++|+|...++.+++|+++ |++||+|..|+++... . .. .+||++ ++-|+ |...+.+.+|.|
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 468999999999999999995 8999999999998421 1 11 279999 88888 877888888865
No 153
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.87 E-value=0.00018 Score=72.33 Aligned_cols=76 Identities=25% Similarity=0.316 Sum_probs=61.6
Q ss_pred HHHhhcccCCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC---e
Q 015066 89 ALEKYDFNSELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD---S 164 (414)
Q Consensus 89 ~l~~~~~~l~~G~iV~G~V~~v~~-~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~---~ 164 (414)
.+++| .-+.|++|+|+|.+++. ++++|++| +.+|+||.+|.. +.+. |.+|+.++|+|..++...+ +
T Consensus 130 i~~ey--~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqi------p~E~-~~~Gdrik~~i~~V~~~~k~gp~ 199 (374)
T PRK12328 130 IFEKY--KKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRI------KGEK-FKVGDVVKAVLKRVKIDKNNGIL 199 (374)
T ss_pred HHHHH--HHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcC------CCCc-CCCCCEEEEEEEEEecCCCCCCE
Confidence 34444 45799999999999997 56999998 599999999874 3344 8999999999999987655 7
Q ss_pred EEEEeeehhh
Q 015066 165 LVLSLRMIQY 174 (414)
Q Consensus 165 i~LS~k~~~~ 174 (414)
+.||+.....
T Consensus 200 IilSRt~p~~ 209 (374)
T PRK12328 200 IELSRTSPKF 209 (374)
T ss_pred EEEEcCCHHH
Confidence 8899876654
No 154
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.83 E-value=8.2e-05 Score=67.26 Aligned_cols=87 Identities=24% Similarity=0.351 Sum_probs=69.8
Q ss_pred cceEEeehhhhhhhHHhhccccEEEEEEEEEEeeceEEEEECC-----------EEEEEeecccCcccccCcccccCCCC
Q 015066 244 QSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-----------INGLLHVSQISHDRVADIATVLQPGD 312 (414)
Q Consensus 244 ~~ri~LS~K~~l~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~g-----------v~Glvh~sels~~~~~~~~~~~~~G~ 312 (414)
.++...|.+.... ...-++.|++|-|.|+++....+.|++-+ ..|-+|+|+++...+++.++.|++||
T Consensus 45 ~~n~~~~V~p~~~-~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GD 123 (188)
T COG1096 45 DKNRVISVKPGKK-TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGD 123 (188)
T ss_pred ccceEEEeccCCC-CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccccccccccccc
Confidence 3444445443322 33568899999999999999999999842 56789999999999999999999999
Q ss_pred EEEEEEEEEeCCCCeEEEEEee
Q 015066 313 TLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 313 ~V~vkVl~id~e~~ri~LS~K~ 334 (414)
.|+|+|++.- ..+.||++.
T Consensus 124 ivrA~Vis~~---~~~~Lst~~ 142 (188)
T COG1096 124 IVRARVISTG---DPIQLSTKG 142 (188)
T ss_pred EEEEEEEecC---CCeEEEecC
Confidence 9999999984 567788774
No 155
>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=97.80 E-value=4.6e-05 Score=78.28 Aligned_cols=62 Identities=32% Similarity=0.580 Sum_probs=53.2
Q ss_pred hhccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCcc------------cccCcccccCCCCEEEEEEEEE
Q 015066 260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~~------------~~~~~~~~~~~G~~V~vkVl~i 321 (414)
....+|++|.|+|.++.++ ||||+++ +-.||+|++++.+. +..++.+.+++||.|.|.|.+-
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 3456899999999999999 9999999 79999999998653 2345667899999999999983
No 156
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.80 E-value=0.00011 Score=55.12 Aligned_cols=61 Identities=18% Similarity=0.192 Sum_probs=37.8
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
.|++.+.+|.+.++.|+|++.+...+-+||.+|+.. . +.+|+.+++.|+. +.++++..|++
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~-------~--~~~Gd~v~VFvY~--D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE-------P--LKVGDEVEVFVYL--DKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG---------------TTSEEEEEEEE---TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC-------C--CCCCCEEEEEEEE--CCCCCEEEecC
Confidence 489999999999999999999888999999998842 1 6899999999976 46778888864
No 157
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.80 E-value=7.1e-05 Score=67.63 Aligned_cols=85 Identities=21% Similarity=0.237 Sum_probs=65.1
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC----------CccccCccCCcEEEEEEEEEeCCC--
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK----------HVEEAGIVPGLKEEFVIIGENEAD-- 162 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~----------~~~e~~~~vG~~v~v~Vl~id~~~-- 162 (414)
+....|++|.|.|+++.+.|+||.+|. .+||+|.+++.+.+.. .-+...+.+|+.|+++|+..+...
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence 356789999999999999999999996 8999999999877322 111222778999999999886544
Q ss_pred ---CeEEEEeeehhh-hHHHHH
Q 015066 163 ---DSLVLSLRMIQY-ELAWER 180 (414)
Q Consensus 163 ---~~i~LS~k~~~~-~~~~~~ 180 (414)
.++.+|+|+.-. ...|-.
T Consensus 156 ~~~~~I~lTmrq~~LGklew~~ 177 (183)
T COG1095 156 PRESKIGLTMRQPGLGKLEWIE 177 (183)
T ss_pred cccceEEEEeccccCCcchhhh
Confidence 578889887643 344643
No 158
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.72 E-value=0.00013 Score=57.28 Aligned_cols=70 Identities=7% Similarity=0.098 Sum_probs=61.7
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEc-CccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 97 SELGTKVKGTVFCTDNRGALVDI-TAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp-~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
.++|+.+. .|+.+.+.|+||.+ ..+.+|+|. .+|++-.++++..+. + +|..+.++|+++|..+|.+-||.
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kl-l-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKK-L-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhh-h-cCCeeEEEEEEECCCCCEEEeEc
Confidence 47899998 89999999999998 345899888 999998888888776 5 99999999999999999999884
No 159
>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=97.69 E-value=9.1e-05 Score=58.81 Aligned_cols=60 Identities=20% Similarity=0.430 Sum_probs=41.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-------------------CEEEEEeecccCccccc--CcccccCCCCEEEEEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-------------------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVMILS 320 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-------------------gv~Glvh~sels~~~~~--~~~~~~~~G~~V~vkVl~ 320 (414)
+++|++|.|+|+++++.-+++++- ...|++|.+++...... .+.+.|++||.|+|+|++
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence 468999999999999988888762 26899999998765444 368889999999999998
Q ss_pred E
Q 015066 321 H 321 (414)
Q Consensus 321 i 321 (414)
+
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 5
No 160
>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=97.66 E-value=0.00028 Score=76.85 Aligned_cols=73 Identities=14% Similarity=0.158 Sum_probs=60.6
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCCCC
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
.-+.|+.++|+|+++.++|+||.+. .+.+|++|.+++.+.+. ++.... +++|++|+++|+++|..++
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~-~~lGD~V~Vki~~vd~~~~ 647 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKV-YRIGDRVTVKLTEVNMETR 647 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcE-ECCCCEEEEEEEEEecccC
Confidence 3467999999999999999999997 67999999999976431 111122 8899999999999999999
Q ss_pred eEEEEe
Q 015066 164 SLVLSL 169 (414)
Q Consensus 164 ~i~LS~ 169 (414)
++.+++
T Consensus 648 ~I~f~l 653 (654)
T TIGR00358 648 SIIFEL 653 (654)
T ss_pred eEEEEE
Confidence 998875
No 161
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.59 E-value=0.0004 Score=63.79 Aligned_cols=77 Identities=21% Similarity=0.206 Sum_probs=61.3
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCC
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
+....|+++.|+|+++++.|++|+++. .+|+++.+++...+.. +.... +.+|+.++++|++++...+
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-i~~Gd~VrvrV~~v~~~~~ 154 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRV-LKVGDVVRARIVAVSLKER 154 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEcccC
Confidence 356789999999999999999999985 9999999998754321 11222 7889999999999986543
Q ss_pred -----eEEEEeeehh
Q 015066 164 -----SLVLSLRMIQ 173 (414)
Q Consensus 164 -----~i~LS~k~~~ 173 (414)
.+.+|++..-
T Consensus 155 ~~~~~~I~ls~~~~~ 169 (187)
T PRK08563 155 RPRGSKIGLTMRQPG 169 (187)
T ss_pred CCCCCEEEEEecCCC
Confidence 7888998653
No 162
>PRK11642 exoribonuclease R; Provisional
Probab=97.57 E-value=0.00045 Score=76.79 Aligned_cols=72 Identities=14% Similarity=0.127 Sum_probs=60.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~k-~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
++|++++|+|++++++|+||.+... .+|++|.+++.+.+.. .... .|.+|+.|+|+|+.+|..++++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~-~~~lGD~V~VkV~~vD~~~rkI 720 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQ-TYRLGDRVEVRVEAVNMDERKI 720 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCc-EECCCCEEEEEEEEeecCCCeE
Confidence 7899999999999999999999764 9999999999764211 1112 2889999999999999999999
Q ss_pred EEEee
Q 015066 166 VLSLR 170 (414)
Q Consensus 166 ~LS~k 170 (414)
.+++-
T Consensus 721 ~f~l~ 725 (813)
T PRK11642 721 DFSLI 725 (813)
T ss_pred EEEEe
Confidence 99985
No 163
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.55 E-value=0.00039 Score=63.38 Aligned_cols=74 Identities=14% Similarity=0.132 Sum_probs=57.7
Q ss_pred ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcc-cc-----------cCcccccCCCCEEEEEEEEEeCCC--Ce
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD-RV-----------ADIATVLQPGDTLKVMILSHDRER--GR 327 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~-~~-----------~~~~~~~~~G~~V~vkVl~id~e~--~r 327 (414)
+-.|+++.|.|+++.++|+||+++-+++++|.++|... .+ .+-...++.|+.|++||.++..+. .+
T Consensus 79 Pf~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~ 158 (176)
T PTZ00162 79 PFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF 158 (176)
T ss_pred cCCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence 55799999999999999999999878899999999643 11 112346899999999998876443 34
Q ss_pred EEEEEeeC
Q 015066 328 VSLSTKKL 335 (414)
Q Consensus 328 i~LS~K~~ 335 (414)
+..|||+-
T Consensus 159 ~i~T~~~~ 166 (176)
T PTZ00162 159 AIATINSD 166 (176)
T ss_pred EEEEecCC
Confidence 66677753
No 164
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.44 E-value=0.00038 Score=76.59 Aligned_cols=73 Identities=25% Similarity=0.506 Sum_probs=62.3
Q ss_pred hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCe
Q 015066 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGR 327 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~r 327 (414)
.-.+|+.+.|+|+++..||+||.+. +++|++|++.+..+++ ......|+.||.|+|+|.+++...++
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~ 698 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK 698 (706)
T ss_pred HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence 4568999999999999999999997 5899999999985422 23345799999999999999999999
Q ss_pred EEEEEe
Q 015066 328 VSLSTK 333 (414)
Q Consensus 328 i~LS~K 333 (414)
+.+++-
T Consensus 699 i~~~~v 704 (706)
T COG0557 699 IDFELV 704 (706)
T ss_pred eEEEec
Confidence 988763
No 165
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=97.44 E-value=0.00034 Score=75.95 Aligned_cols=67 Identities=13% Similarity=0.225 Sum_probs=55.3
Q ss_pred cEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISH--DRV-----A---DI--ATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~--~~~-----~---~~--~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
|+.+.|.|+.+.++|+||++. |++|+||.+.+.. +.+ . .+ ...|+.||.|+|+|.++|.++++|.+
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 458999999999999999995 7999999999865 211 1 11 12699999999999999999999876
Q ss_pred E
Q 015066 331 S 331 (414)
Q Consensus 331 S 331 (414)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 4
No 166
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.41 E-value=0.00053 Score=64.58 Aligned_cols=76 Identities=30% Similarity=0.465 Sum_probs=66.6
Q ss_pred hhccccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRV----ADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~----~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
-.+++||+|-|.|..+...+-.|++++ ..+++|.|++-+..+ .+.+..|++||.|.|+|..+|+ .+...|++|+
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~ 138 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKD 138 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEeec
Confidence 457899999999999999999999995 999999999966543 4678889999999999999996 7889999976
Q ss_pred CC
Q 015066 335 LE 336 (414)
Q Consensus 335 ~~ 336 (414)
.-
T Consensus 139 ~~ 140 (239)
T COG1097 139 EG 140 (239)
T ss_pred CC
Confidence 43
No 167
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.38 E-value=0.0015 Score=66.88 Aligned_cols=72 Identities=13% Similarity=0.132 Sum_probs=58.9
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeC---C--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC---CeEEE
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDIT---A--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD---DSLVL 167 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig---~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~---~~i~L 167 (414)
.-+.|++|+|+|.+++.++++|+++ + +.+|+||.+|.. +.+. |++|+.++|+|.+++... -++.|
T Consensus 149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~-y~~Gdrika~i~~V~~~~~kGpqIil 221 (449)
T PRK12329 149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDN-YRANATFKVFLKEVSEGPRRGPQLFV 221 (449)
T ss_pred HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCc-CCCCCEEEEEEEEeecCCCCCCEEEE
Confidence 4579999999999999999999993 3 489999998874 3344 899999999999997652 26899
Q ss_pred Eeeehhh
Q 015066 168 SLRMIQY 174 (414)
Q Consensus 168 S~k~~~~ 174 (414)
|+.....
T Consensus 222 SRt~p~l 228 (449)
T PRK12329 222 SRANAGL 228 (449)
T ss_pred EcCCHHH
Confidence 9876554
No 168
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.35 E-value=0.00015 Score=75.40 Aligned_cols=72 Identities=22% Similarity=0.475 Sum_probs=64.0
Q ss_pred HhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 259 ~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
..+++.|.+|.|+|+++..||+||+++ -+.||+|.++++.. ..|.+|+.+-|.|..+.++++.|++....++
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 467999999999999999999999999 79999999998763 2578999999999999998898888777665
No 169
>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=97.35 E-value=0.0012 Score=52.92 Aligned_cols=72 Identities=21% Similarity=0.140 Sum_probs=59.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+++||+|-|+|+.+...+.+|+|+ -..|++|.+.+... ..+.+..|++||.|-|+|.++|++ ....||+.+.
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~ 76 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS 76 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence 578999999999999999999998 48999999887433 233456799999999999999974 5688888763
No 170
>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=97.29 E-value=0.002 Score=51.98 Aligned_cols=62 Identities=16% Similarity=0.158 Sum_probs=45.9
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCc----------cccCccCCcEEEEEEEEEeCC
Q 015066 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------EEAGIVPGLKEEFVIIGENEA 161 (414)
Q Consensus 99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~----------~e~~~~vG~~v~v~Vl~id~~ 161 (414)
.|+++.|+|.++++.|+||.+|. .++|++...+..+...++ .+..+..|+.|+|+|+.+..+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 72 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVD 72 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEc
Confidence 48999999999999999999986 778887777754432222 122256788888888877544
No 171
>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=97.28 E-value=0.0006 Score=70.15 Aligned_cols=62 Identities=21% Similarity=0.234 Sum_probs=50.4
Q ss_pred cCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEcCcccccc------------ccCCccccCccCCcEEEEEEEEE
Q 015066 96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~--G~~Vdig~k~~g~lp~sEls~~------------~~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
...+|+++.|+|.++.++ ||||+||.+..||+|.+++... ...+..+. +++|+.+-|.|...
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISEL-LRPGQSVLVQVVKE 97 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHh-CcCCCEEEEEEeeC
Confidence 456899999999999997 9999999999999999998542 11223334 78899999999874
No 172
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=97.27 E-value=0.00079 Score=74.80 Aligned_cols=117 Identities=16% Similarity=0.084 Sum_probs=90.1
Q ss_pred HHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhc-ccCCCCCEEEEEEEEEeCCe---EEEEeCCCeeEEEcCcccc
Q 015066 58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYD-FNSELGTKVKGTVFCTDNRG---ALVDITAKSSAYLPTQEAC 133 (414)
Q Consensus 58 ~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~-~~l~~G~iV~G~V~~v~~~G---~~Vdig~k~~g~lp~sEls 133 (414)
..|.+|..|+...-.+-+......+.++.=.++..-. ..+..|.+|.++|.+++..- +-|.+..+.+||||..+++
T Consensus 943 ~tl~dI~~ELsdgykd~R~~f~~l~~eeiF~mLTget~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S 1022 (1299)
T KOG1856|consen 943 NTLYDIRLELSDGYKDLRNPFHELTGEEIFDMLTGETPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS 1022 (1299)
T ss_pred chHHHHHHHhhcchhhhccccCCCCHHHHHHHHhCCChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC
Confidence 4566666666555545455444566665555665444 35899999999999998855 5568888899999999999
Q ss_pred ccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhh
Q 015066 134 IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE 175 (414)
Q Consensus 134 ~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~ 175 (414)
+..+.+|.+. +++|+.+.|+|++++.+.=.+.||++.+...
T Consensus 1023 d~~v~~p~~~-v~vgq~v~~kvi~id~e~f~v~Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1023 DRDVRRPENR-VKVGQTVYCKVIKIDKERFSVELSCRTSDLK 1063 (1299)
T ss_pred hhhccCHHHh-hccCceEEEEeeeeeHhhhhhhhhhhhHHhh
Confidence 9888888887 8899999999999997766788899887653
No 173
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.24 E-value=0.0018 Score=65.16 Aligned_cols=67 Identities=16% Similarity=0.244 Sum_probs=55.4
Q ss_pred cCCeEEEEEEEEEec-CcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccc---eEEeehhhh
Q 015066 186 SEDVVVKGKVVGANK-GGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS---RLVLSNRKA 254 (414)
Q Consensus 186 ~~g~iv~G~V~~v~~-~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~---ri~LS~K~~ 254 (414)
..|++++|+|.++.. ++++|++|+..|+||.++...... ...|+.++|.|.+|+...+ .+.||+...
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~E~--~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p 207 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKGEK--FKVGDVVKAVLKRVKIDKNNGILIELSRTSP 207 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCCCc--CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence 358899999999986 569999999999999998774422 2279999999999998766 689998754
No 174
>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=97.23 E-value=0.0025 Score=51.07 Aligned_cols=73 Identities=19% Similarity=0.005 Sum_probs=58.5
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~ 171 (414)
..++||.|-|+|+.+...++.|||+....|++|..++... .+..... +.+|+.|-++|..+++. ....||+..
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~-L~~GDlV~ArV~~~~~~-~~~eLtc~~ 75 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPN-LNVGDLVYARVVKANRD-MEPELSCVD 75 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-ccccccc-CCCCCEEEEEEEecCCC-CCeEEEEeC
Confidence 4689999999999999999999999988999999876432 2222222 88999999999998754 557888764
No 175
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.11 E-value=0.0023 Score=47.89 Aligned_cols=59 Identities=27% Similarity=0.411 Sum_probs=35.5
Q ss_pred CeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 188 g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K 252 (414)
|++.+.+|+..++.|+|++.+ +-+.|||.+++..... +|++|.| ++..|.+ +|+..|++
T Consensus 2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~~----~Gd~v~V-FvY~D~~-~rl~AT~k 61 (61)
T PF13509_consen 2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPLK----VGDEVEV-FVYLDKE-GRLVATTK 61 (61)
T ss_dssp -------EEEE-SSEEEEEETT-EEEEEEGGG----------TTSEEEE-EEEE-TT-S-EEEE--
T ss_pred CCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCCC----CCCEEEE-EEEECCC-CCEEEecC
Confidence 568889999999999999998 5999999999874432 8999999 5688864 57777754
No 176
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=97.11 E-value=0.00046 Score=76.58 Aligned_cols=77 Identities=21% Similarity=0.307 Sum_probs=67.9
Q ss_pred hhccccEEEEEEEEEEeece---EEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 260 AQLGIGSVVIGTVQSLKPYG---AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G---~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.+.+|.+|.++|++++..- +-|.+. |+.|+||.+++|+..+.+|...+++||+|.|||+++|.++=-+.||.|..
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 46889999999999998643 346677 99999999999999999999999999999999999998887888898876
Q ss_pred C
Q 015066 336 E 336 (414)
Q Consensus 336 ~ 336 (414)
+
T Consensus 1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred H
Confidence 4
No 177
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.07 E-value=0.0006 Score=64.55 Aligned_cols=77 Identities=19% Similarity=0.227 Sum_probs=70.8
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
.+++++|-+.|.++..-|+||.+ .++.+|++-.+|||-.+++++... .++|..--|.|+.+|.++|.+-||.++...
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kl-irVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKL-IRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHH-HhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 57899999999999999999998 567999999999999999888887 899999999999999999999999998754
No 178
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.06 E-value=0.0023 Score=58.38 Aligned_cols=68 Identities=21% Similarity=0.264 Sum_probs=50.1
Q ss_pred CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--Ccc----c-------cc---cCCeEEEEEEEeeccc--ceEE
Q 015066 187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STA----E-------EL---LGKDLPLKFVEVDEEQ--SRLV 248 (414)
Q Consensus 187 ~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~----~-------~~---vGq~V~vkVl~vD~e~--~ri~ 248 (414)
.|+++.|.|+++++.|+||.+|-+++|||.+++.+. ++. . .. .|+.|++||+.+..+. -.+.
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i 160 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAI 160 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEE
Confidence 468999999999999999999989999999999843 111 0 11 4888888887765433 3355
Q ss_pred eehhhh
Q 015066 249 LSNRKA 254 (414)
Q Consensus 249 LS~K~~ 254 (414)
.|+|+.
T Consensus 161 ~T~~~~ 166 (176)
T PTZ00162 161 ATINSD 166 (176)
T ss_pred EEecCC
Confidence 566543
No 179
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.84 E-value=0.0065 Score=57.32 Aligned_cols=74 Identities=22% Similarity=0.253 Sum_probs=61.1
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc----CCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~----~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
|..++||.|-|.|+.+...++.|||++...|++|.+++..... .+.... +.+||.+-++|..+| .++.+.|++|
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~-l~vGD~v~AkV~~vd-~~~~~~L~~k 137 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPF-LNVGDLVYAKVVDVD-RDGEVELTLK 137 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccc-cccCCEEEEEEEEcc-CCCceEEEee
Confidence 4678999999999999999999999999999999999833221 233333 789999999999998 5677888884
No 180
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.78 E-value=0.0092 Score=62.53 Aligned_cols=149 Identities=14% Similarity=0.157 Sum_probs=102.7
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~ 174 (414)
++++.|....|+|.++.+.|+||+++..+.|+++.++++.. ..+.+|+++-+.+..+.+.++.+-+....+..
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~-------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~ 190 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDR 190 (715)
T ss_pred hhcccceeeeccccchhhhcceeecChhhhccccccccCCC-------CCCCCCCeEEEEeeccCCCCCccceeecCCcc
Confidence 47899999999999999999999999999999999998741 12789999999999998887876665544431
Q ss_pred ------hH-----HHHHhhhcccCCeEEEEEEEEEe-cCc-EEEEECCEEEEEeccccCCC---CccccccCCeEEEEEE
Q 015066 175 ------EL-----AWERCRQLQSEDVVVKGKVVGAN-KGG-VVAEVEGLRGFVPFSQISSK---STAEELLGKDLPLKFV 238 (414)
Q Consensus 175 ------~~-----~~~~l~~~~~~g~iv~G~V~~v~-~~G-~~V~i~gi~GfIp~sels~~---~~~~~~vGq~V~vkVl 238 (414)
++ ....+.+..-.-..++|.|+.+. ..| -+..+-.=.|+++..-+... ..|.-.+|+.|.+ +=
T Consensus 191 Y~~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGvRAyP~IevGdiV~V-iG 269 (715)
T COG1107 191 YREVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEV-IG 269 (715)
T ss_pred chhhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCcccCCCCCCCceEEE-EE
Confidence 11 12223332212236789999983 334 33455555677776655532 2344458999887 45
Q ss_pred EeecccceEEeeh
Q 015066 239 EVDEEQSRLVLSN 251 (414)
Q Consensus 239 ~vD~e~~ri~LS~ 251 (414)
.++...+++.+-.
T Consensus 270 ~V~~r~g~lQiE~ 282 (715)
T COG1107 270 EVTRRDGRLQIEI 282 (715)
T ss_pred EEeecCCcEEEee
Confidence 6676777776543
No 181
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.64 E-value=0.0042 Score=68.73 Aligned_cols=65 Identities=25% Similarity=0.456 Sum_probs=52.1
Q ss_pred ccccEEEEEEEEEEee--ceEEEEEC-CEEEEEeecccCccccc---------CcccccCCCCEEEEEEEEEeCCCC
Q 015066 262 LGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVA---------DIATVLQPGDTLKVMILSHDRERG 326 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~--~G~fV~l~-gv~Glvh~sels~~~~~---------~~~~~~~~G~~V~vkVl~id~e~~ 326 (414)
-.+|.||.|+|.+|.+ .++||+|+ |..||+|++++....+. +..+.++.||.|-|.|.+-...++
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtK 112 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK 112 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCC
Confidence 3589999999999997 58999999 89999999998643322 235579999999999998654333
No 182
>PRK05054 exoribonuclease II; Provisional
Probab=96.48 E-value=0.014 Score=63.52 Aligned_cols=63 Identities=19% Similarity=0.341 Sum_probs=52.2
Q ss_pred CeEEEEEEEEEecCcEEEEEC--CEEEEEeccccCCC---C----c--------c-ccccCCeEEEEEEEeecccceEEe
Q 015066 188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---S----T--------A-EELLGKDLPLKFVEVDEEQSRLVL 249 (414)
Q Consensus 188 g~iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~---~----~--------~-~~~vGq~V~vkVl~vD~e~~ri~L 249 (414)
|+.+.|.|++++.+|+||.+. ++.||||.+.+.+. + + . ...+||.|+|+|.++|.++++|.+
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 469999999999999999995 89999999998642 1 1 0 112799999999999999998876
Q ss_pred e
Q 015066 250 S 250 (414)
Q Consensus 250 S 250 (414)
+
T Consensus 642 ~ 642 (644)
T PRK05054 642 R 642 (644)
T ss_pred E
Confidence 5
No 183
>PRK11712 ribonuclease G; Provisional
Probab=96.40 E-value=0.0075 Score=63.31 Aligned_cols=63 Identities=29% Similarity=0.496 Sum_probs=50.5
Q ss_pred hhccccEEEEEEEEEEee--ceEEEEEC-CEEEEEeecccCcc------------cccCcccccCCCCEEEEEEEEEe
Q 015066 260 AQLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVMILSHD 322 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~--~G~fV~l~-gv~Glvh~sels~~------------~~~~~~~~~~~G~~V~vkVl~id 322 (414)
....+|.||.|+|.+|.| .+|||+++ +-.||+|.+++... ...++.+.++.||.|-|.|.+--
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~ 111 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDP 111 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCC
Confidence 345689999999999998 48999999 89999999987321 11234566999999999999853
No 184
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.33 E-value=0.025 Score=58.10 Aligned_cols=67 Identities=19% Similarity=0.245 Sum_probs=53.9
Q ss_pred cCCeEEEEEEEEEecCcEEEEE----C--CEEEEEeccccCCCCccccccCCeEEEEEEEeeccc---ceEEeehhhh
Q 015066 186 SEDVVVKGKVVGANKGGVVAEV----E--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQ---SRLVLSNRKA 254 (414)
Q Consensus 186 ~~g~iv~G~V~~v~~~G~~V~i----~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~---~ri~LS~K~~ 254 (414)
..|++++|+|.++.+++++|++ | ++.|+||.++...... ...|+.++|.|.+|+... -.|.||+...
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~--y~~Gdrika~i~~V~~~~~kGpqIilSRt~p 226 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDN--YRANATFKVFLKEVSEGPRRGPQLFVSRANA 226 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCc--CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence 3588999999999999999998 4 3999999998764422 127999999999998763 2589998654
No 185
>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=96.21 E-value=0.02 Score=45.52 Aligned_cols=60 Identities=18% Similarity=0.176 Sum_probs=38.4
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeC------------------CCeeEEEcCccccccccCC--ccccCccCCcEEEEEEEE
Q 015066 98 ELGTKVKGTVFCTDNRGALVDIT------------------AKSSAYLPTQEACIHKIKH--VEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig------------------~k~~g~lp~sEls~~~~~~--~~e~~~~vG~~v~v~Vl~ 157 (414)
++|++|.|+|+++....++++|- ....|.|+.+++....... +.+- |++||.|.++|++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~-FrpGDIVrA~ViS 81 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC-FRPGDIVRARVIS 81 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT---SSSEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc-cCCCCEEEEEEee
Confidence 68999999999999999988872 1246788888776544333 2333 8999999999987
Q ss_pred E
Q 015066 158 E 158 (414)
Q Consensus 158 i 158 (414)
+
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 4
No 186
>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=96.20 E-value=0.029 Score=45.96 Aligned_cols=67 Identities=21% Similarity=0.227 Sum_probs=51.8
Q ss_pred HHHHHHHHhhcc---cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066 84 EEFHSALEKYDF---NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 84 ~~f~~~l~~~~~---~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
+.|++++...-. --..|.+|.|+|..+..+-+|+|+|+|-.++|+..+... +. +..|.+|.+++...
T Consensus 5 ~sFaslLR~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~-y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 5 ESFASLLRNSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EK-YVRGSRVRLRLKDL 74 (104)
T ss_pred ccHHHHhcCChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cc-cccCCEEEEEECCH
Confidence 568887754331 225899999999999999999999999999999765421 22 77899998888554
No 187
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=95.93 E-value=0.034 Score=50.57 Aligned_cols=72 Identities=21% Similarity=0.170 Sum_probs=60.9
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~----------k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
-++.|++|-|.|+++....+.|.+-+ -..|-+|.++....+.++.++. |.+||.++++|++.- ..+
T Consensus 61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~-f~~GDivrA~Vis~~---~~~ 136 (188)
T COG1096 61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDA-FRIGDIVRARVISTG---DPI 136 (188)
T ss_pred CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccc-cccccEEEEEEEecC---CCe
Confidence 46889999999999999999988721 1467899999999888888887 999999999999964 568
Q ss_pred EEEeee
Q 015066 166 VLSLRM 171 (414)
Q Consensus 166 ~LS~k~ 171 (414)
.||.+.
T Consensus 137 ~Lst~~ 142 (188)
T COG1096 137 QLSTKG 142 (188)
T ss_pred EEEecC
Confidence 888864
No 188
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.81 E-value=0.022 Score=63.22 Aligned_cols=60 Identities=20% Similarity=0.279 Sum_probs=47.6
Q ss_pred CCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccccC---------CccccCccCCcEEEEEEEEE
Q 015066 98 ELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIK---------HVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~~~---------~~~e~~~~vG~~v~v~Vl~i 158 (414)
.+|.|+.|+|.++.+ +++||+||.+..||||.++....... +..+. +++|+.|-|.|...
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~-Lk~GqeILVQV~KE 107 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDKE 107 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccc-cCCCCEEEEEEeec
Confidence 589999999999998 69999999999999999988532211 11222 67899999998774
No 189
>PRK11712 ribonuclease G; Provisional
Probab=95.79 E-value=0.021 Score=60.04 Aligned_cols=62 Identities=21% Similarity=0.331 Sum_probs=47.6
Q ss_pred cCCCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccc------------cCCccccCccCCcEEEEEEEEE
Q 015066 96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHK------------IKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~------------~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
...+|.++.|+|.++.+ ++||||||.+..||+|.+++.... .....+. +++|+.+-|.|+..
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISEL-VRQGQDIMVQVVKD 110 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHh-ccCCCEEEEEEEeC
Confidence 44689999999999999 689999999999999999873100 0112233 77899999888764
No 190
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=95.20 E-value=0.13 Score=46.17 Aligned_cols=72 Identities=19% Similarity=0.296 Sum_probs=55.8
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC---------CEEEEEeecccCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHD--RVADIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~---------gv~Glvh~sels~~--~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
+.+|+||+++|.++..--+-|+|- -..|++|..++... --..+.+.|++||.|.|+|++.+ .+....|
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~-~~~~y~L 144 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG-DGSNYLL 144 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC-CCCcEEE
Confidence 568999999999998877777762 28999999988653 12356677999999999999964 4667777
Q ss_pred EEee
Q 015066 331 STKK 334 (414)
Q Consensus 331 S~K~ 334 (414)
|.-+
T Consensus 145 TtAe 148 (193)
T KOG3409|consen 145 TTAE 148 (193)
T ss_pred EEec
Confidence 7654
No 191
>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=94.99 E-value=0.13 Score=44.05 Aligned_cols=62 Identities=15% Similarity=0.099 Sum_probs=44.7
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC------------CccccCccCCcEEEEEEEEEeC
Q 015066 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK------------HVEEAGIVPGLKEEFVIIGENE 160 (414)
Q Consensus 99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~------------~~~e~~~~vG~~v~v~Vl~id~ 160 (414)
+|+++.|+|.+.+..|+.|.++.-.+-|||.+.|.....- .-.+.-+..|+.|+|+|.++.-
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 6999999999999999999999888999999988631100 1112225679999999988753
No 192
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=94.86 E-value=0.1 Score=57.59 Aligned_cols=84 Identities=10% Similarity=0.059 Sum_probs=63.0
Q ss_pred HHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEcCccccccccCC-c---------cccCccCCcEEEEE
Q 015066 86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIKH-V---------EEAGIVPGLKEEFV 154 (414)
Q Consensus 86 f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k-~~g~lp~sEls~~~~~~-~---------~e~~~~vG~~v~v~ 154 (414)
+...|......-.+|+...|+|.++..+|+||.+... .+|+++.+.+...+... . ....+..|+.++++
T Consensus 609 ~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~ 688 (706)
T COG0557 609 VIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK 688 (706)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence 3344433333567999999999999999999999765 89999999998532211 1 11127789999999
Q ss_pred EEEEeCCCCeEEEEe
Q 015066 155 IIGENEADDSLVLSL 169 (414)
Q Consensus 155 Vl~id~~~~~i~LS~ 169 (414)
|.+++...+++.+++
T Consensus 689 v~~v~~~~~~i~~~~ 703 (706)
T COG0557 689 VTSVDLDERKIDFEL 703 (706)
T ss_pred EEEEcccccceEEEe
Confidence 999998888888765
No 193
>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=94.58 E-value=0.2 Score=54.64 Aligned_cols=71 Identities=13% Similarity=0.149 Sum_probs=54.1
Q ss_pred CCC--CEEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccc--ccc---CCc------cccCccCCcEEEEEEEEEeCCCC
Q 015066 98 ELG--TKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--HKI---KHV------EEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 98 ~~G--~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~--~~~---~~~------~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
++| +...|.|+.+..+|+||.+ ..+.+|++|.+.+.+ ... .+- ....|..|++|+++|.++|...+
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence 454 5899999999999999999 566999999998864 111 000 11137889999999999998888
Q ss_pred eEEEE
Q 015066 164 SLVLS 168 (414)
Q Consensus 164 ~i~LS 168 (414)
++.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 87653
No 194
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.97 E-value=0.33 Score=43.13 Aligned_cols=64 Identities=20% Similarity=0.301 Sum_probs=46.3
Q ss_pred ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCc----ccccC-c------ccccCCCCEEEEEEEEEeCCCCe
Q 015066 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISH----DRVAD-I------ATVLQPGDTLKVMILSHDRERGR 327 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~----~~~~~-~------~~~~~~G~~V~vkVl~id~e~~r 327 (414)
.|+++.|+|+.+...|+|++.+-++-++..-.+.. ..-+| | .+..++|..|.++|+...-+...
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~ 155 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE 155 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeee
Confidence 69999999999999999999997776665433321 11222 1 12688999999999987654444
No 195
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=93.71 E-value=0.095 Score=55.27 Aligned_cols=73 Identities=29% Similarity=0.456 Sum_probs=57.2
Q ss_pred hhccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCcccccCc-----ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066 260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHDRVADI-----ATVLQPGDTLKVMILSHDRERGRVSLS 331 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~~~~~~~-----~~~~~~G~~V~vkVl~id~e~~ri~LS 331 (414)
....+|.+|.|+|++|.|. .+||+++ +-.||+|.+++.+ +...+ +..++.||.+-|.|+.-....+--.||
T Consensus 33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred cEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCccccccce
Confidence 4556899999999999984 7899999 7999999999988 43333 458999999999999876544433444
Q ss_pred Ee
Q 015066 332 TK 333 (414)
Q Consensus 332 ~K 333 (414)
..
T Consensus 112 ~~ 113 (487)
T COG1530 112 TD 113 (487)
T ss_pred eE
Confidence 33
No 196
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=93.17 E-value=0.53 Score=37.62 Aligned_cols=63 Identities=21% Similarity=0.361 Sum_probs=51.4
Q ss_pred EEEEEEEEEeeceEE-EEEC-CEEEEEeecc-cCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 267 VVIGTVQSLKPYGAF-IDIG-GINGLLHVSQ-ISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 267 iv~g~V~~i~~~G~f-V~l~-gv~Glvh~se-ls~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
.+.|+|+.+.+.+.| |+|+ |..-+.|+|- |...+ -.+.+||.|+|-+--+|.++++|..-.|.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r-----IrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR-----IRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee-----EEecCCCEEEEEECcccCCceeEEEEecC
Confidence 478999999999888 6887 8888888874 32222 24679999999999999999999998884
No 197
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.02 E-value=0.58 Score=41.64 Aligned_cols=63 Identities=17% Similarity=0.207 Sum_probs=41.2
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc----ccCC-c-----cccCccCCcEEEEEEEEEe
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH----KIKH-V-----EEAGIVPGLKEEFVIIGEN 159 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~----~~~~-~-----~e~~~~vG~~v~v~Vl~id 159 (414)
..-.|++|.|+|+++.+.|+|+++|. .+-|+...-...+ +-.+ | .+....+|.+|+++|+...
T Consensus 78 kpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 78 KPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred eecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 34579999999999999999999986 5555543322211 1111 0 0102567888888887764
No 198
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=92.90 E-value=0.48 Score=42.57 Aligned_cols=73 Identities=19% Similarity=0.147 Sum_probs=52.2
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe---CC-----CeeEEEcCccccccccCCcc-ccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066 97 SELGTKVKGTVFCTDNRGALVDI---TA-----KSSAYLPTQEACIHKIKHVE-EAGIVPGLKEEFVIIGENEADDSLVL 167 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdi---g~-----k~~g~lp~sEls~~~~~~~~-e~~~~vG~~v~v~Vl~id~~~~~i~L 167 (414)
...|++|+++|.+++...+.|+| ++ ..+|+|+..++-......++ -.+|.+|+.|.++|++... .....|
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~L 144 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYLL 144 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEEE
Confidence 46899999999999999888877 22 35799998887532221111 1238899999999999654 445666
Q ss_pred Eee
Q 015066 168 SLR 170 (414)
Q Consensus 168 S~k 170 (414)
|.-
T Consensus 145 TtA 147 (193)
T KOG3409|consen 145 TTA 147 (193)
T ss_pred EEe
Confidence 653
No 199
>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=92.60 E-value=0.58 Score=35.79 Aligned_cols=58 Identities=31% Similarity=0.493 Sum_probs=46.5
Q ss_pred EEEEEEEEEeeceEE-EEEC-CEEEEEeecc-cCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066 267 VVIGTVQSLKPYGAF-IDIG-GINGLLHVSQ-ISHDRVADIATVLQPGDTLKVMILSHDRERGRVS 329 (414)
Q Consensus 267 iv~g~V~~i~~~G~f-V~l~-gv~Glvh~se-ls~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~ 329 (414)
.+.|.|+...+.+.| |++. |..-++|++- |... .-.+.+||.|.|-+-..|.++++|.
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 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMH-----YIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhc-----cEEECCCCEEEEEECcccCCcEeEE
Confidence 478999999999888 6887 8999999874 3222 2247899999999999999888875
No 200
>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=92.28 E-value=0.71 Score=39.53 Aligned_cols=56 Identities=18% Similarity=0.233 Sum_probs=42.2
Q ss_pred CCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC--Cc---------c---ccc---cCCeEEEEEEEeec
Q 015066 187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--ST---------A---EEL---LGKDLPLKFVEVDE 242 (414)
Q Consensus 187 ~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~--~~---------~---~~~---vGq~V~vkVl~vD~ 242 (414)
.|+++.|+|++.++.|+.|.++ --+-|||.+.|... ++ . .++ .|++|++||.++..
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 3789999999999999999998 56789999999843 11 1 111 59999999998865
No 201
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=91.63 E-value=1.3 Score=38.47 Aligned_cols=69 Identities=17% Similarity=0.196 Sum_probs=53.8
Q ss_pred HHHHHHHHHhhc---ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066 83 LEEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159 (414)
Q Consensus 83 ~~~f~~~l~~~~---~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id 159 (414)
.+.|++++.... ..-..|..|.|+|..+..+-+|+|+|+|..+.|..-++. .++ |..|.+|..+++..+
T Consensus 63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n------~e~--Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN------GEA--YQKGARVRLRLIDLE 134 (173)
T ss_pred hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC------HHH--hhcCceEEEEEcChh
Confidence 568999885433 234679999999999999999999999999999876663 222 677888888886643
No 202
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=89.41 E-value=0.55 Score=49.63 Aligned_cols=73 Identities=21% Similarity=0.214 Sum_probs=52.5
Q ss_pred cCCCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccccCCccc----cCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIKHVEE----AGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~~~~~~e----~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
...+|.++.|+|.++.+ ..+|||||....||+|.++...+ .+.+.+ ..++.|+.+-+.|+......+-..||.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~-~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~ 112 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPY-FRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTT 112 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccchh-hhhcccccceeeecCCceEEEEEEeecCcccccccee
Confidence 34689999999999999 47999999999999999999873 222222 226778888777776543333333333
No 203
>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=88.85 E-value=2 Score=35.41 Aligned_cols=53 Identities=17% Similarity=0.345 Sum_probs=44.1
Q ss_pred cccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066 263 GIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322 (414)
Q Consensus 263 ~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id 322 (414)
..|.+|.|+|..+.+.-+||++++ ..+.|....... +.|.+|.+|.+++....
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 479999999999999999999996 999998665432 35889999999887654
No 204
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=88.38 E-value=2.2 Score=34.14 Aligned_cols=64 Identities=17% Similarity=0.163 Sum_probs=46.6
Q ss_pred eEEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066 189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 189 ~iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K 252 (414)
-.++|+|+....++.| |.+. |..-+.++|==.......-+.|+.|.+.+-.+|..+++|+.-.+
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 4688999999888877 6875 65555544432222233445799999999999999999987665
No 205
>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=86.62 E-value=4 Score=31.23 Aligned_cols=60 Identities=18% Similarity=0.246 Sum_probs=42.3
Q ss_pred eEEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEE
Q 015066 189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLV 248 (414)
Q Consensus 189 ~iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~ 248 (414)
-.+.|+|+....++.| |.+. |..-+.+.+-=.......-..|+.|.+.+-.+|.++++|+
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 3678999999888877 6875 6555554443222223333469999999999998888875
No 206
>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=85.95 E-value=2.4 Score=31.48 Aligned_cols=64 Identities=27% Similarity=0.347 Sum_probs=40.8
Q ss_pred cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
|+..+-.|..++..|-..--+ .+.|+. +...|+..-...+-+||++++-|+.+|.-+-.+..|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 455666677766555443333 366652 2223444445568899999999999997666666664
No 207
>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=83.99 E-value=14 Score=27.37 Aligned_cols=50 Identities=14% Similarity=0.214 Sum_probs=35.0
Q ss_pred EEEEEEEEeC--CeEEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 103 VKGTVFCTDN--RGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 103 V~G~V~~v~~--~G~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
.+|+|...++ +.-|+.- ++..+-|+|.+++...... .+..|+.|+|.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~-----~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFR-----SLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSST-----S--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccc-----cCCCCCEEEEEEEE
Confidence 4799999987 3345544 4445899999998754311 26789999999977
No 208
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=82.55 E-value=8.8 Score=29.94 Aligned_cols=64 Identities=28% Similarity=0.430 Sum_probs=48.5
Q ss_pred EEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 266 SVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
-.+.|+|....+.+-| |.+. |..-+.|++-=-.. -.--+.+||.|.|..-..|.++++|..-.+
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 4588999999988876 8887 88889898742211 122368999999999999988888766554
No 209
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=82.45 E-value=5.7 Score=37.03 Aligned_cols=63 Identities=17% Similarity=0.055 Sum_probs=49.4
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id 159 (414)
|-..+||.|-|.|+.....+..|||++-..|.+|.--+.....++-. ++++|+.+-++|...+
T Consensus 61 YiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a~ 123 (230)
T KOG1004|consen 61 YIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDAN 123 (230)
T ss_pred ecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--ccccccEEEEEEEecC
Confidence 46789999999999999999999999877888887655433222222 2789999999998765
No 210
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=81.01 E-value=19 Score=26.73 Aligned_cols=48 Identities=29% Similarity=0.515 Sum_probs=35.4
Q ss_pred EEEEEEEEee---ceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEE
Q 015066 268 VIGTVQSLKP---YGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320 (414)
Q Consensus 268 v~g~V~~i~~---~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~ 320 (414)
.+|+|+...+ || ||.-. +-+-++|++++.... ...+..|+.|...+..
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 3799999885 44 55555 369999999997654 3467899999998887
No 211
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=77.37 E-value=19 Score=27.94 Aligned_cols=61 Identities=23% Similarity=0.274 Sum_probs=43.3
Q ss_pred EEEEEEEee-ceE-EEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 269 IGTVQSLKP-YGA-FIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 269 ~g~V~~i~~-~G~-fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+|+|+...+ .|. ||.-. +-+-++|+|.+...- ...+..||.|...+..-. +++-...+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGP--KGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEECC--CCceeeEEEEC
Confidence 488888765 455 67665 589999999996542 235789999999877643 56655556555
No 212
>PRK15464 cold shock-like protein CspH; Provisional
Probab=76.47 E-value=8.9 Score=29.43 Aligned_cols=49 Identities=14% Similarity=0.119 Sum_probs=34.7
Q ss_pred EEEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 191 VKGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 191 v~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.+|+|+..+. .|+ |+.. + +-+.|+|++.+..........|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEE
Confidence 4799999965 354 5544 3 6899999999964422223379999997655
No 213
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=75.51 E-value=11 Score=31.20 Aligned_cols=63 Identities=13% Similarity=0.218 Sum_probs=46.5
Q ss_pred cEEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 265 GSVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
...+.|+|+.....+.| |.+. |..-|+|++- ++.. .--++.||.|.|-....|..+++|..-+
T Consensus 20 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~ 84 (100)
T PRK04012 20 EGEVFGVVEQMLGANRVRVRCMDGVERMGRIPG----KMKK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 34588999999998887 5776 8888988864 2222 3357899999999988886666655443
No 214
>PRK10943 cold shock-like protein CspC; Provisional
Probab=74.89 E-value=26 Score=26.64 Aligned_cols=51 Identities=20% Similarity=0.309 Sum_probs=36.3
Q ss_pred EEEEEEEEEeC-Ce-EEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 102 KVKGTVFCTDN-RG-ALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 102 iV~G~V~~v~~-~G-~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
.++|+|...+. .| =|+.- +++.+.|+|.+.+....... +..|+.|++.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKT-----LAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCC-----CCCCCEEEEEEEE
Confidence 57899999877 33 25544 44579999999886432222 5789999998866
No 215
>PRK15464 cold shock-like protein CspH; Provisional
Probab=74.63 E-value=23 Score=27.14 Aligned_cols=50 Identities=18% Similarity=0.329 Sum_probs=36.1
Q ss_pred EEEEEEEEeC-CeE-EEEeC-CCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 103 VKGTVFCTDN-RGA-LVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 103 V~G~V~~v~~-~G~-~Vdig-~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
++|+|...+. .|. |+.-. ++.+.|+|.+.+.....+. +.+|+.|++.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~-----l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEV-----LIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCC-----CCCCCEEEEEEEE
Confidence 4899999887 343 66554 4578999999985432222 5789999999966
No 216
>PRK10943 cold shock-like protein CspC; Provisional
Probab=74.11 E-value=12 Score=28.56 Aligned_cols=50 Identities=22% Similarity=0.302 Sum_probs=34.8
Q ss_pred EEEEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 190 VVKGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 190 iv~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.++|+|+..+. .|+ |+.- + +-+.|+|+|.+..........|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEE
Confidence 56899999865 343 4433 3 7899999999985422222379999997655
No 217
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=73.84 E-value=49 Score=32.75 Aligned_cols=114 Identities=21% Similarity=0.319 Sum_probs=72.4
Q ss_pred cCCeEEEEEEEEEe-cCcEE-EEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhhHHhhcc
Q 015066 186 SEDVVVKGKVVGAN-KGGVV-AEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLG 263 (414)
Q Consensus 186 ~~g~iv~G~V~~v~-~~G~~-V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~~~~l~ 263 (414)
+.+.+++|+|..-. .+|+. +.++...-.+|.-. .-+|+.++++|-.-| +.+.+++.. ...
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~~~--------a~~g~~~R~~I~a~D-----Vslal~~P~-----~~S 291 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKLD--------APVGARLRIRIQARD-----VSLALQKPE-----QTS 291 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecCceEEEeeccC--------CCCCCcEEEEEEccc-----eEEEecCcc-----ccc
Confidence 45789999999885 45665 34454444444322 227999999885543 556655432 233
Q ss_pred ccEEEEEEEEEEeeceEE----EEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066 264 IGSVVIGTVQSLKPYGAF----IDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~f----V~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id 322 (414)
.-.+..|+|++|.+.+-- ++++|-.=...++.++.+. -.+++||.|-+.|.++.
T Consensus 292 irNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~srd~-----L~l~~G~~v~AqIKsVs 349 (352)
T COG4148 292 IRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWARDE-----LALKPGQWVYAQIKSVS 349 (352)
T ss_pred hhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhhHHh-----hcCCCCCeEEEEEEEEE
Confidence 445788889988865433 3334555555666665543 24899999999998774
No 218
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=73.74 E-value=26 Score=26.68 Aligned_cols=51 Identities=20% Similarity=0.360 Sum_probs=35.9
Q ss_pred EEEEEEEEEeC-Ce-EEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 102 KVKGTVFCTDN-RG-ALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 102 iV~G~V~~v~~-~G-~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
.++|+|...+. .| =|+.- +++.+.|+|.+.+.....+. +.+|+.|++.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKT-----LAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCC-----CCCCCEEEEEEEE
Confidence 57899999876 33 25554 44578999999885432222 5789999998866
No 219
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=72.84 E-value=5.3 Score=37.40 Aligned_cols=83 Identities=20% Similarity=0.271 Sum_probs=55.6
Q ss_pred ccCCC--CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccc-cccccCCcccc----CccCCcEEEEEEEEEeCCCCeEEE
Q 015066 95 FNSEL--GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEA-CIHKIKHVEEA----GIVPGLKEEFVIIGENEADDSLVL 167 (414)
Q Consensus 95 ~~l~~--G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEl-s~~~~~~~~e~----~~~vG~~v~v~Vl~id~~~~~i~L 167 (414)
+.++. |+++.|++.+..+.|+.++++ +...-+|.++| ...+ ..+.++ ++-.-..++++|+..+.. ....|
T Consensus 68 ~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~-g~~~Qi~~rFG~V~hlPvev~~v~~~~~-~~~rl 144 (225)
T PF09883_consen 68 YSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGP-GSPRQIRRRFGLVQHLPVEVEFVKVEDG-IEARL 144 (225)
T ss_pred chhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCC-CCHHHHHHHhCcccCCceEEEEEEcccC-ccccc
Confidence 34555 999999999999999999997 67888899888 4332 333322 234456778899887643 44555
Q ss_pred EeeehhhhHHHHH
Q 015066 168 SLRMIQYELAWER 180 (414)
Q Consensus 168 S~k~~~~~~~~~~ 180 (414)
|-++...-..|.+
T Consensus 145 td~q~d~l~~W~~ 157 (225)
T PF09883_consen 145 TDEQVDRLYEWTR 157 (225)
T ss_pred CHHHHHHHHHHhh
Confidence 5554444344543
No 220
>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=72.78 E-value=14 Score=28.87 Aligned_cols=60 Identities=13% Similarity=0.227 Sum_probs=43.4
Q ss_pred EEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 268 VIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 268 v~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
+.|+|+.....+.| |.+. |..-++|++- ++.. .--+++||.|.|.....|..+++|.--+
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~g----K~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRG----KMRK-RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 56899999988887 6776 8888888764 1222 3357899999999888876555554433
No 221
>PRK15463 cold shock-like protein CspF; Provisional
Probab=71.44 E-value=16 Score=28.00 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=35.9
Q ss_pred EEEEEEEEeC-CeE-EEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 103 VKGTVFCTDN-RGA-LVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 103 V~G~V~~v~~-~G~-~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
++|+|...+. .|. |+.- +++.+.|+|.+.+.....+. +.+|+.|++.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~-----l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEE-----LTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCC-----CCCCCEEEEEEEE
Confidence 4899999887 332 5555 44578999999986432222 5789999998865
No 222
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=71.16 E-value=30 Score=26.82 Aligned_cols=60 Identities=13% Similarity=0.159 Sum_probs=39.4
Q ss_pred EEEEEEEeC-CeE-EEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 104 KGTVFCTDN-RGA-LVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 104 ~G~V~~v~~-~G~-~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
+|+|...+. .|. |+.. +++.+.|+|.+.+.....+. +..|+.|++.+.. ..+|.-.....
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~-----l~~G~~V~f~~~~--~~~G~~A~~V~ 65 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT-----LKAGQSVQFDVHQ--GPKGNHASVIV 65 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCC-----CCCCCEEEEEEEE--CCCCceeeEEE
Confidence 588998876 332 5544 45688999999885432222 6789999999866 34554444333
No 223
>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=70.68 E-value=15 Score=26.91 Aligned_cols=47 Identities=30% Similarity=0.406 Sum_probs=32.0
Q ss_pred CEEEEEEEEEeCCe----EEEEeCCC--eeEEEcCccccccccCCccccCccCCcEEEEEE
Q 015066 101 TKVKGTVFCTDNRG----ALVDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (414)
Q Consensus 101 ~iV~G~V~~v~~~G----~~Vdig~k--~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~V 155 (414)
-.+.|+|..+...| +++++++. ..+.++...+ .+.++.+|+++.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~--------~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA--------EELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH--------HHCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH--------HHcCCCCCCEEEEEE
Confidence 46899999999988 66777765 3456655433 344578999998876
No 224
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=70.37 E-value=35 Score=25.93 Aligned_cols=50 Identities=16% Similarity=0.229 Sum_probs=34.9
Q ss_pred EEEEEEEEeC-Ce-EEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 103 VKGTVFCTDN-RG-ALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 103 V~G~V~~v~~-~G-~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
++|+|...++ .| =|+.- +++.+.|+|.+.+....... +.+|+.|++.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKS-----LDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCC-----CCCCCEEEEEEEE
Confidence 4899999875 22 35554 44578999999886432222 6789999998865
No 225
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.90 E-value=13 Score=34.72 Aligned_cols=84 Identities=21% Similarity=0.190 Sum_probs=54.5
Q ss_pred ccCCCCCEEEEEEEEEeC--CeEEEEeCCC----eeEEEcCccccccccCCc-cc----cCccCCcEEEEEEEEEeCCCC
Q 015066 95 FNSELGTKVKGTVFCTDN--RGALVDITAK----SSAYLPTQEACIHKIKHV-EE----AGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~--~G~~Vdig~k----~~g~lp~sEls~~~~~~~-~e----~~~~vG~~v~v~Vl~id~~~~ 163 (414)
.+++.|+++-|+.....+ .|+||+++-. .++++|..+|....-.++ .+ .++-.-..+++.|..+|...+
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~ 150 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQ 150 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhh
Confidence 478899999999999987 5677777542 468999998865443333 22 223445778899988876544
Q ss_pred eE--EEEeeehhhhHHH
Q 015066 164 SL--VLSLRMIQYELAW 178 (414)
Q Consensus 164 ~i--~LS~k~~~~~~~~ 178 (414)
.+ .|+-+....-..|
T Consensus 151 EIea~ltd~qvd~l~gw 167 (247)
T COG4044 151 EIEARLTDKQVDKLKGW 167 (247)
T ss_pred hhhhhhhHHHHHHHHhh
Confidence 43 3444433333334
No 226
>PRK15463 cold shock-like protein CspF; Provisional
Probab=69.30 E-value=15 Score=28.16 Aligned_cols=49 Identities=14% Similarity=0.123 Sum_probs=34.5
Q ss_pred EEEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 191 VKGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 191 v~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.+|+|+..+. .|+ |+.. + +-+.|+|++.+...-......|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEE
Confidence 4799999965 344 4444 3 7899999999985422223379999997654
No 227
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=68.78 E-value=19 Score=27.37 Aligned_cols=50 Identities=22% Similarity=0.286 Sum_probs=34.4
Q ss_pred EEEEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 190 VVKGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 190 iv~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.++|+|+..+. .|+ |+.- + +-+.|+|+|.+..........|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEE
Confidence 46799999864 343 4444 3 6899999999975422222379999997655
No 228
>PRK09890 cold shock protein CspG; Provisional
Probab=68.57 E-value=46 Score=25.36 Aligned_cols=50 Identities=14% Similarity=0.228 Sum_probs=35.0
Q ss_pred EEEEEEEEeC-Ce-EEEEeC-CCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 103 VKGTVFCTDN-RG-ALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 103 V~G~V~~v~~-~G-~~Vdig-~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
.+|+|...++ .| =|+.-. ++.+.|+|.+.+.....+. +.+|+.|++.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~-----l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRT-----LNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCC-----CCCCCEEEEEEEE
Confidence 4899999876 23 355544 4578999999886443222 5789999998755
No 229
>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=68.20 E-value=30 Score=28.35 Aligned_cols=69 Identities=22% Similarity=0.379 Sum_probs=40.1
Q ss_pred EEEEEEEEEeece--EEEEEC-C---EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 267 VVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 267 iv~g~V~~i~~~G--~fV~l~-g---v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
.+.|+|.++...| +|+++. | +..++...+............+..|+.|.|.=.=....++.+.|..+.+
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~ 77 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEF 77 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEe
Confidence 4789999998765 789986 3 6666654443222222333348899998764322222345555544433
No 230
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=67.03 E-value=12 Score=34.19 Aligned_cols=62 Identities=13% Similarity=0.106 Sum_probs=45.4
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCC----------------ccccCccCCcEEEEEEEEE
Q 015066 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKH----------------VEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~----------------~~e~~~~vG~~v~v~Vl~i 158 (414)
.=+|+++.|+|.+-...|+-|.++.-.+-|+|..-|....... .++.-+-+|..|+|+|.+.
T Consensus 79 PF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 79 PFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 4579999999999999999999998788999988664321111 1222245688888888765
No 231
>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=66.32 E-value=29 Score=25.84 Aligned_cols=64 Identities=22% Similarity=0.261 Sum_probs=40.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEE-EcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 100 GTKVKGTVFCTDNRGALVDITAKSSAY-LPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 100 G~iV~G~V~~v~~~G~~Vdig~k~~g~-lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
|+.++-.|..+..+|-.+--++...|. +..+.. +....++.+|+++++.|+.+|--+-++.+|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~Atry------H~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRY------HKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEE------EecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 677788888877766544445444443 222211 1223337799999999999997666666663
No 232
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=66.15 E-value=22 Score=33.27 Aligned_cols=60 Identities=25% Similarity=0.219 Sum_probs=44.1
Q ss_pred ccccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCc-ccccCcccccCCCCEEEEEEEEEeC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISH-DRVADIATVLQPGDTLKVMILSHDR 323 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~-~~~~~~~~~~~~G~~V~vkVl~id~ 323 (414)
+.+||.|-|.|+.-...+.-|+++| -.+.++.-.+.. .+-+.| .+++||.|-|+|..-++
T Consensus 63 P~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--ccccccEEEEEEEecCC
Confidence 5689999999999999999999997 555554432221 122333 48999999999997753
No 233
>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=64.52 E-value=38 Score=24.91 Aligned_cols=49 Identities=27% Similarity=0.398 Sum_probs=35.6
Q ss_pred EEEEEEEee-ceE-EEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066 269 IGTVQSLKP-YGA-FIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 269 ~g~V~~i~~-~G~-fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i 321 (414)
.|+|+...+ .|. ||... |-+-++|.+.+...- ...+++||.|...+..-
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 588888765 233 55554 789999999997542 24678999999977665
No 234
>PRK14998 cold shock-like protein CspD; Provisional
Probab=63.73 E-value=50 Score=25.46 Aligned_cols=57 Identities=12% Similarity=0.159 Sum_probs=37.9
Q ss_pred EEEEEEEeC-Ce-EEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066 104 KGTVFCTDN-RG-ALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL 167 (414)
Q Consensus 104 ~G~V~~v~~-~G-~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~L 167 (414)
+|+|...+. .| =|+.- +++.+.|+|.+.+.....+. +..|+.|++.+.. ..+|.-..
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~-----l~~G~~V~f~~~~--~~~G~~A~ 62 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT-----LKAGQSVRFDVHQ--GPKGNHAS 62 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCC-----CCCCCEEEEEEEE--CCCCceeE
Confidence 589998876 33 25544 44578999999885432222 6789999999866 34554333
No 235
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.45 E-value=9.8 Score=35.42 Aligned_cols=76 Identities=20% Similarity=0.346 Sum_probs=52.6
Q ss_pred hhccccEEEEEEEEEEee--ceEEEEEC--C---EEEEEeecccCcccccCc----ccc--cCCCCEEEEEEEEEeCCCC
Q 015066 260 AQLGIGSVVIGTVQSLKP--YGAFIDIG--G---INGLLHVSQISHDRVADI----ATV--LQPGDTLKVMILSHDRERG 326 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~--~G~fV~l~--g---v~Glvh~sels~~~~~~~----~~~--~~~G~~V~vkVl~id~e~~ 326 (414)
.+++.|++|-|+.....+ ||++|.++ | .++|++..+|....-..| ... +-..-.|.|-|..+|+..+
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~ 150 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQ 150 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhh
Confidence 578899999999999875 67777776 3 789999988866544333 222 3345567888888887655
Q ss_pred eE--EEEEeeC
Q 015066 327 RV--SLSTKKL 335 (414)
Q Consensus 327 ri--~LS~K~~ 335 (414)
.| .|+=|++
T Consensus 151 EIea~ltd~qv 161 (247)
T COG4044 151 EIEARLTDKQV 161 (247)
T ss_pred hhhhhhhHHHH
Confidence 54 4444443
No 236
>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=62.42 E-value=45 Score=25.20 Aligned_cols=49 Identities=14% Similarity=0.231 Sum_probs=34.0
Q ss_pred EEEEEEEeC-CeE-EEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 104 KGTVFCTDN-RGA-LVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 104 ~G~V~~v~~-~G~-~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
+|+|...+. .|. |+.- +++.+.|+|.+.+.....+. +..|+.|++.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~-----l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRT-----LKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCC-----CCCCCEEEEEEEE
Confidence 589998875 332 5554 44578999999985432222 5789999998865
No 237
>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=61.99 E-value=27 Score=25.48 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=27.2
Q ss_pred EEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 193 GKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 193 G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
|++....++-.||... +-+-|||..++....+ |++|.|+++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~~-----gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGAMD-----GDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS-T-----T-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCCCC-----CCEEEEEEec
Confidence 4455554443455553 8999999999886654 9999999988
No 238
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=59.65 E-value=56 Score=25.52 Aligned_cols=61 Identities=21% Similarity=0.274 Sum_probs=41.0
Q ss_pred EEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEee
Q 015066 190 VVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLS 250 (414)
Q Consensus 190 iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS 250 (414)
.+.|+|.....++-| |.+. |..-.-|++-=.......-..|+.|.+....+|.++++|.--
T Consensus 8 e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~R 70 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYR 70 (75)
T ss_pred EEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEE
Confidence 689999999888876 7774 544333332211111233346999999999999888887654
No 239
>PRK14998 cold shock-like protein CspD; Provisional
Probab=59.22 E-value=29 Score=26.81 Aligned_cols=49 Identities=18% Similarity=0.151 Sum_probs=33.6
Q ss_pred EEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEEe
Q 015066 192 KGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240 (414)
Q Consensus 192 ~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~v 240 (414)
+|+|+..+. .|+ |+.. + +-+.|+|+|.+..........|+.|.+.+..=
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEEC
Confidence 488998864 344 4444 3 78999999999744222233799999987653
No 240
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=58.97 E-value=24 Score=30.74 Aligned_cols=54 Identities=19% Similarity=0.393 Sum_probs=45.2
Q ss_pred ccccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id 322 (414)
--.|.+|.|+|-.+...-+||+|++ ..+.|....+.. +.|..|..|..+++...
T Consensus 80 ~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~-------e~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 80 DAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNG-------EAYQKGARVRLRLIDLE 134 (173)
T ss_pred CcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCH-------HHhhcCceEEEEEcChh
Confidence 3468999999999999999999995 888888776653 35789999999998765
No 241
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=58.30 E-value=17 Score=27.36 Aligned_cols=62 Identities=15% Similarity=0.065 Sum_probs=41.2
Q ss_pred CEEEEEEEEEeCCeEEEEeCC-CeeEEEc-CccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066 101 TKVKGTVFCTDNRGALVDITA-KSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (414)
Q Consensus 101 ~iV~G~V~~v~~~G~~Vdig~-k~~g~lp-~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~ 164 (414)
...+++|..+.+..+.|.+.. ..-.++| .+++.+-+..+.+ . +++|+.+.+.+...+...+.
T Consensus 2 S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~se-k-lkvG~~l~v~lk~~~~~~~g 65 (69)
T cd05701 2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSE-K-LSVGQCLDVTLKDPNCLAGG 65 (69)
T ss_pred CccchhhhhhhhceEEEEeeccccEEEEEchhhccccccccce-e-eeccceEEEEEecCccCccc
Confidence 345678888899999998854 2334555 5666554433323 2 89999999999776544433
No 242
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=58.20 E-value=16 Score=35.16 Aligned_cols=39 Identities=26% Similarity=0.337 Sum_probs=35.4
Q ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccc
Q 015066 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC 133 (414)
Q Consensus 95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls 133 (414)
|.-++||+|-|+|+.+...-+-|+++.+.+++++.+-+.
T Consensus 81 Y~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvN 119 (301)
T KOG3013|consen 81 YAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVN 119 (301)
T ss_pred cCCccCCEEEEEeeeeecceeEEecccccceEEEeeccc
Confidence 477899999999999999999999999999999987653
No 243
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=57.16 E-value=1.3e+02 Score=29.02 Aligned_cols=102 Identities=15% Similarity=0.229 Sum_probs=60.7
Q ss_pred CHHHHHHHHHhhcccCCCCCEEEEEEEEEeCC--eEEEE--eCCC---eeEEEcCccccccccCCccccCccCCcEEEEE
Q 015066 82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNR--GALVD--ITAK---SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFV 154 (414)
Q Consensus 82 ~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~--G~~Vd--ig~k---~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~ 154 (414)
....+...+..+......-..+.|+|.++... ...|+ +..+ ..+.|...- .++..+.+|+.+.+.
T Consensus 109 ~~~~l~~~l~~~~~k~SarN~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s--------~~~L~l~~G~~v~~~ 180 (263)
T PRK10676 109 PLDSLLAAISRFSLQTSARNQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQS--------AERLGLDEGKEVLVL 180 (263)
T ss_pred chHHHHHHHHHhccCcchhhcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHH--------HhhcCCCCCCeEEEE
Confidence 44555666777765556667899999999865 44444 4322 334443321 233447899998888
Q ss_pred EEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEE
Q 015066 155 IIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAE 206 (414)
Q Consensus 155 Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~ 206 (414)
|-. ..+.++...... .... -.+.|+|.++..+|..+.
T Consensus 181 Ika-----~~V~l~~~~~~~---------~Sar-N~l~g~V~~i~~~~~~~~ 217 (263)
T PRK10676 181 IKA-----PWVGITQDPAVA---------QAAD-NQLPGTISHIERGAEQSE 217 (263)
T ss_pred EEC-----CEEEEEcCCCCC---------CChh-heEEEEEEEEEeCCCcEE
Confidence 744 235665322111 1112 279999999987766543
No 244
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=55.16 E-value=42 Score=24.40 Aligned_cols=55 Identities=18% Similarity=0.217 Sum_probs=31.3
Q ss_pred cccCCeEEEEEEEeecccceEEeehhhh---hhhHHhhccccEEEEEEEEEEeeceEEEE
Q 015066 227 ELLGKDLPLKFVEVDEEQSRLVLSNRKA---MADSQAQLGIGSVVIGTVQSLKPYGAFID 283 (414)
Q Consensus 227 ~~vGq~V~vkVl~vD~e~~ri~LS~K~~---l~~~~~~l~~G~iv~g~V~~i~~~G~fV~ 283 (414)
.++|++++|.|.+.. ..+...--...- ........ .|+.+..+|++..++-++=+
T Consensus 2 ~~~G~~~~VlVe~~~-~~g~~~gr~~~~~~V~v~~~~~~-iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 2 SYVGKTLEVLVEELG-DEGQGIGRTDNGKVVFVPGGLPL-IGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp --TTEEEEEEEEEE--TTSEEEEEET-TEEEEETT--T---TEEEEEEEEEE-SSEEEEE
T ss_pred ccCCcEEEEEEEEec-CCCEEEEEeCCCeEEEECCCCCC-CCCEEEEEEEEeeCCcEEEE
Confidence 357999999999888 444444332211 11111122 69999999999998877643
No 245
>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=53.87 E-value=22 Score=26.31 Aligned_cols=53 Identities=19% Similarity=0.245 Sum_probs=30.6
Q ss_pred EEEEEEEEEEeeceEEEEEC-CEEEE-EeecccCcccccCcccccCCCCEEEEEEEE
Q 015066 266 SVVIGTVQSLKPYGAFIDIG-GINGL-LHVSQISHDRVADIATVLQPGDTLKVMILS 320 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~fV~l~-gv~Gl-vh~sels~~~~~~~~~~~~~G~~V~vkVl~ 320 (414)
..+.|+|.++...|.++++. .+.|- .-...++..... .-.+++|+.|.+.+..
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~--~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA--ELGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh--hCCCCCCCEEEEEEEC
Confidence 46899999998888776653 12111 111122221111 2247899999987754
No 246
>PRK09890 cold shock protein CspG; Provisional
Probab=53.19 E-value=54 Score=24.96 Aligned_cols=49 Identities=18% Similarity=0.195 Sum_probs=33.5
Q ss_pred EEEEEEEEec-C--cEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 191 VKGKVVGANK-G--GVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 191 v~G~V~~v~~-~--G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.+|+|+..+. . |++-.-+ +-+.|+|+|.+..........|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEE
Confidence 4799999864 3 4443333 6899999999985422222379999996544
No 247
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=52.23 E-value=5.1 Score=41.56 Aligned_cols=146 Identities=14% Similarity=0.157 Sum_probs=86.2
Q ss_pred hhhhcCccCCCCCCc--cCcccchhhhhhhhhhc---ccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCC
Q 015066 6 QQFTGLRCPPISHTR--LSRRKSITQIQQKLLNS---RKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVS 80 (414)
Q Consensus 6 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~ 80 (414)
|.|+-.+.-|.|+-- |+-|| ||+.|- ++ |-.++.--+++-+-.-.++-+++..-+.|.-+..+-++
T Consensus 473 qsfae~~t~p~PHFglGl~~YA--TWTSPI--RKY~DMiNHRLlKavi~~~~~~kPqedi~v~lae~Rr~nrmaE----- 543 (645)
T COG4776 473 QSFAEISTEPGPHFGLGLEAYA--TWTSPI--RKYGDMINHRLLKAVIKGETAEKPQEDITVQLAERRRLNRMAE----- 543 (645)
T ss_pred HhHHhhccCcCccccccchhee--eccchh--hhhhhHHHHHHHHHHHcCCCcCCCchHHHHHHHHHHHhhhhhh-----
Confidence 678888888888766 78888 566543 22 33333333445555555666777766666544333221
Q ss_pred CCHHHHHH-HHHhhcc-cCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccccccC---Ccc--------ccCcc
Q 015066 81 FTLEEFHS-ALEKYDF-NSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIK---HVE--------EAGIV 146 (414)
Q Consensus 81 ~~~~~f~~-~l~~~~~-~l~~G~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~~~~~---~~~--------e~~~~ 146 (414)
-+... ++.+|.. .........+.|..+...|+-|.+ .++..+|||..-+...+.. +.+ +..++
T Consensus 544 ---Rdv~DWLY~r~L~~k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk 620 (645)
T COG4776 544 ---RDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYK 620 (645)
T ss_pred ---hhhHHHHHHHHhccccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEe
Confidence 12221 2244432 334566788999999999999987 5668899998755432110 111 11255
Q ss_pred CCcEEEEEEEEEeCCCC
Q 015066 147 PGLKEEFVIIGENEADD 163 (414)
Q Consensus 147 vG~~v~v~Vl~id~~~~ 163 (414)
+|+.+++.+.++..+.+
T Consensus 621 ~~D~i~V~l~eVr~etR 637 (645)
T COG4776 621 VGDVIDVTLAEVRMETR 637 (645)
T ss_pred eccEEEEEeHHHHHhhh
Confidence 66777766666554443
No 248
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=51.64 E-value=55 Score=24.88 Aligned_cols=49 Identities=20% Similarity=0.199 Sum_probs=33.5
Q ss_pred EEEEEEEEec---CcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 191 VKGKVVGANK---GGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 191 v~G~V~~v~~---~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.+|+|+..+. +|++-.-+ +-+.|+|.|.+..........|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEE
Confidence 4799999853 34443333 6899999999985422222379999997654
No 249
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=51.32 E-value=67 Score=25.44 Aligned_cols=62 Identities=13% Similarity=0.177 Sum_probs=44.0
Q ss_pred EEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 266 SVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
..+.|+|+.....+.| |.+. |..-++|++- ++.+ .--++.||.|.|.....+..+++|..-+
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipg----K~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r~ 68 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADGKERLARIPG----KMRK-KVWIRRGDIVLVDPWDFQDVKADIIYKY 68 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEecCCCCCEEEEEEEe
Confidence 3478999999988887 6776 8888888764 1222 3347899999998887775555554433
No 250
>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=49.67 E-value=71 Score=25.00 Aligned_cols=60 Identities=13% Similarity=0.159 Sum_probs=41.6
Q ss_pred EEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEE-eCCCCeEEEEE
Q 015066 268 VIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH-DRERGRVSLST 332 (414)
Q Consensus 268 v~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i-d~e~~ri~LS~ 332 (414)
+-|+|+.....+.| |.+. |..-|+|++-= ...- --++.||.|.|..... |+.+++|..-+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK----~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~r~ 64 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPGK----LRKN-IWIKRGDFLIVDPIEEGEDVKADIIFVY 64 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEchh----hccC-EEEcCCCEEEEEecccCCCceEEEEEEe
Confidence 45889999888887 6776 88888888641 1111 3478999999988777 55555554433
No 251
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=49.21 E-value=1.1e+02 Score=26.79 Aligned_cols=58 Identities=24% Similarity=0.300 Sum_probs=37.3
Q ss_pred ccEEEEEEEEEEeece---------EEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 015066 264 IGSVVIGTVQSLKPYG---------AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRV 328 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G---------~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri 328 (414)
.|.+.+-+|..+.+.| +.|+|+ +-..+.|+.. .++ +.+++|.+|++.+.....++..+
T Consensus 63 ~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~------~~p-~~v~iGm~V~~v~~~~~~~~~~~ 130 (140)
T COG1545 63 EGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD------VDP-DDVEIGMKVEAVFRKREEDGGRG 130 (140)
T ss_pred CeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe------cCc-ccccCCCEEEEEEEEccccCCce
Confidence 4666666666665544 466776 4457777655 112 35799999999999876554443
No 252
>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=48.69 E-value=53 Score=24.14 Aligned_cols=48 Identities=21% Similarity=0.302 Sum_probs=30.9
Q ss_pred CEEEEEEEEEeCCeEE----EEeCCC--eeEEEcCccccccccCCccccCccCCcEEEEEEE
Q 015066 101 TKVKGTVFCTDNRGAL----VDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156 (414)
Q Consensus 101 ~iV~G~V~~v~~~G~~----Vdig~k--~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl 156 (414)
-.+.|+|.++...|.+ +++++. ..+.++...+ .+..+.+|+.+.+.+-
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 4689999999876644 444432 3445554332 3344789999888773
No 253
>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=48.68 E-value=68 Score=23.24 Aligned_cols=47 Identities=28% Similarity=0.485 Sum_probs=29.1
Q ss_pred EEEEEEEEEEeece----EEEEECC---EEEEEeecccCcccccCcccccCCCCEEEEEEE
Q 015066 266 SVVIGTVQSLKPYG----AFIDIGG---INGLLHVSQISHDRVADIATVLQPGDTLKVMIL 319 (414)
Q Consensus 266 ~iv~g~V~~i~~~G----~fV~l~g---v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl 319 (414)
..+.|+|..+.+.| +.+++++ +...+...... .-.+++||+|.+.+.
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-------~L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-------ELGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-------HCT-STT-EEEEEE-
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-------HcCCCCCCEEEEEEe
Confidence 46899999999999 4555554 45555433221 123789999988653
No 254
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=47.79 E-value=85 Score=22.28 Aligned_cols=66 Identities=15% Similarity=0.320 Sum_probs=38.5
Q ss_pred EEEEEEEEeec-----eEEEEECCEE-EEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 268 VIGTVQSLKPY-----GAFIDIGGIN-GLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 268 v~g~V~~i~~~-----G~fV~l~gv~-Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.|.|.++... -+++.+.+.. |-+.+.-... ........+..|+.+.+. -.++..+++..|.+.++
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~-~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~~~ 73 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGE-LAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVESI 73 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEch-HHHHHHhhccCCCEEEEE-EEEEecCCeEEEEeeee
Confidence 45677776543 3566665544 5555543332 222234568999998877 55665566666666543
No 255
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=47.18 E-value=50 Score=30.23 Aligned_cols=55 Identities=15% Similarity=0.280 Sum_probs=41.3
Q ss_pred CCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC--Cc----------------cccc---cCCeEEEEEEEee
Q 015066 187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--ST----------------AEEL---LGKDLPLKFVEVD 241 (414)
Q Consensus 187 ~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~--~~----------------~~~~---vGq~V~vkVl~vD 241 (414)
.|+++.|+|++....|+-|.++ -=+-|||.+-|... +. ..++ +|..|++||.+.+
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~ 157 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDES 157 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeec
Confidence 4789999999999999999998 45789998887743 11 1122 5888888887753
No 256
>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=46.93 E-value=1.1e+02 Score=22.33 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=35.4
Q ss_pred EEEEEEEeC--CeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066 104 KGTVFCTDN--RGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 104 ~G~V~~v~~--~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
.|+|...++ +.-|+.... +.+-|+|.+++...... .+.+|+.|++.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~-----~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFR-----SLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCC-----cCCCCCEEEEEEEEC
Confidence 588988877 334555544 78899999998643211 167899999988663
No 257
>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=46.57 E-value=45 Score=25.20 Aligned_cols=48 Identities=19% Similarity=0.137 Sum_probs=32.5
Q ss_pred EEEEEEEec-CcE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 192 KGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 192 ~G~V~~v~~-~G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
+|+|+..+. .|+ |+.. + +-+.|+|.|.+..........|+.|.+.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEE
Confidence 589999853 344 4444 3 7899999999974322222379999997544
No 258
>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=45.02 E-value=1.1e+02 Score=22.83 Aligned_cols=55 Identities=24% Similarity=0.224 Sum_probs=37.0
Q ss_pred EEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 267 iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
-++|+|++|.+...-|.|..-.-+--..+.. -+.+++|.+|.+..-..+ ++|+.=
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~lp~ef~-------~~~L~~G~kV~V~yd~~~--gk~vit 58 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKLPEEFD-------FDGLKPGMKVVVFYDEVD--GKRVIT 58 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEECCCccc-------ccccCCCCEEEEEEEccC--CcEEee
Confidence 4789999999999999998323332223332 235799999987666555 555543
No 259
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=44.24 E-value=2.5e+02 Score=27.96 Aligned_cols=79 Identities=22% Similarity=0.232 Sum_probs=48.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHH
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA 177 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~ 177 (414)
+.|.+++|+|...++....-.+..+ ...+...++ ...+|..++++|-.- -+.+++++.+....
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~-~~~l~v~~~-----------~a~~g~~~R~~I~a~-----DVslal~~P~~~Si 292 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALG-DQHLWVPKL-----------DAPVGARLRIRIQAR-----DVSLALQKPEQTSI 292 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecC-ceEEEeecc-----------CCCCCCcEEEEEEcc-----ceEEEecCccccch
Confidence 5689999999998885433333221 222222221 146899999998553 37787777655321
Q ss_pred HHHhhhcccCCeEEEEEEEEEecCcE
Q 015066 178 WERCRQLQSEDVVVKGKVVGANKGGV 203 (414)
Q Consensus 178 ~~~l~~~~~~g~iv~G~V~~v~~~G~ 203 (414)
- .++.|+|+.+.+.+-
T Consensus 293 ---------r-NiLp~~v~~i~~~~~ 308 (352)
T COG4148 293 ---------R-NILPGKVVGIEDDDG 308 (352)
T ss_pred ---------h-hccceeEEEEEcCCC
Confidence 1 267889999866543
No 260
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=43.72 E-value=2.1e+02 Score=30.41 Aligned_cols=86 Identities=19% Similarity=0.350 Sum_probs=58.8
Q ss_pred EEEEEEEEEEeece--EEEEEC---C-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC---
Q 015066 266 SVVIGTVQSLKPYG--AFIDIG---G-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE--- 336 (414)
Q Consensus 266 ~iv~g~V~~i~~~G--~fV~l~---g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~--- 336 (414)
-.+-|+|..+..+| +|..+. | +.-++...++...........+..||.|-|+--=.--..+.+++....+.
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLs 143 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLS 143 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeec
Confidence 45789999999888 788886 2 77788877776666666677788999998765444434676666555432
Q ss_pred ------CCCCcccCCchhhhh
Q 015066 337 ------PTPGDMIRNPKLVFE 351 (414)
Q Consensus 337 ------~~p~~~~~~~~~~~~ 351 (414)
|+-|-.+.+++..+.
T Consensus 144 KsL~pLPeK~hgL~D~E~RyR 164 (502)
T COG1190 144 KSLRPLPEKFHGLTDKEIRYR 164 (502)
T ss_pred ccCCCCChhhcCCccHHHHHH
Confidence 333556666665543
No 261
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=43.48 E-value=1e+02 Score=25.31 Aligned_cols=52 Identities=13% Similarity=0.236 Sum_probs=36.9
Q ss_pred cEEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066 265 GSVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 265 G~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i 321 (414)
...+.|+|+.....+.| |.+. |..-++|++- ++.. .--++.||.|.|.....
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~iwI~~GD~VlVsp~d~ 71 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPG----KLKK-RIWIREGDVVIVKPWEF 71 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEEccC
Confidence 34588999999988887 5776 8888888764 1222 33478999999844333
No 262
>COG1278 CspC Cold shock proteins [Transcription]
Probab=43.23 E-value=1e+02 Score=23.54 Aligned_cols=49 Identities=14% Similarity=0.138 Sum_probs=32.9
Q ss_pred EEEEEEEeC--CeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 104 KGTVFCTDN--RGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 104 ~G~V~~v~~--~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
+|+|.-.+. +.-|+.-.+ ..+.|+|.+.+.....+. +..||+|++.+..
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 577777765 223444433 378999999885443332 5789999999865
No 263
>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=41.82 E-value=34 Score=25.59 Aligned_cols=57 Identities=23% Similarity=0.324 Sum_probs=36.9
Q ss_pred EEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 015066 267 VVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRV 328 (414)
Q Consensus 267 iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri 328 (414)
.+.|.|+.....+.| |.+. |..=++|++-=... .--++.||.|.|-+-..|+.+++|
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~-----~iwI~~GD~V~V~~~~~d~~kG~I 62 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPGKFRK-----RIWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHT-----CC---TTEEEEEEESTTCTTEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceee-----eEecCCCCEEEEEecccCCCeEEE
Confidence 467899999888776 7777 88888887642111 114789999998876666555554
No 264
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=41.47 E-value=1.6e+02 Score=24.86 Aligned_cols=68 Identities=16% Similarity=0.157 Sum_probs=36.2
Q ss_pred CEEEEEEEEEeCCe--EEEEeCCCeeEE-EcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066 101 TKVKGTVFCTDNRG--ALVDITAKSSAY-LPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (414)
Q Consensus 101 ~iV~G~V~~v~~~G--~~Vdig~k~~g~-lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~ 171 (414)
-..+|+|.+++... +.++-+. +.++ -|.--+...-.....-..+++|+.+.|.+.. ..++.++.+.++
T Consensus 43 ~~~~G~V~~vd~~~~~iti~H~p-Ip~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~~--~~~~~~i~~i~~ 113 (115)
T PRK09838 43 ISGTGVVKGIDLESKKITIHHEP-IPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQ--QGNLSLLQDIKV 113 (115)
T ss_pred EEEEEEEEEEeCCCCEEEEeecc-cccCCCCCccccccCCChhhhccCCCCCEEEEEEEE--cCCcEEEEEEee
Confidence 34689999998866 4444332 3232 2222222111111111237899999999875 345555555543
No 265
>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=41.17 E-value=72 Score=23.18 Aligned_cols=43 Identities=16% Similarity=0.078 Sum_probs=28.4
Q ss_pred EEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 105 GTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 105 G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
|++....++..||.... ..+-|||..+|.. ..-|++|.++++.
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 55666666667887765 6888999988742 3469999999988
No 266
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=40.77 E-value=1.1e+02 Score=22.27 Aligned_cols=43 Identities=37% Similarity=0.475 Sum_probs=30.9
Q ss_pred EEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEE
Q 015066 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKF 237 (414)
Q Consensus 190 iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkV 237 (414)
.++|+|..+.+.-++++++ |..-++|.+.+..-. .++++++.+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~~l~-----~~~~v~l~t 48 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLSELP-----EGGEVKLYT 48 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHHTS------TTSEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHHhCC-----CCCEEEEEE
Confidence 5789999999999999997 788899877655432 244555543
No 267
>CHL00010 infA translation initiation factor 1
Probab=38.99 E-value=1.7e+02 Score=22.78 Aligned_cols=60 Identities=15% Similarity=0.307 Sum_probs=34.7
Q ss_pred EEEEEEEEEecCc-EEEEEC-C--EEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeeh
Q 015066 190 VVKGKVVGANKGG-VVAEVE-G--LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN 251 (414)
Q Consensus 190 iv~G~V~~v~~~G-~~V~i~-g--i~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~ 251 (414)
.++|.|++....| +.|.+. | +.+.++-.- ........+|+.|.+.+...+..+++|+--.
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGkl--r~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKI--RRNSIRILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccce--ecCCcccCCCCEEEEEEcccCCCeEEEEEEe
Confidence 4679999988545 446653 4 333332211 1112334589999998766666666665433
No 268
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=38.94 E-value=1.6e+02 Score=24.29 Aligned_cols=64 Identities=14% Similarity=0.034 Sum_probs=42.9
Q ss_pred eEEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhh
Q 015066 189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRK 253 (414)
Q Consensus 189 ~iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~ 253 (414)
..+.|+|+....++.| |.+. |..-+++.+-=... ..+-..|+.|.+.....|..+++|+.-...
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKK-RMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc-cEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 3699999999888877 6765 65555443321111 223336999999999999877777655443
No 269
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=38.44 E-value=1.8e+02 Score=22.17 Aligned_cols=61 Identities=20% Similarity=0.254 Sum_probs=34.3
Q ss_pred eEEEEEEEEEecCc-EEEEE-CCEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEe
Q 015066 189 VVVKGKVVGANKGG-VVAEV-EGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVL 249 (414)
Q Consensus 189 ~iv~G~V~~v~~~G-~~V~i-~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~L 249 (414)
-..+|.|++...++ +.|.+ +|..-.++..---........+|+.|.+.+-..+..+++|+.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 35679999988775 44555 343222221111111122245899999987666665666653
No 270
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=37.91 E-value=2.3e+02 Score=25.97 Aligned_cols=54 Identities=15% Similarity=0.118 Sum_probs=37.9
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
.+.|+|..+.++.+.++.++ +-+-++|.+.+. + +..|+.+.+.+..+-.++...
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~--------~--l~~g~~v~l~t~~~vred~~~ 58 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAY--------E--LNLEQKAQVFTHLVVREDAEL 58 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHH--------h--cCCCCeEEEEEEEEEecCCce
Confidence 57999999999999999976 445667665542 1 345888888776554455433
No 271
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=37.44 E-value=1.6e+02 Score=28.44 Aligned_cols=117 Identities=11% Similarity=0.140 Sum_probs=61.8
Q ss_pred EEEEEEEEEecC--cEEEE--EC--C--EEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhhHHhh
Q 015066 190 VVKGKVVGANKG--GVVAE--VE--G--LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ 261 (414)
Q Consensus 190 iv~G~V~~v~~~--G~~V~--i~--g--i~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~~~~ 261 (414)
.+.|+|.++..+ +..|. +. + +.+.|...-+. .+.-..|+.+.+.|-. ..+.++.-.. ..
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~---~L~l~~G~~v~~~Ika-----~~V~l~~~~~-----~~ 195 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAE---RLGLDEGKEVLVLIKA-----PWVGITQDPA-----VA 195 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHh---hcCCCCCCeEEEEEEC-----CEEEEEcCCC-----CC
Confidence 789999999766 34444 32 2 44444332211 1122269998887644 3344542111 11
Q ss_pred ccccEEEEEEEEEEeeceEEEEEC-CE-EEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIG-GI-NGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~-gv-~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i 321 (414)
...-..+.|+|.++...|..+++. .+ .|-.-...++..... .-.+++|+.|.+.+..-
T Consensus 196 ~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~--~L~L~~G~~V~a~iKas 255 (263)
T PRK10676 196 QAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAA--RLSLQQGDAVTAYFNAD 255 (263)
T ss_pred CChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHH--hcCCCCCCEEEEEEEcc
Confidence 233468999999998766654432 11 111111122222111 22478999999877643
No 272
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=36.89 E-value=13 Score=38.80 Aligned_cols=63 Identities=17% Similarity=0.375 Sum_probs=46.0
Q ss_pred cCCeEEEEEEEEEecCcEEEEE--CCEEEEEeccccCCCC-----ccc-----------cccCCeEEEEEEEeecccceE
Q 015066 186 SEDVVVKGKVVGANKGGVVAEV--EGLRGFVPFSQISSKS-----TAE-----------ELLGKDLPLKFVEVDEEQSRL 247 (414)
Q Consensus 186 ~~g~iv~G~V~~v~~~G~~V~i--~gi~GfIp~sels~~~-----~~~-----------~~vGq~V~vkVl~vD~e~~ri 247 (414)
..+..+.+.|..++++|+-|++ +|-.+|||..-+-... +.+ ..+|+.+.+++.+|..+.+.|
T Consensus 560 ~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRsi 639 (645)
T COG4776 560 GTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRSI 639 (645)
T ss_pred ccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhhhh
Confidence 3456889999999999999998 4999999998877532 111 115777777777777665544
Q ss_pred E
Q 015066 248 V 248 (414)
Q Consensus 248 ~ 248 (414)
+
T Consensus 640 i 640 (645)
T COG4776 640 I 640 (645)
T ss_pred h
Confidence 3
No 273
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=36.75 E-value=1.8e+02 Score=21.73 Aligned_cols=63 Identities=21% Similarity=0.273 Sum_probs=38.2
Q ss_pred EEEEEEEEe--ece-EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEE-eCCCCeEEEEEeeC
Q 015066 268 VIGTVQSLK--PYG-AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSH-DRERGRVSLSTKKL 335 (414)
Q Consensus 268 v~g~V~~i~--~~G-~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i-d~e~~ri~LS~K~~ 335 (414)
+.|.|+++. ..| +|+.|.+ +++.+..+.+ ......++.|+.|.+...-- +..++++.|...++
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~-----~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i 74 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNA-----RRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEI 74 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchh-----hhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEE
Confidence 566666654 355 6788853 5555554332 33456789999986644322 43356777777655
No 274
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=36.74 E-value=63 Score=27.66 Aligned_cols=57 Identities=21% Similarity=0.321 Sum_probs=36.2
Q ss_pred EEEEEEEEEEeeceEE--EEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEE--EEEEEe
Q 015066 266 SVVIGTVQSLKPYGAF--IDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKV--MILSHD 322 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~f--V~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~v--kVl~id 322 (414)
.-+.|+|+.+.+.|-. ++-. |++-|+|+.-=+.. .-+-....++.||.|++ .++.+|
T Consensus 40 AP~~G~v~~i~~T~HA~~i~~~~G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~D 102 (124)
T cd00210 40 APVDGTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFD 102 (124)
T ss_pred CcCCeEEEEEccCCCEEEEEeCCCcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 4568999999875533 4444 89999999642221 11122334678888875 566776
No 275
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=35.72 E-value=1.8e+02 Score=22.59 Aligned_cols=48 Identities=25% Similarity=0.409 Sum_probs=35.8
Q ss_pred ccCCeEEEEEEEEEecCcE-EEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeec
Q 015066 185 QSEDVVVKGKVVGANKGGV-VAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDE 242 (414)
Q Consensus 185 ~~~g~iv~G~V~~v~~~G~-~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~ 242 (414)
.+.|++++.+|..+.+.|= ...+.|+.-|+|-.+ .|++++++|..+-+
T Consensus 13 VeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~----------~Gd~V~vkI~~v~~ 61 (73)
T COG3269 13 VEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAE----------VGDEVKVKITKVKP 61 (73)
T ss_pred cccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCC----------CCCeeeEEEEEeec
Confidence 3578899999999976642 344558888888554 79999999988743
No 276
>PRK01712 carbon storage regulator; Provisional
Probab=35.61 E-value=1.2e+02 Score=22.98 Aligned_cols=30 Identities=20% Similarity=0.355 Sum_probs=25.3
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.+.+..|+.+.++|+.+. ++++.|.+.+-
T Consensus 8 ~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP 37 (64)
T PRK01712 8 VGESLMIGDDIEVTVLGVK--GNQVRIGINAP 37 (64)
T ss_pred CCCEEEeCCCEEEEEEEEe--CCEEEEEEECC
Confidence 4556788999999999998 78999999863
No 277
>COG1278 CspC Cold shock proteins [Transcription]
Probab=35.28 E-value=96 Score=23.66 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=30.4
Q ss_pred EEEEEEEecC-cE-EEEE-C-CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 192 KGKVVGANKG-GV-VAEV-E-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 192 ~G~V~~v~~~-G~-~V~i-~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
+|+|+-.+.. |+ |+.- + +-+.|+|+|.+...-...-.-||+|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEec
Confidence 5778877533 32 3332 3 5899999999974422222359999987644
No 278
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=35.16 E-value=1.5e+02 Score=23.97 Aligned_cols=69 Identities=25% Similarity=0.332 Sum_probs=48.1
Q ss_pred ccEEEEEEEEEEee--c-eEEEEECC----EEEEEeecccCcccccCcc-cccCCCCEEEEEE-EEEeCCCCeEEEEEee
Q 015066 264 IGSVVIGTVQSLKP--Y-GAFIDIGG----INGLLHVSQISHDRVADIA-TVLQPGDTLKVMI-LSHDRERGRVSLSTKK 334 (414)
Q Consensus 264 ~G~iv~g~V~~i~~--~-G~fV~l~g----v~Glvh~sels~~~~~~~~-~~~~~G~~V~vkV-l~id~e~~ri~LS~K~ 334 (414)
..--|.|.|++++. . .+|..|-+ +.+.+..+.. ..+. ..++.|++|.|.. +++.+..++++|...+
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~-----~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~ 96 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRA-----RRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVED 96 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHH-----hhCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEE
Confidence 34568899999876 3 45667642 6666665543 2333 5689999998765 3567778999999988
Q ss_pred CCC
Q 015066 335 LEP 337 (414)
Q Consensus 335 ~~~ 337 (414)
++|
T Consensus 97 i~P 99 (99)
T PF13742_consen 97 IDP 99 (99)
T ss_pred eEC
Confidence 764
No 279
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.79 E-value=2.7e+02 Score=25.70 Aligned_cols=59 Identities=14% Similarity=0.109 Sum_probs=39.3
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k 170 (414)
.+.|+|..+.++.+.++.++ +-+-++|.+.+. . +..|+.+.+.+..+-.++.....-..
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~--------~--l~~g~~v~l~t~~~vrEd~~~LyGF~ 63 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLA--------R--LVEGQEAELHTRLVVREDALSLYGFP 63 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHHHH--------H--cCCCCeEEEEEEEEEccCCceeeCcC
Confidence 57899999999999999976 345566654332 1 34688888877665555554333333
No 280
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=34.16 E-value=1.3e+02 Score=26.84 Aligned_cols=63 Identities=17% Similarity=0.195 Sum_probs=44.1
Q ss_pred ccEEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066 264 IGSVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST 332 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~ 332 (414)
.|+ +-|+|+.....|.| |.+. |..-|+|++-=-.. .--+..||.|.|..-..+..+++|..-+
T Consensus 31 egq-~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK-----~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 31 EGQ-EYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRK-----RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred CCc-EEEEEEEEcCCCEEEEEECCCCEEEEEeecccee-----eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 454 67899999988887 6776 89999998742111 1347899999998766765555555443
No 281
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=32.85 E-value=2.2e+02 Score=21.56 Aligned_cols=63 Identities=19% Similarity=0.244 Sum_probs=30.3
Q ss_pred EEEEEEeCC--eEEEEeCCCeeE-EEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC-eEEEEee
Q 015066 105 GTVFCTDNR--GALVDITAKSSA-YLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD-SLVLSLR 170 (414)
Q Consensus 105 G~V~~v~~~--G~~Vdig~k~~g-~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~-~i~LS~k 170 (414)
|+|.+++.. -+.+.-+. ..+ ..|.-.+...-.....-..+++|+.|.|.+...+ .+ ..+..++
T Consensus 1 G~V~~vd~~~~~iti~H~p-Ip~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~--~~~~~I~~i~ 67 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEP-IPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTD--DGSYVITAIE 67 (70)
T ss_dssp EEEEEEETTTTEEEEEE---BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEET--TCEEEEEEEE
T ss_pred CEEEEEecCCCEEEEecCc-cccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECC--CCcEEEEEEE
Confidence 788999853 34444332 222 2333333332222222234889999999997743 45 3444443
No 282
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=32.69 E-value=88 Score=26.69 Aligned_cols=57 Identities=19% Similarity=0.303 Sum_probs=35.6
Q ss_pred EEEEEEEEEEeeceEE--EEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEE--EEEEEe
Q 015066 266 SVVIGTVQSLKPYGAF--IDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKV--MILSHD 322 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~f--V~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~v--kVl~id 322 (414)
.-+.|+|+.+.+.+-- ++-. |++-|+|+.-=+.. .-+--...++.||+|++ .++.+|
T Consensus 40 AP~~G~v~~v~~T~HA~gi~~~~G~evLiHiGidTV~L~G~gF~~~v~~Gd~V~~G~~l~~~D 102 (121)
T TIGR00830 40 APVDGKIGKIFPTKHAFGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKKGDPLLEFD 102 (121)
T ss_pred ccCCeEEEEEccCCCEEEEEeCCCcEEEEEeeeceeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 3467899999885543 3444 89999999642211 11122334678888875 566666
No 283
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=32.66 E-value=1.5e+02 Score=22.81 Aligned_cols=67 Identities=10% Similarity=0.035 Sum_probs=40.9
Q ss_pred ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCE-EEEEEEEEeCCCCeEEEEEeeC
Q 015066 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDT-LKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~-V~vkVl~id~e~~ri~LS~K~~ 335 (414)
...|..+.|++..|...|+.+.+.. -++..+.-.-.+. ....+.. +.++|..+.+..+...+.++-.
T Consensus 19 ~~~~~~~~~~~~diS~~G~~~~~~~---~~~~~~~v~l~~~----~~~~~~~~~~~~V~~~~~~~~~~~~g~~f~ 86 (102)
T PF07238_consen 19 DPGGSSFQGTIVDISEGGCAFRSPK---PLEPGDRVRLSFS----LPGGGFPIVTGRVVRIQKDSDGYRVGVEFV 86 (102)
T ss_dssp EETTEEEEEEEEEETTSEEEEEECT---G--TTSEEEEEEE----CTTTSCEEEEEEEEEEEEESSEEEEEEEEC
T ss_pred ecCCcEEEEEEEEECccceEEEECC---CCCCCCEEEEEEE----eCCCCeeEEEEEEEEEECCCCceEEEEEEe
Confidence 3457788999999999999999854 1111110000000 0112222 8899999887777777777754
No 284
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=32.25 E-value=59 Score=28.17 Aligned_cols=56 Identities=25% Similarity=0.346 Sum_probs=31.6
Q ss_pred EEEEEEEEeeceEEE--EEC-CEEEEEeecccCcc-cccCcccccCCCCEEEE--EEEEEeC
Q 015066 268 VIGTVQSLKPYGAFI--DIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKV--MILSHDR 323 (414)
Q Consensus 268 v~g~V~~i~~~G~fV--~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~v--kVl~id~ 323 (414)
+.|+|+.+.+.+-.+ +-. |++-|+|+.-=+-. .-.-....++.||+|++ .++.+|.
T Consensus 46 ~~G~v~~i~~T~HAi~i~s~~G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~~G~~L~~~D~ 107 (132)
T PF00358_consen 46 VDGTVTMIFPTKHAIGIRSDNGVEILIHIGIDTVKLNGEGFETLVKEGDKVKAGQPLIEFDL 107 (132)
T ss_dssp SSEEEEEE-TTSSEEEEEETTSEEEEEE-SBSGGGGTTTTEEESS-TTSEE-TTEEEEEE-H
T ss_pred eeEEEEEEcCCCCEEEEEeCCCCEEEEEEccchhhcCCcceEEEEeCCCEEECCCEEEEEcH
Confidence 569999998854443 444 89999999632221 11223445678888875 5666663
No 285
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=31.99 E-value=99 Score=30.14 Aligned_cols=49 Identities=29% Similarity=0.393 Sum_probs=39.8
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i 158 (414)
....|.+-+|-|++..+.|.+|++|....+.++.. +.+|.++.++|.+.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~~--------------~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSSP--------------APPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceeccCC--------------CCCCceEEEEEEec
Confidence 35789999999999999999999997555554432 56899999999886
No 286
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=31.51 E-value=39 Score=32.61 Aligned_cols=75 Identities=23% Similarity=0.344 Sum_probs=57.8
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc--c--cc------cCcccccCCCCEEEEEEEEEeCCCCeE
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH--D--RV------ADIATVLQPGDTLKVMILSHDRERGRV 328 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~--~--~~------~~~~~~~~~G~~V~vkVl~id~e~~ri 328 (414)
-..++||+|-|+|..|.+.---|+++ ...+.+..|-+.- . |- .+.++.|+.||.|-+-|-++-. ++-+
T Consensus 81 Y~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~-dGs~ 159 (301)
T KOG3013|consen 81 YAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH-DGSL 159 (301)
T ss_pred cCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc-CCeE
Confidence 45779999999999999999999998 5777777776532 1 11 1356679999999999998854 7888
Q ss_pred EEEEeeC
Q 015066 329 SLSTKKL 335 (414)
Q Consensus 329 ~LS~K~~ 335 (414)
+|-.+-+
T Consensus 160 sLhTRS~ 166 (301)
T KOG3013|consen 160 SLHTRSL 166 (301)
T ss_pred EEEecch
Confidence 8866654
No 287
>PLN00208 translation initiation factor (eIF); Provisional
Probab=31.32 E-value=1.6e+02 Score=26.03 Aligned_cols=61 Identities=18% Similarity=0.170 Sum_probs=42.9
Q ss_pred ccEEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 264 IGSVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 264 ~G~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
.|+ +-|.|+.....|.| |.+. |..-|+|++-=-.. .--++.||.|.|.+-..+..+++|..
T Consensus 31 egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRK-----rIWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 31 DGQ-EYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRK-----KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred CCc-EEEEEEEEcCCCEEEEEECCCCEEEEEEecccee-----eEEecCCCEEEEEccCCCCCEEEEEE
Confidence 454 67899999888887 6776 89999998642111 23478999999997777755444443
No 288
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=31.28 E-value=2.4e+02 Score=21.94 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=33.3
Q ss_pred hccccEEEEEEEEEEeeceE-EEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeC
Q 015066 261 QLGIGSVVIGTVQSLKPYGA-FIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323 (414)
Q Consensus 261 ~l~~G~iv~g~V~~i~~~G~-fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~ 323 (414)
-++.|++|+-.|..+.+.|= ..++.|.--|++ ..++||+|+++|..+.+
T Consensus 12 PVeeGe~y~V~I~d~g~~GDGiarveGfvVFVp--------------~a~~Gd~V~vkI~~v~~ 61 (73)
T COG3269 12 PVEEGETYEVEIEDVGDQGDGIARVEGFVVFVP--------------GAEVGDEVKVKITKVKP 61 (73)
T ss_pred CcccCCEEEEEEEEeccCCCceEEEEEEEEEeC--------------CCCCCCeeeEEEEEeec
Confidence 46789999999988876542 112224333333 24799999999999864
No 289
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.99 E-value=68 Score=24.27 Aligned_cols=56 Identities=16% Similarity=0.117 Sum_probs=37.0
Q ss_pred EEEEEEEEEeeceEEEEEC--C-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeC
Q 015066 267 VVIGTVQSLKPYGAFIDIG--G-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323 (414)
Q Consensus 267 iv~g~V~~i~~~G~fV~l~--g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~ 323 (414)
.++++|..+...-+.|.+. | +..+=-.|++.+.+. .-++.+++||.+.|.+...+.
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfr-f~seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFR-FDSEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred ccchhhhhhhhceEEEEeeccccEEEEEchhhcccccc-ccceeeeccceEEEEEecCcc
Confidence 4566777777777788886 3 444444456655432 224578999999998887654
No 290
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=30.83 E-value=1.9e+02 Score=30.77 Aligned_cols=68 Identities=18% Similarity=0.276 Sum_probs=41.1
Q ss_pred EEEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 266 SVVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 266 ~iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
-.+.|+|.++...| +|+.|.+ +..++....+.......... +..|+.|.|.=.=.....+.+.|..+.
T Consensus 57 v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v~G~v~~t~~ge~el~~~~ 130 (491)
T PRK00484 57 VSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKK-LDLGDIIGVEGTLFKTKTGELSVKATE 130 (491)
T ss_pred EEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhc-CCCCCEEEEEEEEEEcCCCcEEEEEeE
Confidence 35789999999877 7999952 66666655443222222333 889999876422222235555554443
No 291
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.77 E-value=3.6e+02 Score=24.73 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=33.3
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~ 157 (414)
.+.|+|..+.++.+.++.++ +-+-++|.+.+. . +..|+.+.+.+..
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~--------~--l~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLS--------T--CKIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHH--------h--hCCCCeEEEEEEE
Confidence 58999999999999999976 345566654442 1 3568888877654
No 292
>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=30.19 E-value=2.2e+02 Score=22.10 Aligned_cols=61 Identities=8% Similarity=0.042 Sum_probs=38.8
Q ss_pred EEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066 191 VKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (414)
Q Consensus 191 v~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K 252 (414)
+.|+|+....++.| |.+. |..-+++.+-=.. ...+-..|+.|.+.....|..+++|+--..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~r-k~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~ 64 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMR-KRVWINEGDIVLVAPWDFQDDKADIIYKYT 64 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhc-ccEEEcCCCEEEEEeccccCCEEEEEEEcC
Confidence 56899999888877 6765 5444433222111 123333699999998888877777765444
No 293
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=29.62 E-value=2.5e+02 Score=21.30 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=36.4
Q ss_pred EEEEEEEEEeece-EEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066 267 VVIGTVQSLKPYG-AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL 330 (414)
Q Consensus 267 iv~g~V~~i~~~G-~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L 330 (414)
.+.|.|.+....+ ..|.+. |..=.+|+.-- +........+||.|.+.+-..+..+++|..
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gk----lr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISGK----MRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEccc----eeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 4678999887664 445554 65555554321 111122268999999987666765666654
No 294
>PRK13605 endoribonuclease SymE; Provisional
Probab=29.60 E-value=83 Score=26.47 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=31.3
Q ss_pred CCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh--hhhHHHHHhhhc
Q 015066 138 KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI--QYELAWERCRQL 184 (414)
Q Consensus 138 ~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~--~~~~~~~~l~~~ 184 (414)
.++++.+|..|+.+.++| +.|.++++.... +....|..|++.
T Consensus 45 ~WLeeAGF~tG~~V~V~V-----~~G~LVIt~~~~~~~~~el~~~l~~v 88 (113)
T PRK13605 45 QWLEAAGFATGTAVDVRV-----MEGCIVLTAQPPAAEESELMQSLRQV 88 (113)
T ss_pred hhHHhhCCCCCCeEEEEE-----eCCEEEEEeCCCCcccHHHHHHHHHH
Confidence 356778899999999988 458999998876 334566666654
No 295
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.57 E-value=3.9e+02 Score=24.55 Aligned_cols=59 Identities=10% Similarity=0.152 Sum_probs=39.1
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~ 169 (414)
.+.|+|..+.++.+.++.++ +-+-++|.+.+. +. ...|+.+.+.+..+-.++.....-.
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~--------~l-~~~g~~~~l~t~~~vrEd~~~LyGF 63 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPA--------LI-GGLGQRVRVFTHLHVREDALSLFGF 63 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHH--------hc-ccCCCeEEEEEEEEEecCCceeeCC
Confidence 58999999999999999976 445677765442 11 1358888877765544555433333
No 296
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.15 E-value=3.9e+02 Score=24.62 Aligned_cols=56 Identities=13% Similarity=0.052 Sum_probs=37.8
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~ 166 (414)
.+.|+|..+.++.+.++.++ +-+-++|.+.+. +. ..+|+.+.+.+..+-.++....
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~--------~l-~~~g~~v~l~t~~~vrEd~~~L 60 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLA--------AI-GAIGDEVFLYTHLIVREDALTL 60 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHH--------Hh-ccCCCeEEEEEEEEEecCCcee
Confidence 58999999999999999976 345566654432 11 1468888877765544554433
No 297
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=28.58 E-value=96 Score=22.72 Aligned_cols=67 Identities=22% Similarity=0.311 Sum_probs=37.3
Q ss_pred EEEEEEEEE-ee--ceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCe-EEEEEeeC
Q 015066 267 VVIGTVQSL-KP--YGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGR-VSLSTKKL 335 (414)
Q Consensus 267 iv~g~V~~i-~~--~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~r-i~LS~K~~ 335 (414)
.+.|.|+++ .. .-+|+.+.+-+|-+...-.. +......+.+++|+.|.+. =.+...+++ +.|....+
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~-~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l~~~~i 72 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFN-EEYERFREKLKEGDIVRVR-GKVKRYNGGELELIVPKI 72 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET-HHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEEEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECCccEEEEEcc-HHhhHHhhcCCCCeEEEEE-EEEEEECCccEEEEECEE
Confidence 367888888 43 34566776322444333222 1233445678999999765 233333455 77776553
No 298
>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=28.18 E-value=61 Score=23.58 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=25.3
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066 304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~ 336 (414)
+.+.+..|+.+.++|++++ ++++.|.+.+-.
T Consensus 8 ~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~ 38 (54)
T PF02599_consen 8 VGESIVIGDDIEITVLEIS--GGQVKLGIDAPK 38 (54)
T ss_dssp TT-EEEETTTEEEEEEEEE--TTEEEEEEEECT
T ss_pred CCCEEEECCCEEEEEEEEc--CCEEEEEEECCC
Confidence 4456778999999999998 899999998743
No 299
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=28.16 E-value=2.4e+02 Score=20.54 Aligned_cols=31 Identities=16% Similarity=0.364 Sum_probs=24.1
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccc
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEA 132 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEl 132 (414)
-+.|+|..+.++.+.++.++ +-+-++|.+.+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~ 35 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL 35 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHH
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchH
Confidence 47899999999999999986 34567776544
No 300
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=28.15 E-value=1e+02 Score=22.33 Aligned_cols=48 Identities=23% Similarity=0.389 Sum_probs=30.2
Q ss_pred EEEEEEEEEEeeceEEEEEC---CEEE-EEeecccCcccccCcccccCCCCEEEEE
Q 015066 266 SVVIGTVQSLKPYGAFIDIG---GING-LLHVSQISHDRVADIATVLQPGDTLKVM 317 (414)
Q Consensus 266 ~iv~g~V~~i~~~G~fV~l~---gv~G-lvh~sels~~~~~~~~~~~~~G~~V~vk 317 (414)
.-+.++|..+...|..++++ ...| ++.+ +|+.+. ..-.+..||.|.++
T Consensus 5 ~~l~a~V~~v~~~G~~vRlEl~~~~~~~~iEv-el~~~~---~~l~l~~G~~V~l~ 56 (58)
T PF12857_consen 5 GGLPARVRRVRPVGPEVRLELKRLDDGEPIEV-ELPRER---RQLGLQPGDRVYLR 56 (58)
T ss_pred CcEeEEEEEEEecCCeEEEEEEECCCCCEEEE-EeCHhH---HhcCCCCCCEEEEE
Confidence 35789999999999998875 1111 2222 344433 22246679999765
No 301
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=27.88 E-value=3.2e+02 Score=28.24 Aligned_cols=91 Identities=14% Similarity=0.192 Sum_probs=58.7
Q ss_pred cEEEEEEEEEEeec--e-EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEE-EEEeCCCCeEEEEEeeCC
Q 015066 265 GSVVIGTVQSLKPY--G-AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMI-LSHDRERGRVSLSTKKLE 336 (414)
Q Consensus 265 G~iv~g~V~~i~~~--G-~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkV-l~id~e~~ri~LS~K~~~ 336 (414)
.=-|.|.|++++.. | +|..|-+ +.+.+..+... .....++.|+.|.|.. +++-+..++++|...+++
T Consensus 25 ~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~-----~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~~i~ 99 (438)
T PRK00286 25 QVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR-----RLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVEEIE 99 (438)
T ss_pred cEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh-----cCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEee
Confidence 45688999998743 5 7888852 66666655432 3344588999997754 455667899999999887
Q ss_pred CCCCcccCCchhhhhhHHHHHHHHHHHHHHHHHh
Q 015066 337 PTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAM 370 (414)
Q Consensus 337 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 370 (414)
+.-- -+.....+..++++.+.|-.
T Consensus 100 ~~g~----------G~l~~~~~~lk~~L~~eGlf 123 (438)
T PRK00286 100 PAGI----------GALAAAFEQLKEKLAAEGLF 123 (438)
T ss_pred eCCc----------cHHHHHHHHHHHHHHHCCCC
Confidence 5310 12233344556666655533
No 302
>CHL00010 infA translation initiation factor 1
Probab=27.41 E-value=3e+02 Score=21.38 Aligned_cols=64 Identities=23% Similarity=0.321 Sum_probs=39.4
Q ss_pred EEEEEEEEeeceE-EEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 268 VIGTVQSLKPYGA-FIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 268 v~g~V~~i~~~G~-fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
+.|.|.++.+.|. .|.+. |..=.+|+.-- +..-.....+||.|.+.+-..+..+++|..-.+..
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGk----lr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISGK----IRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEeccc----eecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 6789998885444 45664 65555554321 11112336789999998766676667776655543
No 303
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.74 E-value=4.6e+02 Score=24.29 Aligned_cols=53 Identities=11% Similarity=0.080 Sum_probs=35.1
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~ 164 (414)
.++|+|..+.++.+.++.++ +.+-++|.+-+. . +..|+.+.+.+.-+=.++..
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~~--------~--l~~g~~v~l~t~~~vrED~~ 57 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCLA--------E--LRLLEDVEILTYLHTREDEL 57 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHHH--------h--cCCCCcEEEEEEEEEecCCc
Confidence 58999999999999999976 345566654331 1 34588887766444334443
No 304
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.36 E-value=4.4e+02 Score=24.09 Aligned_cols=53 Identities=13% Similarity=0.192 Sum_probs=35.5
Q ss_pred EEEEEEEEEeCCeEEEE-eCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066 102 KVKGTVFCTDNRGALVD-ITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vd-ig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~ 164 (414)
.+.|+|..+.++.+.++ .++ +-+-++|.+.+. . +..|+.+...+.-+-.++..
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~~~~~~--------~--l~~g~~v~l~t~~~vrEd~~ 58 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFISLFCSA--------K--IQKGEKHELFITQIIKEDSN 58 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEecHHHHH--------H--cCCCCeEEEEEEEEEecCCc
Confidence 58999999999999999 454 345566654332 1 34688888776555444443
No 305
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=25.94 E-value=1.6e+02 Score=22.29 Aligned_cols=42 Identities=21% Similarity=0.147 Sum_probs=29.0
Q ss_pred EEEEeecccceEEeehhhhhh-h--------------HHhhccccEEEEEEEEEEee
Q 015066 236 KFVEVDEEQSRLVLSNRKAMA-D--------------SQAQLGIGSVVIGTVQSLKP 277 (414)
Q Consensus 236 kVl~vD~e~~ri~LS~K~~l~-~--------------~~~~l~~G~iv~g~V~~i~~ 277 (414)
.|..+|.+.+.+.+++-+.-. . ....+++|+.|.-.+....+
T Consensus 2 ~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 2 VVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDD 58 (70)
T ss_dssp EEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETT
T ss_pred EEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCC
Confidence 578999999999999876521 0 12689999999998887644
No 306
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=25.80 E-value=6.7e+02 Score=29.60 Aligned_cols=67 Identities=27% Similarity=0.431 Sum_probs=40.5
Q ss_pred EEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 267 VVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 267 iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
.+.|.|.++...| +|+.|.+ +..++..+.+...........+..||.|.|.=.=....++.+.+..+
T Consensus 655 ~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~~~ 727 (1094)
T PRK02983 655 SVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVT 727 (1094)
T ss_pred EEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEEEe
Confidence 5789999999887 7999862 66666655543322222334578999987642222223455554333
No 307
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=25.31 E-value=53 Score=30.67 Aligned_cols=18 Identities=28% Similarity=0.663 Sum_probs=15.5
Q ss_pred eceEEEEEC-CEEEEEeec
Q 015066 277 PYGAFIDIG-GINGLLHVS 294 (414)
Q Consensus 277 ~~G~fV~l~-gv~Glvh~s 294 (414)
+.||||-|+ |.+|||-+.
T Consensus 49 DiGCFvlFDGGFsGLVviN 67 (229)
T PF11813_consen 49 DIGCFVLFDGGFSGLVVIN 67 (229)
T ss_pred CcceEEEecCCcceEEEEe
Confidence 589999998 799999764
No 308
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=24.96 E-value=2.7e+02 Score=29.57 Aligned_cols=68 Identities=18% Similarity=0.280 Sum_probs=40.3
Q ss_pred EEEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066 266 SVVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333 (414)
Q Consensus 266 ~iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K 333 (414)
-.+.|+|.++...| +|+.|.+ +..++..+.+...........+..|+.|.|.=.=.....+.+.|..+
T Consensus 56 v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~ 129 (496)
T TIGR00499 56 VSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVT 129 (496)
T ss_pred EEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEee
Confidence 35789999999776 7999962 67777665543322111223478999987632112233554554443
No 309
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=24.89 E-value=1.8e+02 Score=23.30 Aligned_cols=49 Identities=27% Similarity=0.403 Sum_probs=31.1
Q ss_pred EEEEEEEEEeece---EEEEEC-C---EEEEEeecc--cCcccccCcccccCCCCEEEE
Q 015066 267 VVIGTVQSLKPYG---AFIDIG-G---INGLLHVSQ--ISHDRVADIATVLQPGDTLKV 316 (414)
Q Consensus 267 iv~g~V~~i~~~G---~fV~l~-g---v~Glvh~se--ls~~~~~~~~~~~~~G~~V~v 316 (414)
.+.|+|.++...| +|+.|. + +..+++..+ ...... ..-..++.|+.|.|
T Consensus 3 ~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~-~~~~~l~~es~V~V 60 (102)
T cd04320 3 LIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMV-KWAGSLSKESIVDV 60 (102)
T ss_pred EEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHH-HHHhcCCCccEEEE
Confidence 4789999999887 899996 2 666665433 111111 11134788888765
No 310
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.30 E-value=1.9e+02 Score=26.61 Aligned_cols=52 Identities=19% Similarity=0.248 Sum_probs=37.9
Q ss_pred EEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEEEEeecccc
Q 015066 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS 245 (414)
Q Consensus 190 iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ 245 (414)
.+.|+|..+.+..++++++ |+.-++|.+.+..-.. .|+++.+.+..+-.++.
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~~l~~----~g~~~~l~t~~~vrEd~ 57 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPALIGG----LGQRVRVFTHLHVREDA 57 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHHhccc----CCCeEEEEEEEEEecCC
Confidence 5899999999999999997 7788888766543211 58888877665544443
No 311
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=24.02 E-value=2e+02 Score=26.58 Aligned_cols=45 Identities=18% Similarity=0.191 Sum_probs=33.7
Q ss_pred eeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC-CCeEEEEeeehhh
Q 015066 123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA-DDSLVLSLRMIQY 174 (414)
Q Consensus 123 ~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~-~~~i~LS~k~~~~ 174 (414)
.+|++|..++. +.+. +.+|+++.+.+.++... +|++.+|+.....
T Consensus 2 ~~~~l~~~~~~------~~e~-~~~g~ri~~~~~~v~~~~~g~~~~srt~~~~ 47 (190)
T COG0195 2 VEAILPKREQI------PGEN-FKVGDRIRALLYEVQKEAKGQIELSRTIPEL 47 (190)
T ss_pred ceeEcchhhcC------CCcc-cccCcEEEEEEeeeeecCcccEEEEeccHHH
Confidence 57899998874 2333 89999999999998753 3568888766554
No 312
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=23.77 E-value=1.9e+02 Score=26.60 Aligned_cols=51 Identities=24% Similarity=0.255 Sum_probs=37.4
Q ss_pred EEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEEEEeecccc
Q 015066 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS 245 (414)
Q Consensus 190 iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ 245 (414)
.+.|+|..+....++++++ |+.-++|.+.+..-. .|+++.+.+-.+=.++.
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~~l~-----~g~~v~l~t~~~vred~ 56 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYELN-----LEQKAQVFTHLVVREDA 56 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHhcC-----CCCeEEEEEEEEEecCC
Confidence 5899999999999999997 778888876654221 38888877655544433
No 313
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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.
Probab=23.47 E-value=2.1e+02 Score=23.12 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=28.5
Q ss_pred EEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEE
Q 015066 267 VVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKV 316 (414)
Q Consensus 267 iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~v 316 (414)
.+.|+|.++...| +|+.|.+ +..++..+ .+....... ..+..|+.|.+
T Consensus 3 ~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~-~~~~~~~~~-~~l~~~s~v~V 56 (103)
T cd04319 3 TLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKD-LNEEAYREA-KKVGIESSVIV 56 (103)
T ss_pred EEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCC-CCHHHHHHH-hCCCCCCEEEE
Confidence 5789999998765 8999963 44444332 211111111 24678998865
No 314
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=23.08 E-value=2.6e+02 Score=29.03 Aligned_cols=69 Identities=14% Similarity=0.229 Sum_probs=40.9
Q ss_pred EEEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEE--EEEEeCCCCeEEEEEeeC
Q 015066 266 SVVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVM--ILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 266 ~iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vk--Vl~id~e~~ri~LS~K~~ 335 (414)
-.+.|+|.++...| +|+.|.. +...++.++.+..-+... ..+..|+.|.|. |..-....+.+.|..+.+
T Consensus 15 v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~i 91 (428)
T TIGR00458 15 VTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWA-KKLNLESVVAVRGIVKIKEKAPGGFEIIPTKI 91 (428)
T ss_pred EEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHH-hCCCCCcEEEEEEEEEecCCCCCcEEEEEeEE
Confidence 34679999999887 8999852 667776554433222222 357889998763 332111235566555543
No 315
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.78 E-value=2e+02 Score=26.63 Aligned_cols=51 Identities=18% Similarity=0.308 Sum_probs=37.1
Q ss_pred EEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEEEEeeccc
Q 015066 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQ 244 (414)
Q Consensus 190 iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~ 244 (414)
.++|+|..+....++++++ |+.-++|.+.+..-.. +|+.+.+.+..+=.++
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~~l~~----~g~~v~l~t~~~vrEd 56 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLAAIGA----IGDEVFLYTHLIVRED 56 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHHhcc----CCCeEEEEEEEEEecC
Confidence 5899999999999999997 6788888665543211 6888887765543343
No 316
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=22.35 E-value=1.9e+02 Score=28.27 Aligned_cols=50 Identities=26% Similarity=0.291 Sum_probs=40.0
Q ss_pred hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322 (414)
Q Consensus 260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id 322 (414)
.+...|.+-+|.|.+....|++|+++ +--+.++- -+.+|..|.++|.+..
T Consensus 101 ~~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~-------------~~~~~~RvTvri~~~~ 151 (272)
T COG2106 101 TSPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSS-------------PAPPGARVTVRIISRS 151 (272)
T ss_pred CCccceeecceEEEEecCCceEEEecCCcceeccC-------------CCCCCceEEEEEEecc
Confidence 36778999999999999999999987 44444331 2689999999999873
No 317
>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=22.31 E-value=3.4e+02 Score=20.32 Aligned_cols=45 Identities=27% Similarity=0.395 Sum_probs=30.9
Q ss_pred EEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEE
Q 015066 102 KVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~V 155 (414)
-++|+|.++++...-+.+..+..=-+|. +.. .. .+++|.+|.+..
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~lp~-ef~------~~--~L~~G~kV~V~y 48 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKLPE-EFD------FD--GLKPGMKVVVFY 48 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEECCC-ccc------cc--ccCCCCEEEEEE
Confidence 4799999999999999997765444443 222 11 278999765443
No 318
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=22.00 E-value=3.8e+02 Score=22.21 Aligned_cols=33 Identities=12% Similarity=0.208 Sum_probs=24.2
Q ss_pred cCCCCCEE------EEEEEEEeCCeEEEEeCCCeeEEEc
Q 015066 96 NSELGTKV------KGTVFCTDNRGALVDITAKSSAYLP 128 (414)
Q Consensus 96 ~l~~G~iV------~G~V~~v~~~G~~Vdig~k~~g~lp 128 (414)
++++|+.| -|+|++++++-+.++++.+..--+.
T Consensus 52 ~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~ 90 (106)
T PRK05585 52 SLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQ 90 (106)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEE
Confidence 56788876 5899999998888888765443333
No 319
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=21.90 E-value=1.6e+02 Score=22.81 Aligned_cols=54 Identities=20% Similarity=0.313 Sum_probs=32.1
Q ss_pred EEEEEEEEee----ceEEEEECC-------EEEEEeecccCcccccCcccccCCCCEEEE--EEEEEeCCCCeEEEEE
Q 015066 268 VIGTVQSLKP----YGAFIDIGG-------INGLLHVSQISHDRVADIATVLQPGDTLKV--MILSHDRERGRVSLST 332 (414)
Q Consensus 268 v~g~V~~i~~----~G~fV~l~g-------v~Glvh~sels~~~~~~~~~~~~~G~~V~v--kVl~id~e~~ri~LS~ 332 (414)
++|.|+.+.+ .|.||+=.. .+|+.-.. .. ...+++||.|.+ +|... .+...|+.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~-------~~-~~~~~~Gd~V~vtG~v~ey---~g~tql~~ 68 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYT-------GS-GADVAVGDLVRVTGTVTEY---YGLTQLTA 68 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEec-------CC-CCCCCCCCEEEEEEEEEee---CCeEEEcc
Confidence 7899999887 689988641 34432211 01 345789999875 44444 34444443
No 320
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.84 E-value=4.2e+02 Score=22.96 Aligned_cols=59 Identities=20% Similarity=0.199 Sum_probs=38.9
Q ss_pred CCCCCEEEEEEEEEeCCe---------EEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC
Q 015066 97 SELGTKVKGTVFCTDNRG---------ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD 163 (414)
Q Consensus 97 l~~G~iV~G~V~~v~~~G---------~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~ 163 (414)
-..|.+.+-||+.+...| ++|++.+....+.+... .++++ +.+|++|++........++
T Consensus 61 s~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~------~~p~~--v~iGm~V~~v~~~~~~~~~ 128 (140)
T COG1545 61 SGEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD------VDPDD--VEIGMKVEAVFRKREEDGG 128 (140)
T ss_pred CCCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe------cCccc--ccCCCEEEEEEEEccccCC
Confidence 467888999999988765 46677544445544433 12333 6889999998877654443
No 321
>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=21.75 E-value=2.4e+02 Score=20.93 Aligned_cols=56 Identities=18% Similarity=0.153 Sum_probs=34.0
Q ss_pred EEEEEEEEEecCcEE-EEEC-C--EEEEEeccccCCCCccccccCCeEEEEEEEeecccceEE
Q 015066 190 VVKGKVVGANKGGVV-AEVE-G--LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLV 248 (414)
Q Consensus 190 iv~G~V~~v~~~G~~-V~i~-g--i~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~ 248 (414)
.+.|+|++...++.| |.+. | +.+.+|.. .. ....-..|+.|.|.+-..|..+++|+
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK-~r--~~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPGK-FR--KRIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-HH-HH--TCC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccc-ee--eeEecCCCCEEEEEecccCCCeEEEE
Confidence 578999999888876 6775 5 45555544 21 12222259998887766665555543
No 322
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.48 E-value=5.1e+02 Score=23.70 Aligned_cols=54 Identities=15% Similarity=0.035 Sum_probs=36.9
Q ss_pred EEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066 102 KVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (414)
Q Consensus 102 iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i 165 (414)
.+.|+|..+..+.+.++. |-+.+-++|.+-+. . +..|+++.+.+..+-.++...
T Consensus 4 ~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~~--------~--l~~g~~v~l~t~~~vrEd~~~ 59 (188)
T PRK14606 4 GISGRVLKKSGNVLLVETKSGVVFEIVCDVQTSE--------E--VEEGGECFLHTFLSVSQDGIT 59 (188)
T ss_pred eEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHHH--------H--cCCCCeEEEEEEEEEecCCce
Confidence 589999999999999995 33456666654332 1 346898888876554455443
No 323
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=20.75 E-value=4.6e+02 Score=21.24 Aligned_cols=32 Identities=22% Similarity=0.097 Sum_probs=23.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccc
Q 015066 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC 133 (414)
Q Consensus 98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls 133 (414)
++=.++-|+|+++.+ +-|.+.++ ..++.+++-
T Consensus 15 ~p~~i~~G~V~s~~P--L~I~i~~~--liL~~~~L~ 46 (100)
T PF10844_consen 15 NPVDIVIGTVVSVPP--LKIKIDQK--LILDKDFLI 46 (100)
T ss_pred CCceeEEEEEEeccc--EEEEECCe--EEEchHHEE
Confidence 455678999999999 88888774 566665553
No 324
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=20.59 E-value=1.6e+02 Score=20.39 Aligned_cols=34 Identities=9% Similarity=-0.028 Sum_probs=23.6
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcc
Q 015066 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE 131 (414)
Q Consensus 96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sE 131 (414)
.++.|++|... .+..++=.++.. ++..|++|.+-
T Consensus 14 s~~~Gd~i~v~-~~~~~~W~~g~~-~g~~G~~P~~y 47 (49)
T PF14604_consen 14 SFKKGDVITVL-EKSDDGWWYGRN-TGRTGLFPANY 47 (49)
T ss_dssp EB-TTEEEEEE-EESSTSEEEEEE-TTEEEEEEGGG
T ss_pred eEcCCCEEEEE-EeCCCCEEEEEE-CCEEEEECHHh
Confidence 68899999865 333445566776 56999999763
No 325
>PRK00568 carbon storage regulator; Provisional
Probab=20.54 E-value=1.4e+02 Score=23.43 Aligned_cols=30 Identities=23% Similarity=0.380 Sum_probs=25.2
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066 304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKL 335 (414)
Q Consensus 304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~ 335 (414)
..+.+..||.+.++|+++. ++++.|.+.+-
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP 37 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISID--RGSVRLGFEAP 37 (76)
T ss_pred CCCeEEeCCCeEEEEEEEc--CCEEEEEEECC
Confidence 4556788999999999998 78999999753
No 326
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=20.48 E-value=3.8e+02 Score=28.63 Aligned_cols=69 Identities=14% Similarity=0.208 Sum_probs=40.2
Q ss_pred EEEEEEEEEEeece--EEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066 266 SVVIGTVQSLKPYG--AFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334 (414)
Q Consensus 266 ~iv~g~V~~i~~~G--~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~ 334 (414)
-.+.|+|.++...| +|+.|.+ +..++..+++....+......+..|+.|.|.=.=.....+.+.|-.+.
T Consensus 68 v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~ 142 (505)
T PRK12445 68 VSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTE 142 (505)
T ss_pred EEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeE
Confidence 35789999998876 7999852 666666555432211111234789999876322122235656555443
No 327
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=20.40 E-value=3.4e+02 Score=21.10 Aligned_cols=40 Identities=20% Similarity=0.331 Sum_probs=28.4
Q ss_pred EEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEE
Q 015066 268 VIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316 (414)
Q Consensus 268 v~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~v 316 (414)
+.|+|.++.+..+.|+++|+.=-+.+.-+. ..++||.|-+
T Consensus 5 iP~~V~~i~~~~A~v~~~G~~~~v~l~lv~---------~~~vGD~VLV 44 (76)
T TIGR00074 5 IPGQVVEIDENIALVEFCGIKRDVSLDLVG---------EVKVGDYVLV 44 (76)
T ss_pred cceEEEEEcCCEEEEEcCCeEEEEEEEeeC---------CCCCCCEEEE
Confidence 567888888888999988865555544331 2578998865
No 328
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.26 E-value=2.4e+02 Score=25.80 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=34.9
Q ss_pred EEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCccccccCCeEEEEEEE
Q 015066 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (414)
Q Consensus 190 iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~ 239 (414)
.++|+|..+....++++++ |+.-++|.+.+... ..|+++.+.+..
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~~l-----~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLSTC-----KIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHhh-----CCCCeEEEEEEE
Confidence 5899999999999999997 67788886655431 269998887654
Done!