Query 011538
Match_columns 483
No_of_seqs 275 out of 2322
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 02:28:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 2.2E-45 4.7E-50 391.6 29.3 267 158-470 4-286 (541)
2 PRK07400 30S ribosomal protein 100.0 3.9E-44 8.5E-49 365.5 29.4 266 156-465 15-285 (318)
3 PRK07899 rpsA 30S ribosomal pr 100.0 2.6E-42 5.7E-47 368.4 32.3 266 157-466 20-298 (486)
4 PRK06299 rpsA 30S ribosomal pr 100.0 6.3E-40 1.4E-44 357.4 34.9 271 155-471 11-296 (565)
5 COG0539 RpsA Ribosomal protein 100.0 1.9E-40 4.2E-45 353.7 28.0 276 157-475 90-377 (541)
6 PRK06676 rpsA 30S ribosomal pr 100.0 3.4E-38 7.3E-43 329.4 33.5 268 157-468 3-284 (390)
7 PRK13806 rpsA 30S ribosomal pr 100.0 2E-38 4.3E-43 340.6 32.4 275 157-478 15-309 (491)
8 TIGR00717 rpsA ribosomal prote 100.0 1.3E-37 2.8E-42 335.5 32.0 273 158-478 2-289 (516)
9 PRK12269 bifunctional cytidyla 100.0 2.8E-37 6.1E-42 347.7 29.5 271 162-474 388-678 (863)
10 PRK12269 bifunctional cytidyla 100.0 2.5E-36 5.3E-41 340.1 34.3 298 112-471 266-588 (863)
11 PRK00087 4-hydroxy-3-methylbut 100.0 4.2E-36 9E-41 332.2 32.6 280 157-479 287-580 (647)
12 PRK13806 rpsA 30S ribosomal pr 100.0 7.9E-36 1.7E-40 320.6 30.2 268 163-473 106-391 (491)
13 PRK06299 rpsA 30S ribosomal pr 100.0 1.1E-34 2.3E-39 316.5 29.9 270 161-472 190-471 (565)
14 PRK06676 rpsA 30S ribosomal pr 100.0 1.2E-34 2.7E-39 302.6 29.2 254 162-458 95-360 (390)
15 PRK07899 rpsA 30S ribosomal pr 100.0 1.9E-34 4.1E-39 308.2 29.2 247 161-451 111-369 (486)
16 TIGR00717 rpsA ribosomal prote 100.0 3.9E-34 8.4E-39 308.6 30.8 272 160-473 175-458 (516)
17 PRK00087 4-hydroxy-3-methylbut 100.0 9.3E-31 2E-35 289.7 29.4 247 162-451 379-638 (647)
18 PRK07400 30S ribosomal protein 99.9 2.2E-21 4.8E-26 198.4 22.7 186 283-478 18-213 (318)
19 COG2996 Predicted RNA-bindinin 99.8 5.2E-17 1.1E-21 159.7 21.0 212 169-452 2-223 (287)
20 KOG1070 rRNA processing protei 99.7 2.3E-17 5E-22 187.3 12.6 196 252-449 465-673 (1710)
21 COG1098 VacB Predicted RNA bin 99.7 6.2E-18 1.4E-22 148.5 5.4 82 372-454 2-83 (129)
22 KOG1070 rRNA processing protei 99.7 2.2E-16 4.7E-21 179.6 16.2 247 163-448 1058-1326(1710)
23 PTZ00248 eukaryotic translatio 99.7 3E-16 6.4E-21 159.7 10.1 98 372-469 13-113 (319)
24 PRK08582 hypothetical protein; 99.6 1.3E-14 2.9E-19 132.0 11.0 82 372-454 2-83 (139)
25 PTZ00248 eukaryotic translatio 99.5 2.2E-15 4.7E-20 153.4 1.9 138 295-434 16-173 (319)
26 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 4.5E-14 9.7E-19 115.1 8.5 70 373-443 1-74 (74)
27 PF00575 S1: S1 RNA binding do 99.5 2.1E-13 4.6E-18 109.6 9.6 73 372-445 1-74 (74)
28 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 1.3E-13 2.9E-18 111.5 8.4 71 373-445 1-72 (72)
29 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 3.3E-13 7.2E-18 109.2 9.7 71 374-444 2-72 (73)
30 cd05694 S1_Rrp5_repeat_hs2_sc2 99.5 5.5E-13 1.2E-17 108.8 10.3 72 372-449 1-73 (74)
31 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 5.5E-13 1.2E-17 108.3 8.9 70 376-446 1-73 (73)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 4.9E-13 1.1E-17 110.6 8.4 73 371-444 10-83 (83)
33 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 6.7E-13 1.4E-17 105.8 8.6 69 376-445 1-70 (70)
34 PRK07252 hypothetical protein; 99.4 1.1E-12 2.4E-17 116.8 10.7 77 374-451 2-79 (120)
35 PLN00207 polyribonucleotide nu 99.4 2.7E-13 5.9E-18 153.1 8.4 85 372-457 750-835 (891)
36 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 1.7E-12 3.6E-17 104.4 10.3 72 373-445 1-73 (73)
37 cd05684 S1_DHX8_helicase S1_DH 99.4 1.7E-12 3.7E-17 106.2 10.1 75 376-451 1-78 (79)
38 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 1.4E-12 3E-17 103.9 8.6 68 376-444 1-69 (69)
39 cd04452 S1_IF2_alpha S1_IF2_al 99.4 2.4E-12 5.2E-17 103.9 9.9 74 373-446 1-76 (76)
40 PRK05807 hypothetical protein; 99.4 2.7E-12 5.9E-17 116.6 11.0 75 372-448 2-76 (136)
41 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 1.7E-12 3.7E-17 104.7 8.6 68 376-444 1-71 (71)
42 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 3.5E-12 7.5E-17 102.8 9.8 74 374-447 1-75 (77)
43 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 3.6E-12 7.9E-17 101.8 9.5 72 376-448 1-73 (73)
44 cd05707 S1_Rrp5_repeat_sc11 S1 99.3 2.9E-12 6.4E-17 101.8 7.9 67 376-443 1-68 (68)
45 PRK08059 general stress protei 99.3 6.1E-12 1.3E-16 112.2 10.4 79 372-451 4-83 (123)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 3.6E-12 7.8E-17 101.0 7.8 67 376-443 1-69 (69)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 1E-11 2.2E-16 97.3 8.9 69 376-445 1-69 (69)
48 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 1.8E-11 4E-16 97.5 9.1 69 376-445 1-70 (70)
49 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 2.7E-11 5.8E-16 97.1 8.7 70 373-443 1-72 (72)
50 PF00575 S1: S1 RNA binding do 99.3 3.7E-11 8E-16 96.6 9.4 71 294-365 2-74 (74)
51 PHA02945 interferon resistance 99.2 4.8E-11 1E-15 99.6 9.2 75 373-450 9-87 (88)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 2.4E-11 5.2E-16 104.8 7.0 74 373-447 1-97 (100)
53 COG1098 VacB Predicted RNA bin 99.2 2.6E-11 5.5E-16 107.1 7.2 75 294-370 3-79 (129)
54 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 5.6E-11 1.2E-15 98.7 8.5 74 373-447 4-81 (86)
55 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 9.6E-11 2.1E-15 92.9 9.4 66 297-365 1-67 (67)
56 cd05685 S1_Tex S1_Tex: The C-t 99.2 4.9E-11 1.1E-15 93.2 7.6 67 376-443 1-68 (68)
57 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 6.8E-11 1.5E-15 94.1 8.3 65 376-443 1-66 (66)
58 cd04472 S1_PNPase S1_PNPase: P 99.2 1.1E-10 2.3E-15 91.8 8.3 68 376-444 1-68 (68)
59 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 1.9E-10 4E-15 91.3 8.8 66 376-445 1-67 (67)
60 cd05705 S1_Rrp5_repeat_hs14 S1 99.1 1.7E-10 3.8E-15 94.0 8.7 69 294-363 1-74 (74)
61 cd05688 S1_RPS1_repeat_ec3 S1_ 99.1 1.7E-10 3.7E-15 90.4 8.2 67 375-443 1-68 (68)
62 smart00316 S1 Ribosomal protei 99.1 2.6E-10 5.5E-15 89.0 9.0 71 374-445 1-72 (72)
63 PRK03987 translation initiatio 99.1 1.7E-10 3.7E-15 115.5 9.9 79 373-451 6-86 (262)
64 COG1093 SUI2 Translation initi 99.1 4.2E-11 9.2E-16 117.8 5.2 79 373-451 9-89 (269)
65 COG2996 Predicted RNA-bindinin 99.1 1.1E-09 2.3E-14 108.5 14.8 145 168-366 69-217 (287)
66 cd04453 S1_RNase_E S1_RNase_E: 99.1 2.6E-10 5.6E-15 96.1 8.9 73 372-445 4-82 (88)
67 cd05703 S1_Rrp5_repeat_hs12_sc 99.1 3.7E-10 7.9E-15 91.7 9.0 68 297-365 1-72 (73)
68 TIGR02696 pppGpp_PNP guanosine 99.1 1.1E-10 2.4E-15 129.7 7.9 71 372-443 644-718 (719)
69 cd05698 S1_Rrp5_repeat_hs6_sc5 99.1 3.5E-10 7.6E-15 90.0 8.3 68 297-365 1-70 (70)
70 cd04471 S1_RNase_R S1_RNase_R: 99.1 6.4E-10 1.4E-14 90.9 9.6 71 375-445 1-83 (83)
71 PRK11824 polynucleotide phosph 99.1 6.6E-10 1.4E-14 124.8 11.7 76 371-447 617-692 (693)
72 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.1 9E-10 2E-14 87.7 8.9 67 297-364 1-69 (69)
73 cd05694 S1_Rrp5_repeat_hs2_sc2 99.0 8.5E-10 1.8E-14 90.0 8.3 68 294-367 2-71 (74)
74 PRK09202 nusA transcription el 99.0 7.7E-10 1.7E-14 118.9 10.3 108 253-367 85-201 (470)
75 cd04461 S1_Rrp5_repeat_hs8_sc7 99.0 1.1E-09 2.4E-14 90.5 8.7 70 294-364 12-83 (83)
76 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 1.3E-09 2.8E-14 89.9 9.0 73 373-446 4-76 (82)
77 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.0 1.5E-09 3.2E-14 87.6 8.1 67 297-364 1-71 (71)
78 COG2183 Tex Transcriptional ac 99.0 6.3E-10 1.4E-14 123.4 7.6 80 371-451 654-734 (780)
79 cd04473 S1_RecJ_like S1_RecJ_l 99.0 3.9E-09 8.4E-14 86.4 9.9 65 371-444 12-76 (77)
80 cd05707 S1_Rrp5_repeat_sc11 S1 99.0 2.6E-09 5.7E-14 84.8 8.4 66 297-363 1-68 (68)
81 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 3.1E-09 6.8E-14 84.6 8.9 68 297-365 1-70 (70)
82 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 3E-09 6.4E-14 84.7 8.5 64 297-363 1-66 (66)
83 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 2.2E-09 4.9E-14 85.9 7.8 62 376-438 1-64 (70)
84 PRK09521 exosome complex RNA-b 99.0 3.5E-09 7.5E-14 101.1 10.1 90 352-446 42-142 (189)
85 cd05686 S1_pNO40 S1_pNO40: pNO 99.0 3.4E-09 7.5E-14 85.7 8.6 68 295-364 2-72 (73)
86 cd05706 S1_Rrp5_repeat_sc10 S1 99.0 3.6E-09 7.8E-14 85.0 8.6 70 295-365 2-73 (73)
87 COG1185 Pnp Polyribonucleotide 98.9 1.7E-09 3.6E-14 118.5 8.5 77 371-448 615-691 (692)
88 cd04452 S1_IF2_alpha S1_IF2_al 98.9 5.3E-09 1.1E-13 84.3 9.0 71 295-366 2-76 (76)
89 cd00164 S1_like S1_like: Ribos 98.9 4E-09 8.6E-14 80.7 6.8 64 379-443 1-65 (65)
90 cd05708 S1_Rrp5_repeat_sc12 S1 98.9 7.4E-09 1.6E-13 83.3 8.5 71 296-367 2-75 (77)
91 cd05704 S1_Rrp5_repeat_hs13 S1 98.9 6.4E-09 1.4E-13 84.1 8.0 68 295-365 2-72 (72)
92 cd04460 S1_RpoE S1_RpoE: RpoE, 98.9 6.7E-09 1.5E-13 88.8 8.5 80 377-458 1-97 (99)
93 cd05691 S1_RPS1_repeat_ec6 S1_ 98.9 7.7E-09 1.7E-13 82.5 8.3 69 297-366 1-71 (73)
94 cd05690 S1_RPS1_repeat_ec5 S1_ 98.8 1.3E-08 2.8E-13 80.5 8.3 66 297-363 1-69 (69)
95 cd05692 S1_RPS1_repeat_hs4 S1_ 98.8 1.7E-08 3.7E-13 78.9 8.4 67 297-365 1-69 (69)
96 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2E-08 4.3E-13 78.6 8.8 67 296-363 1-68 (68)
97 PRK07252 hypothetical protein; 98.8 1.3E-08 2.9E-13 90.7 8.6 73 295-368 2-76 (120)
98 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 2.8E-08 6E-13 81.9 9.9 76 168-281 2-77 (82)
99 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.8 2.7E-08 5.8E-13 82.6 9.5 80 168-281 2-81 (86)
100 smart00316 S1 Ribosomal protei 98.8 2.6E-08 5.5E-13 77.6 8.8 70 295-365 1-72 (72)
101 TIGR03591 polynuc_phos polyrib 98.8 9E-09 2E-13 115.5 8.0 70 372-442 615-684 (684)
102 PRK08582 hypothetical protein; 98.8 1.5E-08 3.2E-13 92.5 7.9 72 294-367 3-76 (139)
103 PRK05807 hypothetical protein; 98.8 2.5E-08 5.4E-13 90.7 8.3 73 294-368 3-76 (136)
104 TIGR01953 NusA transcription t 98.8 3.2E-08 7E-13 102.6 10.2 108 253-367 82-199 (341)
105 PRK04163 exosome complex RNA-b 98.8 4.4E-08 9.4E-13 96.8 10.6 75 372-447 60-138 (235)
106 cd05685 S1_Tex S1_Tex: The C-t 98.7 5.9E-08 1.3E-12 75.7 8.6 66 297-363 1-68 (68)
107 cd05693 S1_Rrp5_repeat_hs1_sc1 98.7 3.6E-08 7.9E-13 85.1 7.5 72 295-367 2-97 (100)
108 cd05684 S1_DHX8_helicase S1_DH 98.7 5.1E-08 1.1E-12 79.7 7.9 68 297-367 1-74 (79)
109 cd05689 S1_RPS1_repeat_ec4 S1_ 98.7 7.4E-08 1.6E-12 77.1 8.1 68 295-363 2-72 (72)
110 KOG1067 Predicted RNA-binding 98.7 3.5E-08 7.7E-13 105.5 7.0 84 372-456 665-748 (760)
111 COG1093 SUI2 Translation initi 98.6 5.1E-08 1.1E-12 96.3 7.2 71 294-365 9-83 (269)
112 cd04472 S1_PNPase S1_PNPase: P 98.6 1.4E-07 3E-12 73.9 8.4 66 297-364 1-68 (68)
113 PRK08059 general stress protei 98.6 1E-07 2.3E-12 85.0 8.5 74 294-368 5-80 (123)
114 cd04455 S1_NusA S1_NusA: N-uti 98.6 1.7E-07 3.8E-12 74.6 8.7 62 374-443 2-66 (67)
115 cd04455 S1_NusA S1_NusA: N-uti 98.6 1.5E-07 3.3E-12 74.9 8.0 64 295-364 2-67 (67)
116 PHA02945 interferon resistance 98.6 9.4E-08 2E-12 80.0 6.8 69 295-367 10-84 (88)
117 TIGR02696 pppGpp_PNP guanosine 98.6 2.7E-07 5.8E-12 103.2 12.5 95 267-363 612-718 (719)
118 PRK12327 nusA transcription el 98.6 2.3E-07 4.9E-12 97.0 9.4 109 253-367 85-201 (362)
119 PRK09202 nusA transcription el 98.5 2.2E-07 4.7E-12 100.2 9.2 112 320-446 72-200 (470)
120 PLN00207 polyribonucleotide nu 98.5 2.8E-07 6E-12 105.1 10.4 71 294-366 751-824 (891)
121 TIGR00448 rpoE DNA-directed RN 98.5 5E-07 1.1E-11 85.6 10.2 81 374-456 80-177 (179)
122 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.5 4.2E-07 9E-12 77.3 7.8 74 373-447 4-87 (92)
123 cd00164 S1_like S1_like: Ribos 98.5 4.4E-07 9.5E-12 69.3 7.1 63 300-363 1-65 (65)
124 PRK03987 translation initiatio 98.5 4.3E-07 9.4E-12 91.1 8.8 71 294-365 6-80 (262)
125 cd04453 S1_RNase_E S1_RNase_E: 98.5 5.4E-07 1.2E-11 76.0 8.1 70 294-364 5-81 (88)
126 TIGR02063 RNase_R ribonuclease 98.5 5.7E-07 1.2E-11 101.7 10.1 73 372-444 624-708 (709)
127 PRK11824 polynucleotide phosph 98.4 1.2E-06 2.6E-11 98.9 10.4 97 269-367 590-692 (693)
128 cd04471 S1_RNase_R S1_RNase_R: 98.4 1.5E-06 3.3E-11 70.9 7.6 67 297-364 2-82 (83)
129 cd05702 S1_Rrp5_repeat_hs11_sc 98.4 2.3E-06 4.9E-11 68.5 8.4 61 297-358 1-65 (70)
130 PRK11642 exoribonuclease R; Pr 98.3 1.6E-06 3.5E-11 99.2 10.2 76 374-449 642-729 (813)
131 COG1095 RPB7 DNA-directed RNA 98.3 1.7E-06 3.6E-11 81.9 8.0 79 373-453 79-174 (183)
132 PRK09521 exosome complex RNA-b 98.3 2E-06 4.2E-11 82.3 8.6 104 251-366 23-142 (189)
133 TIGR00358 3_prime_RNase VacB a 98.3 2.7E-06 5.8E-11 95.5 10.1 72 373-444 570-653 (654)
134 cd04473 S1_RecJ_like S1_RecJ_l 98.3 6E-06 1.3E-10 67.5 9.0 62 294-364 14-76 (77)
135 PHA02858 EIF2a-like PKR inhibi 98.2 2.8E-06 6.1E-11 70.6 6.4 70 373-444 14-85 (86)
136 COG2183 Tex Transcriptional ac 98.2 2.8E-06 6.1E-11 94.9 7.9 82 285-368 648-731 (780)
137 PRK08563 DNA-directed RNA poly 98.2 5.7E-06 1.2E-10 78.7 9.0 83 373-457 79-178 (187)
138 TIGR03591 polynuc_phos polyrib 98.2 9.1E-06 2E-10 91.7 11.6 92 268-361 586-683 (684)
139 PRK04163 exosome complex RNA-b 98.1 1.3E-05 2.8E-10 79.3 9.6 79 168-280 59-137 (235)
140 COG1185 Pnp Polyribonucleotide 98.1 1.1E-05 2.4E-10 89.1 9.7 98 268-367 587-690 (692)
141 cd04460 S1_RpoE S1_RpoE: RpoE, 98.0 1.1E-05 2.4E-10 69.0 6.7 69 298-367 1-86 (99)
142 TIGR01953 NusA transcription t 98.0 2.9E-05 6.2E-10 80.8 10.3 97 341-447 85-199 (341)
143 PRK12327 nusA transcription el 98.0 1.4E-05 3.1E-10 83.6 7.7 96 341-445 88-199 (362)
144 PRK12328 nusA transcription el 97.9 4.2E-05 9E-10 80.1 9.4 108 253-367 89-207 (374)
145 PF13509 S1_2: S1 domain; PDB: 97.9 5.2E-05 1.1E-09 59.7 7.7 61 172-279 1-61 (61)
146 COG1095 RPB7 DNA-directed RNA 97.9 9.4E-06 2E-10 76.9 3.7 74 294-367 79-168 (183)
147 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.9 8.6E-05 1.9E-09 63.2 8.7 78 168-281 2-87 (92)
148 TIGR00448 rpoE DNA-directed RN 97.8 4.5E-05 9.7E-10 72.3 7.2 73 295-367 80-168 (179)
149 KOG2916 Translation initiation 97.8 5.8E-06 1.2E-10 81.8 1.1 88 372-459 13-102 (304)
150 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.6 0.00037 8.1E-09 58.8 9.2 74 168-280 2-75 (86)
151 PRK05054 exoribonuclease II; P 97.6 0.00024 5.1E-09 79.9 9.7 71 374-444 558-643 (644)
152 COG1096 Predicted RNA-binding 97.6 0.00042 9E-09 66.0 9.4 73 372-446 61-142 (188)
153 TIGR00757 RNaseEG ribonuclease 97.5 0.00022 4.7E-09 76.2 8.2 62 372-434 22-97 (414)
154 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.5 0.00059 1.3E-08 57.6 9.0 59 375-435 1-70 (88)
155 PF13509 S1_2: S1 domain; PDB: 97.5 0.00046 1E-08 54.3 7.7 61 375-445 1-61 (61)
156 COG1097 RRP4 RNA-binding prote 97.5 0.0004 8.6E-09 68.5 8.5 76 372-448 61-140 (239)
157 TIGR02063 RNase_R ribonuclease 97.5 0.00038 8.2E-09 79.1 9.4 70 294-364 625-708 (709)
158 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.4 0.0008 1.7E-08 56.8 8.7 73 373-447 4-76 (86)
159 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00049 1.1E-08 56.1 7.1 67 376-445 1-72 (72)
160 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00048 1E-08 56.2 7.0 65 297-365 1-72 (72)
161 COG1097 RRP4 RNA-binding prote 97.4 0.00072 1.6E-08 66.7 9.5 80 167-280 59-138 (239)
162 PF10447 EXOSC1: Exosome compo 97.4 0.00035 7.6E-09 58.4 6.0 61 374-434 3-82 (82)
163 PRK08563 DNA-directed RNA poly 97.4 0.00024 5.2E-09 67.6 5.6 72 295-367 80-168 (187)
164 PRK12329 nusA transcription el 97.4 0.00075 1.6E-08 72.0 9.4 109 253-367 101-226 (449)
165 PTZ00162 DNA-directed RNA poly 97.3 0.0011 2.3E-08 63.1 9.2 73 373-447 79-166 (176)
166 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.2 0.0014 3E-08 55.4 7.8 34 296-329 1-34 (88)
167 TIGR00358 3_prime_RNase VacB a 97.1 0.0019 4.1E-08 72.8 10.1 68 295-363 571-652 (654)
168 PRK11642 exoribonuclease R; Pr 97.1 0.0014 3.1E-08 75.4 9.0 70 295-365 642-725 (813)
169 KOG1067 Predicted RNA-binding 97.1 0.0022 4.8E-08 69.7 9.3 73 295-369 667-741 (760)
170 TIGR02062 RNase_B exoribonucle 97.1 0.0016 3.5E-08 73.2 8.6 68 376-443 558-638 (639)
171 PHA02858 EIF2a-like PKR inhibi 97.1 0.0018 3.9E-08 54.1 6.6 67 295-364 15-85 (86)
172 COG0557 VacB Exoribonuclease R 97.0 0.0019 4E-08 73.5 8.7 74 372-445 619-704 (706)
173 PRK12328 nusA transcription el 97.0 0.0038 8.3E-08 65.6 10.2 88 168-304 134-226 (374)
174 PTZ00162 DNA-directed RNA poly 96.8 0.0037 8.1E-08 59.4 7.7 73 295-367 80-166 (176)
175 KOG1856 Transcription elongati 96.7 0.0022 4.7E-08 74.4 5.6 76 372-448 982-1061(1299)
176 PRK12329 nusA transcription el 96.6 0.0082 1.8E-07 64.3 9.3 89 168-304 148-245 (449)
177 PRK10811 rne ribonuclease E; R 96.6 0.0045 9.8E-08 71.3 7.6 92 374-473 37-142 (1068)
178 COG1107 Archaea-specific RecJ- 96.6 0.0018 3.9E-08 70.7 4.1 71 371-448 118-189 (715)
179 PF10447 EXOSC1: Exosome compo 96.0 0.023 5.1E-07 47.5 6.9 23 170-192 2-24 (82)
180 TIGR00757 RNaseEG ribonuclease 95.8 0.025 5.5E-07 60.6 7.8 57 295-352 24-96 (414)
181 PRK11712 ribonuclease G; Provi 95.7 0.027 6E-07 61.5 7.4 61 373-434 36-110 (489)
182 PRK05054 exoribonuclease II; P 95.6 0.052 1.1E-06 61.3 9.4 67 297-363 562-642 (644)
183 KOG2916 Translation initiation 95.5 0.016 3.5E-07 57.9 4.7 71 294-365 14-88 (304)
184 KOG1856 Transcription elongati 95.4 0.031 6.6E-07 65.3 6.7 72 294-366 983-1059(1299)
185 COG1096 Predicted RNA-binding 95.0 0.12 2.6E-06 49.5 8.3 105 251-365 23-141 (188)
186 COG1107 Archaea-specific RecJ- 95.0 0.15 3.2E-06 56.3 10.0 150 165-363 115-281 (715)
187 TIGR02062 RNase_B exoribonucle 94.8 0.12 2.5E-06 58.5 9.2 66 297-362 558-637 (639)
188 KOG3013 Exosomal 3'-5' exoribo 94.6 0.058 1.3E-06 53.9 5.4 87 167-281 80-166 (301)
189 KOG3298 DNA-directed RNA polym 93.5 0.58 1.2E-05 44.0 9.4 60 374-435 80-150 (170)
190 PF10246 MRP-S35: Mitochondria 93.3 0.37 7.9E-06 42.0 7.3 32 171-202 22-53 (104)
191 KOG3409 Exosomal 3'-5' exoribo 93.1 0.42 9E-06 45.3 7.9 71 374-445 67-147 (193)
192 COG0557 VacB Exoribonuclease R 92.0 0.57 1.2E-05 53.6 8.8 70 294-363 620-702 (706)
193 PF08292 RNA_pol_Rbc25: RNA po 91.7 0.79 1.7E-05 41.2 7.6 60 296-355 3-76 (122)
194 COG1530 CafA Ribonucleases G a 91.0 0.3 6.5E-06 53.5 5.1 62 372-435 34-102 (487)
195 KOG3409 Exosomal 3'-5' exoribo 90.8 1.1 2.3E-05 42.7 7.7 76 170-281 66-149 (193)
196 KOG3298 DNA-directed RNA polym 90.6 1 2.2E-05 42.3 7.4 34 295-328 80-113 (170)
197 PRK11712 ribonuclease G; Provi 90.0 0.8 1.7E-05 50.3 7.2 58 295-353 37-110 (489)
198 PRK10811 rne ribonuclease E; R 89.9 0.6 1.3E-05 54.6 6.4 61 295-356 37-110 (1068)
199 PF10246 MRP-S35: Mitochondria 89.1 1.7 3.7E-05 37.9 7.0 53 374-434 22-74 (104)
200 PF08292 RNA_pol_Rbc25: RNA po 88.1 3.2 7E-05 37.3 8.5 60 375-435 3-75 (122)
201 PRK12442 translation initiatio 87.0 4.2 9.1E-05 34.5 8.0 64 378-446 8-73 (87)
202 KOG1004 Exosomal 3'-5' exoribo 85.4 4.8 0.0001 39.5 8.6 63 168-269 61-123 (230)
203 TIGR00008 infA translation ini 84.7 5.4 0.00012 32.4 7.3 59 378-441 6-66 (68)
204 PF00313 CSD: 'Cold-shock' DNA 80.4 19 0.00041 28.1 8.9 55 379-439 1-58 (66)
205 COG4148 ModC ABC-type molybdat 76.0 24 0.00053 36.6 10.2 113 295-434 230-348 (352)
206 PRK09937 stationary phase/star 75.7 23 0.0005 29.0 8.3 63 380-447 3-67 (74)
207 PF09883 DUF2110: Uncharacteri 74.1 13 0.00029 36.6 7.5 97 159-289 59-157 (225)
208 COG1530 CafA Ribonucleases G a 73.5 4.4 9.6E-05 44.6 4.7 44 164-207 29-74 (487)
209 cd05700 S1_Rrp5_repeat_hs9 S1_ 73.2 10 0.00022 30.2 5.2 64 376-444 1-65 (65)
210 COG0361 InfA Translation initi 72.7 25 0.00054 29.1 7.7 65 376-445 6-72 (75)
211 PRK15464 cold shock-like prote 70.4 33 0.00071 27.8 8.0 56 379-439 5-62 (70)
212 PRK15463 cold shock-like prote 68.4 21 0.00045 28.9 6.4 51 379-433 5-57 (70)
213 PRK12442 translation initiatio 67.9 18 0.0004 30.7 6.1 62 298-365 7-72 (87)
214 PRK14998 cold shock-like prote 66.2 46 0.001 27.1 8.1 62 380-446 3-66 (73)
215 PRK09890 cold shock protein Cs 66.0 54 0.0012 26.4 8.4 56 379-439 5-62 (70)
216 PRK10943 cold shock-like prote 65.9 51 0.0011 26.4 8.2 52 378-433 3-56 (69)
217 cd04458 CSP_CDS Cold-Shock Pro 65.3 42 0.0009 26.0 7.5 56 380-440 2-59 (65)
218 TIGR00008 infA translation ini 64.7 24 0.00053 28.6 6.0 57 299-361 6-66 (68)
219 KOG4078 Putative mitochondrial 59.6 14 0.00029 34.2 4.1 54 374-435 81-134 (173)
220 KOG4078 Putative mitochondrial 58.4 24 0.00052 32.7 5.5 46 156-201 63-111 (173)
221 PF01330 RuvA_N: RuvA N termin 57.5 66 0.0014 24.9 7.3 48 378-434 4-51 (61)
222 PF13742 tRNA_anti_2: OB-fold 57.2 68 0.0015 27.4 8.0 69 375-449 22-99 (99)
223 PRK10943 cold shock-like prote 55.9 44 0.00095 26.8 6.2 49 299-352 3-56 (69)
224 PF03459 TOBE: TOBE domain; I 55.5 32 0.0007 26.3 5.2 49 377-432 5-58 (64)
225 PRK09507 cspE cold shock prote 54.0 57 0.0012 26.1 6.6 52 378-433 3-56 (69)
226 KOG3013 Exosomal 3'-5' exoribo 53.1 11 0.00024 38.1 2.7 75 372-447 82-166 (301)
227 PRK09507 cspE cold shock prote 49.8 63 0.0014 25.9 6.2 49 299-352 3-56 (69)
228 CHL00010 infA translation init 48.4 1.3E+02 0.0027 24.8 7.9 67 379-450 9-77 (78)
229 PRK15464 cold shock-like prote 48.3 58 0.0012 26.4 5.7 48 300-352 5-57 (70)
230 PRK04012 translation initiatio 48.3 91 0.002 27.1 7.3 64 375-444 19-84 (100)
231 KOG3297 DNA-directed RNA polym 48.3 30 0.00065 33.4 4.6 60 295-354 80-157 (202)
232 PRK15463 cold shock-like prote 47.2 64 0.0014 26.1 5.8 48 300-352 5-57 (70)
233 PRK10354 RNA chaperone/anti-te 46.5 1.5E+02 0.0033 23.7 8.1 51 379-433 5-57 (70)
234 COG4148 ModC ABC-type molybdat 45.9 2.5E+02 0.0053 29.5 11.0 46 255-314 265-310 (352)
235 PF09883 DUF2110: Uncharacteri 45.7 1.5E+02 0.0032 29.5 9.1 81 285-366 61-148 (225)
236 cd04322 LysRS_N LysRS_N: N-ter 45.7 51 0.0011 28.2 5.4 54 378-431 3-60 (108)
237 TIGR02381 cspD cold shock doma 45.4 1.1E+02 0.0024 24.3 7.0 55 380-439 3-59 (68)
238 PF01330 RuvA_N: RuvA N termin 43.6 1.5E+02 0.0033 22.9 7.5 48 299-355 4-53 (61)
239 cd05793 S1_IF1A S1_IF1A: Trans 42.0 99 0.0021 25.5 6.3 58 379-442 2-61 (77)
240 PRK09937 stationary phase/star 41.3 83 0.0018 25.7 5.7 47 301-352 3-54 (74)
241 COG3269 Predicted RNA-binding 41.0 1.2E+02 0.0026 25.0 6.5 47 295-355 14-61 (73)
242 COG1545 Predicted nucleic-acid 40.5 1.6E+02 0.0034 27.0 8.1 53 375-435 63-124 (140)
243 PRK10354 RNA chaperone/anti-te 40.3 1E+02 0.0022 24.7 6.0 48 300-352 5-57 (70)
244 PRK09890 cold shock protein Cs 38.3 1.3E+02 0.0027 24.2 6.3 48 300-352 5-57 (70)
245 PRK10676 DNA-binding transcrip 37.5 2.1E+02 0.0045 28.9 9.1 113 299-433 129-254 (263)
246 KOG1004 Exosomal 3'-5' exoribo 36.7 1E+02 0.0022 30.6 6.4 59 294-355 63-124 (230)
247 PF00313 CSD: 'Cold-shock' DNA 36.6 2E+02 0.0043 22.2 9.1 31 176-206 1-34 (66)
248 TIGR00739 yajC preprotein tran 35.1 85 0.0018 26.3 5.0 34 164-197 32-71 (84)
249 PF03459 TOBE: TOBE domain; I 34.2 1.7E+02 0.0038 22.1 6.4 45 299-350 6-57 (64)
250 COG1278 CspC Cold shock protei 34.1 1.5E+02 0.0032 24.1 5.9 50 380-433 3-54 (67)
251 PRK05585 yajC preprotein trans 32.7 89 0.0019 27.4 4.9 35 164-198 47-87 (106)
252 TIGR00084 ruvA Holliday juncti 32.7 1.3E+02 0.0028 29.0 6.5 48 378-434 4-51 (191)
253 TIGR00187 ribE riboflavin synt 32.4 4.8E+02 0.01 25.4 10.6 132 348-482 10-161 (200)
254 PF08206 OB_RNB: Ribonuclease 32.1 1.2E+02 0.0026 23.2 5.1 44 381-433 1-44 (58)
255 TIGR02381 cspD cold shock doma 32.0 1.2E+02 0.0027 24.1 5.2 47 301-352 3-54 (68)
256 PF08206 OB_RNB: Ribonuclease 31.8 1.3E+02 0.0028 23.1 5.2 42 302-352 1-44 (58)
257 PRK14998 cold shock-like prote 31.8 1.4E+02 0.003 24.3 5.6 48 301-353 3-55 (73)
258 cd04458 CSP_CDS Cold-Shock Pro 31.6 1.4E+02 0.003 23.0 5.5 48 301-353 2-54 (65)
259 PRK14604 ruvA Holliday junctio 31.4 2.1E+02 0.0046 27.7 7.8 27 175-201 4-31 (195)
260 PRK14603 ruvA Holliday junctio 30.9 1.4E+02 0.003 28.9 6.4 48 378-434 4-51 (197)
261 PRK14604 ruvA Holliday junctio 30.8 1.5E+02 0.0032 28.8 6.6 49 378-434 4-52 (195)
262 TIGR00638 Mop molybdenum-pteri 30.4 63 0.0014 24.9 3.3 49 377-432 7-60 (69)
263 PRK10676 DNA-binding transcrip 30.1 4.3E+02 0.0093 26.6 10.0 76 255-351 171-253 (263)
264 cd05701 S1_Rrp5_repeat_hs10 S1 29.8 84 0.0018 25.4 3.8 57 378-434 3-59 (69)
265 PRK05886 yajC preprotein trans 29.8 1.1E+02 0.0024 27.1 5.0 37 165-201 34-76 (109)
266 PRK14600 ruvA Holliday junctio 29.5 1.8E+02 0.0038 28.0 6.8 47 378-433 4-50 (186)
267 COG0361 InfA Translation initi 29.0 1.1E+02 0.0024 25.4 4.5 60 297-362 6-69 (75)
268 PRK14605 ruvA Holliday junctio 29.0 1.7E+02 0.0036 28.3 6.6 49 378-434 4-52 (194)
269 COG2106 Uncharacterized conser 28.3 1.1E+02 0.0024 31.3 5.4 49 372-434 102-150 (272)
270 PRK13901 ruvA Holliday junctio 28.0 1.9E+02 0.0042 28.2 6.8 48 378-434 4-51 (196)
271 PRK14605 ruvA Holliday junctio 27.8 2.7E+02 0.0059 26.9 7.8 27 175-201 4-31 (194)
272 PRK14601 ruvA Holliday junctio 26.8 1.7E+02 0.0038 28.0 6.2 48 378-434 4-52 (183)
273 KOG3297 DNA-directed RNA polym 26.7 91 0.002 30.2 4.2 46 162-207 71-116 (202)
274 PRK10476 multidrug resistance 26.2 3.8E+02 0.0083 27.6 9.2 70 296-388 211-286 (346)
275 cd04318 EcAsnRS_like_N EcAsnRS 26.1 2.8E+02 0.0061 22.2 6.6 50 378-431 3-58 (82)
276 TIGR00084 ruvA Holliday juncti 26.1 2.7E+02 0.0058 26.8 7.4 51 299-358 4-56 (191)
277 smart00652 eIF1a eukaryotic tr 25.6 3.5E+02 0.0076 22.6 7.1 60 377-442 5-66 (83)
278 PRK14603 ruvA Holliday junctio 25.5 3E+02 0.0065 26.7 7.7 26 175-200 4-30 (197)
279 COG4044 Uncharacterized protei 25.4 5.6E+02 0.012 25.5 9.3 108 260-368 31-160 (247)
280 cd04456 S1_IF1A_like S1_IF1A_l 25.4 3.3E+02 0.0072 22.5 6.8 59 379-443 2-63 (78)
281 PRK15136 multidrug efflux syst 24.3 5.9E+02 0.013 27.0 10.3 72 295-388 217-294 (390)
282 COG1862 YajC Preprotein transl 24.2 1.4E+02 0.0031 25.9 4.6 35 165-199 39-79 (97)
283 COG4776 Rnb Exoribonuclease II 23.0 20 0.00044 39.2 -1.0 66 295-360 560-639 (645)
284 PF09953 DUF2187: Uncharacteri 22.5 1.5E+02 0.0033 23.3 4.0 19 176-194 16-34 (57)
285 PRK13901 ruvA Holliday junctio 22.0 3.9E+02 0.0085 26.0 7.7 27 175-201 4-31 (196)
286 PRK14600 ruvA Holliday junctio 21.7 3.7E+02 0.0081 25.8 7.4 46 299-353 4-51 (186)
287 PF02699 YajC: Preprotein tran 21.5 34 0.00073 28.5 0.2 36 161-196 28-69 (82)
288 PF05339 DUF739: Protein of un 21.5 24 0.00052 32.4 -0.7 16 117-132 75-90 (138)
289 PRK14606 ruvA Holliday junctio 21.4 3.7E+02 0.0079 25.9 7.3 77 174-297 3-82 (188)
290 KOG4134 DNA-dependent RNA poly 21.1 72 0.0016 31.8 2.4 58 372-435 104-161 (253)
291 PTZ00329 eukaryotic translatio 21.1 3.2E+02 0.007 25.7 6.6 63 375-444 31-95 (155)
292 PF07076 DUF1344: Protein of u 21.0 4.4E+02 0.0095 21.1 7.1 56 377-442 3-58 (61)
293 PRK14601 ruvA Holliday junctio 20.8 4.1E+02 0.0088 25.5 7.5 27 175-201 4-32 (183)
294 smart00357 CSP Cold shock prot 20.8 3E+02 0.0064 20.2 5.4 47 381-433 2-49 (64)
295 PF01176 eIF-1a: Translation i 20.6 1.7E+02 0.0036 23.1 4.0 49 378-432 4-53 (65)
296 COG3269 Predicted RNA-binding 20.3 4.2E+02 0.0092 21.9 6.3 48 372-435 12-60 (73)
297 PF01938 TRAM: TRAM domain; I 20.2 3.3E+02 0.0072 20.6 5.6 51 341-392 3-57 (61)
298 COG1278 CspC Cold shock protei 20.2 1.7E+02 0.0037 23.8 3.9 47 301-352 3-54 (67)
299 PF07653 SH3_2: Variant SH3 do 20.0 2.4E+02 0.0052 20.9 4.7 17 312-328 36-52 (55)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-45 Score=391.59 Aligned_cols=267 Identities=30% Similarity=0.378 Sum_probs=240.8
Q ss_pred hhhcccc---ccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccce
Q 011538 158 VGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG 234 (483)
Q Consensus 158 ~~~~~~~---~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~ 234 (483)
+|++.+. ...+.+++|++|.|+|+++++++++||+|++++|++|++|+...+
T Consensus 4 ~f~~~~~~~~~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~------------------------- 58 (541)
T COG0539 4 EFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEP------------------------- 58 (541)
T ss_pred hHHHHHHhhhcchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhcccc-------------------------
Confidence 3444444 467889999999999999999999999999999999999986431
Q ss_pred eeeccccccccCCCCCCCCcccCCCEEEEEEEE-EcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEE
Q 011538 235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLG-RTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313 (483)
Q Consensus 235 vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~-~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~f 313 (483)
....+++||.+.+.|.. .+.+|.++||++++...++|..|.++++.|++|+|+|+...++|++
T Consensus 59 ----------------~~~~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~ 122 (541)
T COG0539 59 ----------------VEDVVQVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLT 122 (541)
T ss_pred ----------------ccceecCCCEEEEEEEEEecCCceEEeeHHHHHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEE
Confidence 11258899999999998 4667899999999999999999999999999999999999999999
Q ss_pred EEECCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEE
Q 011538 314 TRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGT 382 (483)
Q Consensus 314 V~I~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~ 382 (483)
|+++|++||+|.|++. +++++... .+|+.+.++|+++|++++++++|||..++ ..++++|++++|+
T Consensus 123 Vdi~gvr~FlP~S~v~~r~v~d~~~---~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~ 199 (541)
T COG0539 123 VDIEGVRAFLPGSLVDVRPVRDLDP---LIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGV 199 (541)
T ss_pred EEECCEEEeccHHHhcccccccccc---cCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEE
Confidence 9999999999999994 55655444 58999999999999999999999998764 2589999999999
Q ss_pred EEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccc
Q 011538 383 VKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVH 461 (483)
Q Consensus 383 V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V 461 (483)
|++|++|||||+|+ |++||||+++|||.|+.+|++.|++||+|+|+|+++| +++||+||||++.+|||+.+.++|++
T Consensus 200 V~~It~~GafVdig--GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~ 277 (541)
T COG0539 200 VKNITDYGAFVDIG--GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPV 277 (541)
T ss_pred EEEeecCcEEEEec--CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCC
Confidence 99999999999999 5999999999999999999999999999999999999 89999999999999999999999999
Q ss_pred ceeeEEEEe
Q 011538 462 IIFLFILLF 470 (483)
Q Consensus 462 ~~~~~~~~~ 470 (483)
++.+.=.+-
T Consensus 278 g~~v~G~Vt 286 (541)
T COG0539 278 GDKVEGKVT 286 (541)
T ss_pred CCEEEEEEE
Confidence 999854443
No 2
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.9e-44 Score=365.47 Aligned_cols=266 Identities=31% Similarity=0.426 Sum_probs=236.4
Q ss_pred chhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538 156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (483)
Q Consensus 156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v 235 (483)
..+|+++|+.+.+.+++|++|.|+|++++++|++||+|++..||||++|++..+. .+
T Consensus 15 ~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~-----------~~------------ 71 (318)
T PRK07400 15 HEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRV-----------EG------------ 71 (318)
T ss_pred HHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccc-----------cC------------
Confidence 3679999986666799999999999999999999999999999999999864311 11
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (483)
Q Consensus 236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV 314 (483)
....+++|+.+.|.|++. +.+|++.||+|++.....|+++.++++.|++|+|+|++++++|++|
T Consensus 72 ---------------~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V 136 (318)
T PRK07400 72 ---------------PEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV 136 (318)
T ss_pred ---------------HHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 123478999999999985 4678999999999877899999999999999999999999999999
Q ss_pred EECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh---hcCCCCCcEEEEEEEEEeCceE
Q 011538 315 RIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---TLNLREGTLLEGTVKKIYPYGA 391 (483)
Q Consensus 315 ~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e---~~~l~vG~iv~G~V~~I~~~Ga 391 (483)
+++|++||||.|++..+. ..+. .+|+.+.|+|+++|++++++.||+|.++. ..++++|+++.|+|++|++||+
T Consensus 137 ~l~Gv~gfip~s~ls~~~--~~~~--~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~ 212 (318)
T PRK07400 137 RIEGLRGFIPGSHISTRK--PKEE--LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGA 212 (318)
T ss_pred EECCEEEEEEHHHcCccC--Cccc--cCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeE
Confidence 999999999999994321 2222 59999999999999999999999998753 3479999999999999999999
Q ss_pred EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceee
Q 011538 392 QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFL 465 (483)
Q Consensus 392 FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~ 465 (483)
||+++ |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++++|||+.+.+++.+|+-+
T Consensus 213 fV~i~--gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~ 285 (318)
T PRK07400 213 FIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKA 285 (318)
T ss_pred EEEEC--CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHH
Confidence 99996 6899999999999999999999999999999999998 789999999999999999999999988643
No 3
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.6e-42 Score=368.44 Aligned_cols=266 Identities=26% Similarity=0.392 Sum_probs=238.2
Q ss_pred hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (483)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv 236 (483)
.+|.+.++..+..+++|++|.|+|+++++++++||+|++.+|+||.+|++...+ .+
T Consensus 20 e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~-----------~~------------- 75 (486)
T PRK07899 20 EDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHD-----------VD------------- 75 (486)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhccccc-----------CC-------------
Confidence 678888888888899999999999999999999999999999999999864310 11
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEE
Q 011538 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (483)
Q Consensus 237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~ 315 (483)
....+++||+|+|.|++. +.+|+++||+|++.....|..+.++++.|++++|+|+++.++|++|+
T Consensus 76 --------------~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vd 141 (486)
T PRK07899 76 --------------PNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILD 141 (486)
T ss_pred --------------hhhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEE
Confidence 123488999999999985 46789999999998889999999999999999999999999999999
Q ss_pred ECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEEE
Q 011538 316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTVK 384 (483)
Q Consensus 316 I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V~ 384 (483)
+ |++||||.|++ +.+..++.. .+|+.|+|+|+++|+++++++||+|..++ ...+++|+++.|+|+
T Consensus 142 l-Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~ 217 (486)
T PRK07899 142 I-GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVS 217 (486)
T ss_pred E-CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEE
Confidence 9 89999999999 555555544 59999999999999999999999996432 147999999999999
Q ss_pred EEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccce
Q 011538 385 KIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHII 463 (483)
Q Consensus 385 ~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~ 463 (483)
+++++|+||+|+ |++||||+++++|.++.++.+.|++||.|+|+|+++| +++||.||+|++.++||+.+.+++++++
T Consensus 218 ~i~~~G~FVdlg--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~ 295 (486)
T PRK07899 218 SIVNFGAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQ 295 (486)
T ss_pred EEECCeEEEEEC--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCC
Confidence 999999999996 6999999999999999999999999999999999998 7899999999999999999999998888
Q ss_pred eeE
Q 011538 464 FLF 466 (483)
Q Consensus 464 ~~~ 466 (483)
.+.
T Consensus 296 vv~ 298 (486)
T PRK07899 296 IVP 298 (486)
T ss_pred EEE
Confidence 773
No 4
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=6.3e-40 Score=357.42 Aligned_cols=271 Identities=26% Similarity=0.354 Sum_probs=242.0
Q ss_pred cchhhhccccccc--cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccc
Q 011538 155 DDKVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK 232 (483)
Q Consensus 155 ~~~~~~~~~~~~~--~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~ 232 (483)
+..+|+++++.+. +++++|++|+|+|+++++++++||+|++.+||||.+|+.+..
T Consensus 11 ~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~----------------------- 67 (565)
T PRK06299 11 MEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ----------------------- 67 (565)
T ss_pred chHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc-----------------------
Confidence 3467999998776 779999999999999999999999999999999999985310
Q ss_pred ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCe
Q 011538 233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGG 311 (483)
Q Consensus 233 v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G 311 (483)
....+++||+++|.|++. +.+|+++||++++.....|+++.++++.|++++|+|+++.++|
T Consensus 68 ------------------~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G 129 (565)
T PRK06299 68 ------------------GELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGG 129 (565)
T ss_pred ------------------ccccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCE
Confidence 012478999999999995 5678999999999999999999999999999999999999999
Q ss_pred EEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEE
Q 011538 312 LLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLE 380 (483)
Q Consensus 312 ~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~ 380 (483)
++|+++|++||||.+++ +.+.+++. ..+|+++.|+|+++|++++++.+|+|++++ ...+++|+++.
T Consensus 130 ~~V~~~g~~gfip~s~~~~~~~~~~~---~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~ 206 (565)
T PRK06299 130 FTVDLNGVEAFLPGSQVDVRPVRDTD---PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVE 206 (565)
T ss_pred EEEEECCEEEEEEHHHccCcCCCChH---HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEE
Confidence 99999999999999999 55555543 369999999999999999999999997643 14799999999
Q ss_pred EEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccc
Q 011538 381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKE 459 (483)
Q Consensus 381 G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~ 459 (483)
|+|++++++|+||+++ |++||+|.++++|.++.++.+.|++||+|+|+|+++| ++++|.||+|++.+|||+.+.+++
T Consensus 207 g~V~~v~~~G~~V~i~--g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~ 284 (565)
T PRK06299 207 GVVKNITDYGAFVDLG--GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKY 284 (565)
T ss_pred EEEEEEeCCeEEEEEC--CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhC
Confidence 9999999999999997 6999999999999999999999999999999999998 789999999999999999999999
Q ss_pred ccceeeEEEEee
Q 011538 460 VHIIFLFILLFN 471 (483)
Q Consensus 460 ~V~~~~~~~~~~ 471 (483)
++++.+.-.+.+
T Consensus 285 ~~G~~v~g~V~~ 296 (565)
T PRK06299 285 PVGSKVKGKVTN 296 (565)
T ss_pred CCCCEEEEEEEE
Confidence 999988444443
No 5
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-40 Score=353.74 Aligned_cols=276 Identities=21% Similarity=0.232 Sum_probs=242.7
Q ss_pred hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (483)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv 236 (483)
-+.++.|.........|.+|.|+|+...+.|+.|+++. ..||||.|++..+. +
T Consensus 90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~--------------------------v 142 (541)
T COG0539 90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRP--------------------------V 142 (541)
T ss_pred HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhcccc--------------------------c
Confidence 35567777777778899999999999999999999964 99999999985331 0
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhHHHHHHhhCCCeEEEEEEEEECCeE
Q 011538 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (483)
Q Consensus 237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~---~~w~~L~~~~k~GeiV~GkV~~v~k~G~ 312 (483)
. .....+|..+.+.|++.| .++++++|+|..... +....+.+.++.|++++|+|++++++|+
T Consensus 143 --~------------d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga 208 (541)
T COG0539 143 --R------------DLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA 208 (541)
T ss_pred --c------------cccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence 0 011348999999999976 578999999998653 2233445567999999999999999999
Q ss_pred EEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----Hhhh--cCCCCCcEEEEEEEE
Q 011538 313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKK 385 (483)
Q Consensus 313 fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----~~e~--~~l~vG~iv~G~V~~ 385 (483)
||+++|++|++|.++| |.|+.+|+++. ++||+|+|+|+++|++++|+.||+|+ ||+. ..+.+|+.+.|+|++
T Consensus 209 fVdigGvdGLlHiseiS~~rv~~P~~vv-kvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~ 287 (541)
T COG0539 209 FVDIGGVDGLLHISEISWKRVDHPSEVV-KVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTN 287 (541)
T ss_pred EEEecCeeeEEehhhccccccCCHHHhc-ccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEE
Confidence 9999999999999999 89999999986 99999999999999999999999997 5654 589999999999999
Q ss_pred EeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccccee
Q 011538 386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIF 464 (483)
Q Consensus 386 I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~ 464 (483)
+++|||||++.+ |++||+|+|||||.+...|++++++||+|.|+|+++| +++||+||||++.+|||+.+.++|++++.
T Consensus 288 i~~~GafVei~~-GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~ 366 (541)
T COG0539 288 LTDYGAFVEIEE-GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDV 366 (541)
T ss_pred eecCcEEEEecC-CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCe
Confidence 999999999999 8999999999999999999999999999999999998 88999999999999999999999999999
Q ss_pred eEEEEeecccc
Q 011538 465 LFILLFNKQYS 475 (483)
Q Consensus 465 ~~~~~~~~~~~ 475 (483)
+.=.+.++..-
T Consensus 367 v~g~v~~~t~~ 377 (541)
T COG0539 367 VEGKVKSITDF 377 (541)
T ss_pred EEEEEeeeccc
Confidence 96666665543
No 6
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.4e-38 Score=329.42 Aligned_cols=268 Identities=31% Similarity=0.413 Sum_probs=237.5
Q ss_pred hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEe-CCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (483)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~Vdi-G~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v 235 (483)
.+|++.+. ...++++|++|.|+|++++++|++|++ |.+.+|+||.+|+...+.
T Consensus 3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~------------------------- 56 (390)
T PRK06676 3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHI------------------------- 56 (390)
T ss_pred HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccc-------------------------
Confidence 46888887 888999999999999999999999999 889999999999863210
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (483)
Q Consensus 236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV 314 (483)
.+....+++|+.|.|+|+..+ .++++.||++++.....|+.+.++++.|++++|+|+++.++|++|
T Consensus 57 -------------~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V 123 (390)
T PRK06676 57 -------------EDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV 123 (390)
T ss_pred -------------cCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 011235889999999999964 567899999999888899999999999999999999999999999
Q ss_pred EECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEE
Q 011538 315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV 383 (483)
Q Consensus 315 ~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V 383 (483)
+++|++||||.+++ +.+..++.. .+|+.+.|+|+++|++++++.+|+|.... ...+++|+++.|+|
T Consensus 124 ~~~G~~gflp~~el~~~~~~~~~~---~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V 200 (390)
T PRK06676 124 DVEGVRGFIPASLISTRFVEDFSD---FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTV 200 (390)
T ss_pred EECCEEEEEEHHHcCCccCCChHH---cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEE
Confidence 99999999999999 555666554 48999999999999999999999997532 14689999999999
Q ss_pred EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI 462 (483)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~ 462 (483)
++++++|+||+++ +++|+||.++++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||+.+.+.++++
T Consensus 201 ~~v~~~G~fV~l~--~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G 278 (390)
T PRK06676 201 ARLTDFGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEG 278 (390)
T ss_pred EEEecceEEEEeC--CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCC
Confidence 9999999999996 5999999999999999999999999999999999998 689999999999999999998899999
Q ss_pred eeeEEE
Q 011538 463 IFLFIL 468 (483)
Q Consensus 463 ~~~~~~ 468 (483)
+.+.-.
T Consensus 279 ~~v~g~ 284 (390)
T PRK06676 279 DVIEGT 284 (390)
T ss_pred cEEEEE
Confidence 888333
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2e-38 Score=340.64 Aligned_cols=275 Identities=24% Similarity=0.292 Sum_probs=237.6
Q ss_pred hhhhcccccccc----CCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccc
Q 011538 157 KVGEDKVSVEYY----EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK 232 (483)
Q Consensus 157 ~~~~~~~~~~~~----~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~ 232 (483)
++|+++++.+.+ .+++|++|+|+|+++++++++||+|++.+|+||.+|+....
T Consensus 15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~----------------------- 71 (491)
T PRK13806 15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD----------------------- 71 (491)
T ss_pred HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc-----------------------
Confidence 578888876653 39999999999999999999999999999999999985210
Q ss_pred ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeE
Q 011538 233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (483)
Q Consensus 233 v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~ 312 (483)
....+++|+++++.|++.+ ++.+.||++.. ....|..+.++++.|++++|+|+++.++|+
T Consensus 72 ------------------~~~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~ 131 (491)
T PRK13806 72 ------------------GELTVAVGDEVELYVVSVN-GQEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGF 131 (491)
T ss_pred ------------------ccccccCCCEEEEEEEEEc-CCEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCE
Confidence 0123789999999999854 46799997754 567999999999999999999999999999
Q ss_pred EEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEE
Q 011538 313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG 381 (483)
Q Consensus 313 fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G 381 (483)
+|+++|++||||.|++ +....++.. .+|+++.|+|+++|++++++.+|+|+.++ ...+++|+++.|
T Consensus 132 ~V~i~g~~~flP~s~~~~~~~~~~~~---~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G 208 (491)
T PRK13806 132 NVEVLGRRAFCPVSQIDLRYVEDPES---YVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEG 208 (491)
T ss_pred EEEECCEEEEEEHHHhccccCCChHH---cCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEE
Confidence 9999999999999999 555666654 48999999999999999999999997642 136999999999
Q ss_pred EEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CC----CeEEEEEecCCCCcCcccc
Q 011538 382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP----DKISLSIADLESEPGLFVS 456 (483)
Q Consensus 382 ~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek----~rI~LSLK~~~~dPw~~l~ 456 (483)
+|+++.++|+||++++ |+.||||.++++|.++.++.+.|++||.|+|+|+++| ++ .||.||+|++.++||+.+.
T Consensus 209 ~V~~v~~~G~fV~l~~-gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~ 287 (491)
T PRK13806 209 TVTRLAPFGAFVELAP-GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVG 287 (491)
T ss_pred EEEEEeCCeEEEEcCC-CcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhh
Confidence 9999999999999987 7999999999999999999999999999999999998 43 4899999999999999999
Q ss_pred cccccceeeEEEEeecccceEE
Q 011538 457 DKEVHIIFLFILLFNKQYSVWF 478 (483)
Q Consensus 457 ~k~~V~~~~~~~~~~~~~~~~~ 478 (483)
+++++++.+.-.+.+-...-.|
T Consensus 288 ~~~~~G~~v~G~V~~v~~~G~f 309 (491)
T PRK13806 288 DRLKAGDKVTGKVVRLAPFGAF 309 (491)
T ss_pred ccCCCCCEEEEEEEEEeCceEE
Confidence 9999999995555444443333
No 8
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=1.3e-37 Score=335.50 Aligned_cols=273 Identities=26% Similarity=0.364 Sum_probs=238.9
Q ss_pred hhhcccccc--ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538 158 VGEDKVSVE--YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (483)
Q Consensus 158 ~~~~~~~~~--~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v 235 (483)
+|+++++.+ ..++++|++|.|+|+++++++++||+|++.+|++|.+|+...
T Consensus 2 ~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~--------------------------- 54 (516)
T TIGR00717 2 SFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA--------------------------- 54 (516)
T ss_pred hHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCC---------------------------
Confidence 578888665 346899999999999999999999999999999999988521
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (483)
Q Consensus 236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV 314 (483)
...+++||++.+.|.+. +..|++.||+++......|..++++++.|++++|+|+++.++|++|
T Consensus 55 ----------------~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V 118 (516)
T TIGR00717 55 ----------------PLEIQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIV 118 (516)
T ss_pred ----------------ccCCCCCCEEEEEEEEEeCCCCcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEEE
Confidence 13478999999999984 4679999999999888999999999999999999999999999999
Q ss_pred EECCeEEEeeccccccc-cCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEE
Q 011538 315 RIEGLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV 383 (483)
Q Consensus 315 ~I~Gi~gFVP~Sel~~r-v~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V 383 (483)
+++|++||||.+++..+ .++. ...+|++++|+|+++|++++++++|+|+.+. ...+++|++++|+|
T Consensus 119 ~i~g~~~flP~s~~~~~~~~~~---~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V 195 (516)
T TIGR00717 119 DLNGVEAFLPGSQVDVKPIKDL---DSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVV 195 (516)
T ss_pred EECCEEEEEeHHHhcCcccCch---hhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEE
Confidence 99999999999999533 2332 2369999999999999999999999997642 14799999999999
Q ss_pred EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI 462 (483)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~ 462 (483)
+++.++|+||+++ |++||+|.++++|.+..++.+.|++||+|.|+|+++| +++++.||+|++.++||+.+.++++++
T Consensus 196 ~~i~~~G~~V~l~--g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G 273 (516)
T TIGR00717 196 KNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVG 273 (516)
T ss_pred EEEECCeEEEEEC--CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCC
Confidence 9999999999996 6899999999999999999999999999999999998 778999999999999999998899999
Q ss_pred eeeEEEEeecccceEE
Q 011538 463 IFLFILLFNKQYSVWF 478 (483)
Q Consensus 463 ~~~~~~~~~~~~~~~~ 478 (483)
+.+.-.+.+-...-.|
T Consensus 274 ~i~~g~V~~v~~~G~f 289 (516)
T TIGR00717 274 DKITGRVTNLTDYGVF 289 (516)
T ss_pred CEEEEEEEEeeCCcEE
Confidence 9995555444443344
No 9
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.8e-37 Score=347.68 Aligned_cols=271 Identities=16% Similarity=0.232 Sum_probs=233.8
Q ss_pred cccccccCCCCCcEEEEEEEEEe--CCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538 162 KVSVEYYEPKPGDFVIGVVVSGN--ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (483)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~V~--~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~ 239 (483)
.|+.....++.|++|+|+|++++ ++|++||+|++.+||||.+|+.... ..+
T Consensus 388 ~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~-----------~~~---------------- 440 (863)
T PRK12269 388 LKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQK-----------VDA---------------- 440 (863)
T ss_pred HHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhcccc-----------ccc----------------
Confidence 34444456789999999999985 4699999999999999999984210 000
Q ss_pred ccccccCCCCCCCCcccCCCEEEEEEEEEc------CCCcEEEEehHHHHHhhhHHHHHHh---hCCCeEEEEEEEEECC
Q 011538 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT------LSGRPLLSTRRLFRKMAWHRVRQIK---QLNEPIEVKFTEWNTG 310 (483)
Q Consensus 240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d------~~G~iiLS~k~~~~~~~w~~L~~~~---k~GeiV~GkV~~v~k~ 310 (483)
....+|+.+++.|+..+ .++++++|+|++..+..|..+.+++ +.|++++|+|.++.++
T Consensus 441 -------------~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~ 507 (863)
T PRK12269 441 -------------PESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSF 507 (863)
T ss_pred -------------hHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCC
Confidence 11248999999998753 3468999999999888998887765 4789999999999999
Q ss_pred eEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEE
Q 011538 311 GLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTV 383 (483)
Q Consensus 311 G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V 383 (483)
|+||+++|++||||.|++ |.++.++.+.. ++||+++|+|+++|++++++.||+|+. |.. ..+++|++++|+|
T Consensus 508 G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V 586 (863)
T PRK12269 508 GAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRV 586 (863)
T ss_pred cEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEE
Confidence 999999999999999999 78888888765 899999999999999999999999964 432 3699999999999
Q ss_pred EEEeCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccc
Q 011538 384 KKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVH 461 (483)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V 461 (483)
++|++||+||++++ |++||+|+|+++| .++.+|.+.|++||+|+|+|+++| +++||+||+|++.+|||+.+.++|++
T Consensus 587 ~~I~~fG~fVeL~~-gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~v 665 (863)
T PRK12269 587 TKIADFGAFIELAE-GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPV 665 (863)
T ss_pred EEEeCCeEEEEecC-CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCC
Confidence 99999999999987 7999999999999 588999999999999999999998 78999999999999999999999999
Q ss_pred ceeeEEEEeeccc
Q 011538 462 IIFLFILLFNKQY 474 (483)
Q Consensus 462 ~~~~~~~~~~~~~ 474 (483)
|+.+.-.+.+-..
T Consensus 666 G~~v~G~V~~i~~ 678 (863)
T PRK12269 666 GARFTRRIVKVTN 678 (863)
T ss_pred CCEEEEEEEEEec
Confidence 9999655555443
No 10
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.5e-36 Score=340.09 Aligned_cols=298 Identities=21% Similarity=0.275 Sum_probs=246.6
Q ss_pred cCCCCChhhhhhhhhcccccCC--ChHHHhhhccccccccccccc--cchhhhcccccc-ccCCCCCcEEEEEEEEEeCC
Q 011538 112 KSEKPDEEEALAPFLKFFKPRD--SAEEVEEEGSEVGVSRESIDV--DDKVGEDKVSVE-YYEPKPGDFVIGVVVSGNEN 186 (483)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~ik~GdiV~G~Vv~V~~~ 186 (483)
.+..++-+|.+.=.++..+.+. .+| ..+ ++.+| ..---..+++.. +..+++|++|+|+|++++++
T Consensus 266 Dts~l~ieevv~~i~~~~~~~~~~~~~--------~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~G~iV~G~Vv~i~~~ 335 (863)
T PRK12269 266 DTSCLTIEEVCERIAREAHRRALWGGE--------RSV--ENQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTVVQVNAG 335 (863)
T ss_pred ECCCCCHHHHHHHHHHHHHhccccccc--------ccc--ccccccCCCchhHHHHHhhccccCCCCCEEEEEEEEEECC
Confidence 3567888999998888888765 211 111 01111 001122444444 78899999999999999999
Q ss_pred eEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCCCCCcccCCCEEEEEEE
Q 011538 187 KLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVL 266 (483)
Q Consensus 187 gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi 266 (483)
++|||+|++.+|++|.+|+.. .+++||+|+|.|+
T Consensus 336 ~v~VdiG~K~eGiI~~~E~~~----------------------------------------------~~kvGd~i~~~V~ 369 (863)
T PRK12269 336 TVFVDIGGKSEGRVPVEEFEA----------------------------------------------PPKAGDGVRVYVE 369 (863)
T ss_pred EEEEEeCCCceEEeEHHHhcc----------------------------------------------CCCCCCEEEEEEE
Confidence 999999999999999888731 1479999999999
Q ss_pred EEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEE--CCeEEEEEC-CeEEEeeccccc-cccCChhhhhhhc
Q 011538 267 GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN--TGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKV 342 (483)
Q Consensus 267 ~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~--k~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~V 342 (483)
+.+.+| +.||++++...+.|+.+.++++.|++|+|+|+++. ++|++|+++ |++||||.||+. ....++. ..+
T Consensus 370 ~~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~---~~v 445 (863)
T PRK12269 370 RVTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE---SLI 445 (863)
T ss_pred EEcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchH---HhC
Confidence 866566 89999999999999999999999999999999974 689999997 899999999994 3333433 358
Q ss_pred CCEEEEEEEEEEC-----CCCceeechhhHhh----------hcCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEecc
Q 011538 343 GRRMYVQITRINE-----DTNDLILSEREAWA----------TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS 407 (483)
Q Consensus 343 Gq~V~vkVl~ID~-----e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiS 407 (483)
|++++|+|+++++ +++++++|+|+.++ ..++++|++|.|+|++++++|+||+++ |++||||.|
T Consensus 446 G~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~--Gv~Gfvp~S 523 (863)
T PRK12269 446 GLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG--GFDGLLHVN 523 (863)
T ss_pred CCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC--CEEEEEEch
Confidence 9999999999975 34689999997532 147889999999999999999999996 699999999
Q ss_pred CcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEEEEee
Q 011538 408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFN 471 (483)
Q Consensus 408 els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~~~~ 471 (483)
+++|.++.++.+.+++||+|+|+|+++| +++|+.||+|++.++||+.+.+++++|+.+.-.+.+
T Consensus 524 eiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~ 588 (863)
T PRK12269 524 DMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTK 588 (863)
T ss_pred hccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEE
Confidence 9999999999999999999999999998 689999999999999999999999999998444433
No 11
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=4.2e-36 Score=332.24 Aligned_cols=280 Identities=29% Similarity=0.377 Sum_probs=244.4
Q ss_pred hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (483)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv 236 (483)
.++.+.++.....+++|++|.|+|.+++++++||++|++.+|+||.+|++... ..+
T Consensus 287 ~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~-----------~~~------------- 342 (647)
T PRK00087 287 NEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDE-----------ISS------------- 342 (647)
T ss_pred HHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc-----------cCC-------------
Confidence 34455567788899999999999999999999999999999999999986321 001
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEE
Q 011538 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (483)
Q Consensus 237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~ 315 (483)
....+++|+.+.++|++. +.+|++.||++++.....|+.+.++++.|+++.|+|+++.++|++|+
T Consensus 343 --------------~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~ 408 (647)
T PRK00087 343 --------------LKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD 408 (647)
T ss_pred --------------hhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence 123488999999999995 46899999999998888999999999999999999999999999999
Q ss_pred ECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCc-eeechhhHhh----------hcCCCCCcEEEEEE
Q 011538 316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTND-LILSEREAWA----------TLNLREGTLLEGTV 383 (483)
Q Consensus 316 I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~r-LiLS~K~~~e----------~~~l~vG~iv~G~V 383 (483)
++|++||||.+++ +.+..++.. .+|+.+.|+|+++|+++++ +.+|+|..+. ..++++|+++.|+|
T Consensus 409 lggi~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V 485 (647)
T PRK00087 409 YGGVRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEV 485 (647)
T ss_pred ECCEEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEE
Confidence 9999999999999 555555543 4899999999999999888 9999998642 13689999999999
Q ss_pred EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI 462 (483)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~ 462 (483)
++++++|+||++ + +++||+|.++++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||..+.++++++
T Consensus 486 ~~v~~~G~fV~l-~-gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G 563 (647)
T PRK00087 486 KRLTDFGAFVDI-G-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVG 563 (647)
T ss_pred EEEeCCcEEEEE-C-CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCC
Confidence 999999999999 5 7999999999999999999999999999999999998 789999999999999999999999999
Q ss_pred eeeEEEEeecccceEEE
Q 011538 463 IFLFILLFNKQYSVWFL 479 (483)
Q Consensus 463 ~~~~~~~~~~~~~~~~~ 479 (483)
+.+.-.+.+-...-+|.
T Consensus 564 ~~v~g~V~~i~~~G~fV 580 (647)
T PRK00087 564 SIVLGKVVRIAPFGAFV 580 (647)
T ss_pred eEEEEEEEEEECCeEEE
Confidence 98866666655555554
No 12
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=7.9e-36 Score=320.59 Aligned_cols=268 Identities=23% Similarity=0.256 Sum_probs=229.9
Q ss_pred ccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccc
Q 011538 163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI 242 (483)
Q Consensus 163 ~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~ 242 (483)
|......++.|++|+|+|.++.++|++|+++ +..||||.+++...+ ..++
T Consensus 106 ~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~-----------~~~~------------------ 155 (491)
T PRK13806 106 AAMLEEAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRY-----------VEDP------------------ 155 (491)
T ss_pred HHHHHHHHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhcccc-----------CCCh------------------
Confidence 3444455679999999999999999999997 689999999985321 0011
Q ss_pred cccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-
Q 011538 243 AMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE- 317 (483)
Q Consensus 243 ~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~- 317 (483)
. -.+|+++.|.|+..| .++++.||++.... ...|..+...++.|++++|+|+++.++|+||+++
T Consensus 156 ----------~-~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~ 224 (491)
T PRK13806 156 ----------E-SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAP 224 (491)
T ss_pred ----------H-HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCC
Confidence 1 128999999999976 46789999998853 4688888788899999999999999999999995
Q ss_pred CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCC----CceeechhhH----hhh--cCCCCCcEEEEEEEEE
Q 011538 318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT----NDLILSEREA----WAT--LNLREGTLLEGTVKKI 386 (483)
Q Consensus 318 Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~----~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I 386 (483)
|+.||||.+++ |.++.++.++. ++|+.|+|+|+++|+++ +++.||+|+. |.. .++++|+++.|+|+++
T Consensus 225 gv~g~v~~sels~~~~~~~~~~~-~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v 303 (491)
T PRK13806 225 GVEGMVHISELSWSRVQKADEAV-SVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRL 303 (491)
T ss_pred CcEEEEEHHHCCCccccChhHhc-CCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEE
Confidence 89999999999 77888887764 89999999999999875 4799999975 543 3789999999999999
Q ss_pred eCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccccee
Q 011538 387 YPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIF 464 (483)
Q Consensus 387 ~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~ 464 (483)
+++|+||++++ |++||+|.++++| .++.++.+.|++||.|+|+|+++| +++||.||+|++.++||+.+.+++++++.
T Consensus 304 ~~~G~fV~l~~-gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~ 382 (491)
T PRK13806 304 APFGAFVEILP-GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTT 382 (491)
T ss_pred eCceEEEEeCC-CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCE
Confidence 99999999987 7999999999999 578899999999999999999998 78999999999999999999999999998
Q ss_pred eEEEEeecc
Q 011538 465 LFILLFNKQ 473 (483)
Q Consensus 465 ~~~~~~~~~ 473 (483)
+.-.+.+..
T Consensus 383 v~G~V~~i~ 391 (491)
T PRK13806 383 VTGTVEKRA 391 (491)
T ss_pred EEEEEEEEe
Confidence 855544443
No 13
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.1e-34 Score=316.49 Aligned_cols=270 Identities=21% Similarity=0.305 Sum_probs=232.7
Q ss_pred ccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccc
Q 011538 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD 240 (483)
Q Consensus 161 ~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d 240 (483)
..+...+.++++|+++.|+|+++.+.|+||++| +.+|+||.+|++..+ ..+
T Consensus 190 ~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~-----------~~~----------------- 240 (565)
T PRK06299 190 EEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKR-----------VNH----------------- 240 (565)
T ss_pred hHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccc-----------cCC-----------------
Confidence 345556778999999999999999999999998 899999999986320 111
Q ss_pred cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-C
Q 011538 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-G 318 (483)
Q Consensus 241 ~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-G 318 (483)
....+++||.|.|+|+..| .++++.||++.+.. .+|..+.+.++.|+++.|+|+++.++|+||+++ |
T Consensus 241 ----------~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~ 309 (565)
T PRK06299 241 ----------PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEG 309 (565)
T ss_pred ----------HhhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence 1234899999999999976 47899999998764 689999888999999999999999999999995 8
Q ss_pred eEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCce
Q 011538 319 LRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYG 390 (483)
Q Consensus 319 i~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~G 390 (483)
+.||+|.+++ |. +..++.... .+|+.|+|+|+++|++++++.||+|+. |.. ..+++|+++.|+|++++++|
T Consensus 310 v~Glv~~sel~~~~~~~~~~~~~-~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G 388 (565)
T PRK06299 310 IEGLVHVSEMSWTKKNKHPSKVV-SVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFG 388 (565)
T ss_pred CEEEEEHHHcCccccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecce
Confidence 9999999999 43 345565543 799999999999999999999999864 432 36789999999999999999
Q ss_pred EEEEECCCceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEEE
Q 011538 391 AQIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFIL 468 (483)
Q Consensus 391 aFV~I~~~gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~ 468 (483)
+||++++ +++|++|.++++|.+. .++.+.|++||.|+|+|+++| ++++|.||+|++..+||..+.+.+++++.+.-.
T Consensus 389 ~fV~l~~-~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~ 467 (565)
T PRK06299 389 AFVGLEG-GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGT 467 (565)
T ss_pred EEEECCC-CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEE
Confidence 9999987 7999999999999877 888999999999999999998 789999999999999999988889999988444
Q ss_pred Eeec
Q 011538 469 LFNK 472 (483)
Q Consensus 469 ~~~~ 472 (483)
+.+.
T Consensus 468 V~~v 471 (565)
T PRK06299 468 VTEV 471 (565)
T ss_pred EEEE
Confidence 4433
No 14
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.2e-34 Score=302.59 Aligned_cols=254 Identities=25% Similarity=0.330 Sum_probs=219.7
Q ss_pred cccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538 162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (483)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~ 241 (483)
.|......+++|+++.|+|+++.++|++|+++ +..||||.+|+...+ ..++
T Consensus 95 ~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~-----------~~~~----------------- 145 (390)
T PRK06676 95 AWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRF-----------VEDF----------------- 145 (390)
T ss_pred hHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCcc-----------CCCh-----------------
Confidence 34444556789999999999999999999995 469999999986321 0011
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC
Q 011538 242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE 317 (483)
Q Consensus 242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~---~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~ 317 (483)
.. .+|+.+.|+|+..+ ..+++.||+|.+... ..|..+...++.|++++|+|+++.++|+||+++
T Consensus 146 -----------~~-~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~ 213 (390)
T PRK06676 146 -----------SD-FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG 213 (390)
T ss_pred -----------HH-cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC
Confidence 11 28999999999865 468899999987442 577877778899999999999999999999999
Q ss_pred CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCce
Q 011538 318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYG 390 (483)
Q Consensus 318 Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~G 390 (483)
|++||||.+++ +.++.++.+.. ++|+.|+|+|+++|++++++.+|+|+. |.. ..+++|+++.|+|++++++|
T Consensus 214 ~v~g~v~~sels~~~~~~~~~~~-~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G 292 (390)
T PRK06676 214 GVDGLVHISELSHERVEKPSEVV-SVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFG 292 (390)
T ss_pred CeEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCce
Confidence 99999999999 67777777764 899999999999999999999999864 432 36899999999999999999
Q ss_pred EEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccc
Q 011538 391 AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK 458 (483)
Q Consensus 391 aFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k 458 (483)
+||++.+ |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++.++||+.+.++
T Consensus 293 ~fV~l~~-gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~ 360 (390)
T PRK06676 293 AFVEVLP-GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR 360 (390)
T ss_pred EEEEECC-CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence 9999987 7999999999999999999999999999999999998 78999999999999999988765
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.9e-34 Score=308.16 Aligned_cols=247 Identities=20% Similarity=0.268 Sum_probs=212.0
Q ss_pred ccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccc
Q 011538 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD 240 (483)
Q Consensus 161 ~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d 240 (483)
+.|+..-...+.|++|+|+|+++.++|++|++| ..||||.+++...+ ..+
T Consensus 111 ~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~-----------~~~----------------- 160 (486)
T PRK07899 111 RAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRR-----------VRD----------------- 160 (486)
T ss_pred chHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccc-----------cCC-----------------
Confidence 445533333458999999999999999999995 68999999874221 000
Q ss_pred cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE
Q 011538 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI 316 (483)
Q Consensus 241 ~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I 316 (483)
..-.+|+.|.|+|+..+ ..++++||+|.... ...|..+...++.|++++|+|+++.++|+||++
T Consensus 161 ------------~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl 228 (486)
T PRK07899 161 ------------LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL 228 (486)
T ss_pred ------------hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE
Confidence 01148999999999976 46789999997543 367888888889999999999999999999999
Q ss_pred CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538 317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY 389 (483)
Q Consensus 317 ~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~ 389 (483)
+|++||||.+++ |.++.++.++. ++||.|+|+|+++|+++++|.||+|+. |.. ..+.+|+++.|+|++|+++
T Consensus 229 ggv~Glv~~Sels~~~v~~~~~~~-kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~f 307 (486)
T PRK07899 229 GGVDGLVHVSELSWKHIDHPSEVV-EVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPF 307 (486)
T ss_pred CCEEEEEEHHHCCCcccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEecc
Confidence 999999999999 78888887764 899999999999999999999999963 543 2577899999999999999
Q ss_pred eEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538 390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP 451 (483)
Q Consensus 390 GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP 451 (483)
|+||++.+ |+.||+|++++++.++.++.+.|++||+|+|+|+++| +++||.||+|++.++-
T Consensus 308 GvFVeL~~-gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 308 GAFVRVEE-GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred EEEEEeCC-CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence 99999987 7999999999999999999999999999999999998 8899999999998764
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=3.9e-34 Score=308.56 Aligned_cols=272 Identities=21% Similarity=0.276 Sum_probs=230.6
Q ss_pred hccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538 160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (483)
Q Consensus 160 ~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~ 239 (483)
+..+...+..+++|++++|+|.++.+.|+||++| +.+|+||.+|++... ..++
T Consensus 175 ~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~-----------~~~~--------------- 227 (516)
T TIGR00717 175 SQAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKR-----------VKHP--------------- 227 (516)
T ss_pred HHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCC-----------CCCH---------------
Confidence 3455666778999999999999999999999997 589999999986321 1111
Q ss_pred ccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-
Q 011538 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE- 317 (483)
Q Consensus 240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~- 317 (483)
...+++|+.+.|+|+..| .++++.||+|.+.. .+|+.+.+.++.|++++|+|+++.++|+||+++
T Consensus 228 ------------~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~ 294 (516)
T TIGR00717 228 ------------SEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEE 294 (516)
T ss_pred ------------HHhccCCCEEEEEEEEEECCCCcEEEEEEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCC
Confidence 124789999999999876 46889999998754 589998888899999999999999999999995
Q ss_pred CeEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538 318 GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY 389 (483)
Q Consensus 318 Gi~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~ 389 (483)
|+.||+|.+++ +. ...++.+.. .+|+.++|+|+++|++++++.||+|++ |.. ..+++|+++.|+|++++++
T Consensus 295 ~v~g~v~~sels~~~~~~~~~~~~-~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~ 373 (516)
T TIGR00717 295 GIEGLVHVSEMSWVKKNSHPSKVV-KKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDF 373 (516)
T ss_pred CCEEEEEHHHcCCccccCCHHHhc-cCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecc
Confidence 89999999999 43 344555443 799999999999999999999999864 432 3588999999999999999
Q ss_pred eEEEEECCCceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEE
Q 011538 390 GAQIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFI 467 (483)
Q Consensus 390 GaFV~I~~~gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~ 467 (483)
|+||++++ +++||+|.++++|.+. .++...|++||.|.|+|+++| +++||.||+|++.+|||..+.+.+++++.+.-
T Consensus 374 G~fV~l~~-~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g 452 (516)
T TIGR00717 374 GAFVELEG-GIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKG 452 (516)
T ss_pred eEEEECCC-CCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEE
Confidence 99999997 7999999999999754 456788999999999999998 78999999999999999999988999998855
Q ss_pred EEeecc
Q 011538 468 LLFNKQ 473 (483)
Q Consensus 468 ~~~~~~ 473 (483)
.+.+..
T Consensus 453 ~V~~v~ 458 (516)
T TIGR00717 453 KVTEIK 458 (516)
T ss_pred EEEEEe
Confidence 554443
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.98 E-value=9.3e-31 Score=289.74 Aligned_cols=247 Identities=24% Similarity=0.335 Sum_probs=212.2
Q ss_pred cccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538 162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (483)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~ 241 (483)
.|......+++|+++.|+|+++.++|++|++|. .+||||.+|+...+- .++
T Consensus 379 ~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~-----------~d~----------------- 429 (647)
T PRK00087 379 AWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYV-----------EDL----------------- 429 (647)
T ss_pred HHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCcccc-----------CCH-----------------
Confidence 344444556899999999999999999999985 999999999864310 011
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEcC-CCc-EEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE
Q 011538 242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGR-PLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI 316 (483)
Q Consensus 242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~-~G~-iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I 316 (483)
.. .+|+.+.|+|+..+. +++ +.+|+|.... ...|....+.++.|+++.|+|+++.++|+||++
T Consensus 430 -----------~~-~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l 497 (647)
T PRK00087 430 -----------SE-YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI 497 (647)
T ss_pred -----------HH-hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE
Confidence 11 289999999998664 567 9999988753 345555666678999999999999999999999
Q ss_pred CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538 317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY 389 (483)
Q Consensus 317 ~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~ 389 (483)
+|++||+|.+++ +.++.++.+.. .+|+.++++|+++|++++++.+|+|+. |.. .++++|+++.|+|++++++
T Consensus 498 ~gv~Gll~~sels~~~~~~~~~~~-~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~ 576 (647)
T PRK00087 498 GGVDGLLHVSEISWGRVEKPSDVL-KVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPF 576 (647)
T ss_pred CCEEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECC
Confidence 999999999999 67777776654 899999999999999999999999964 432 3688999999999999999
Q ss_pred eEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538 390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP 451 (483)
Q Consensus 390 GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP 451 (483)
|+||++.+ ++.||+|.+++++.++.++.+.|++||.|+|+|+++| +++|+.||+|++.++|
T Consensus 577 G~fV~l~~-~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 577 GAFVELEP-GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred eEEEEECC-CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 99999988 7999999999999999999999999999999999998 7899999999999999
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.88 E-value=2.2e-21 Score=198.44 Aligned_cols=186 Identities=17% Similarity=0.123 Sum_probs=150.1
Q ss_pred HHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEECC-eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCce
Q 011538 283 RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDL 360 (483)
Q Consensus 283 ~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~G-i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rL 360 (483)
....|+.+...++.|++++|+|+++.++|++|++++ .+||||.+++ +.+..++.+.. .+|+.++|+|++++++++++
T Consensus 18 f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~-~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 18 FAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVL-QPNETREFFILSDENEDGQL 96 (318)
T ss_pred HHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHcc-CCCCEEEEEEEEEeCCCCeE
Confidence 344555555568999999999999999999999975 8999999999 67777777764 79999999999999999999
Q ss_pred eechhhH-----hhh--cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 361 ILSEREA-----WAT--LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 361 iLS~K~~-----~e~--~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
.||+|+. |+. .....|+++.|+|+++.++|+||+++ |++||||.|+++|.+.. +. .+|+.|+|+|++
T Consensus 97 ~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~~~~~---~~-~vG~~i~~kVl~ 170 (318)
T PRK07400 97 TLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE--GLRGFIPGSHISTRKPK---EE-LVGEELPLKFLE 170 (318)
T ss_pred EEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCccCCc---cc-cCCCEEEEEEEE
Confidence 9999863 543 24457999999999999999999996 69999999999986433 33 499999999999
Q ss_pred Ee-CCCeEEEEEecCCCCcCcccccccccceeeEEEEeecccceEE
Q 011538 434 SM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWF 478 (483)
Q Consensus 434 vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~~~~~~~~~~~ 478 (483)
+| +++||.||+|....++ ...++++|+.+.=.+.+-...-+|
T Consensus 171 id~~~~~i~lS~K~~~~~~---~~~~~k~G~vv~G~V~~I~~~G~f 213 (318)
T PRK07400 171 VDEERNRLVLSHRRALVER---KMNRLEVGEVVVGTVRGIKPYGAF 213 (318)
T ss_pred EEcccCEEEEEhhHhhhhh---hhccCCCCCEEEEEEEEEECCeEE
Confidence 98 7799999999766543 345678888874333333333444
No 19
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.76 E-value=5.2e-17 Score=159.72 Aligned_cols=212 Identities=17% Similarity=0.103 Sum_probs=169.2
Q ss_pred CCCCCcEEEEEEEEEeCCeEEEEeCCcee-eEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 169 EPKPGDFVIGVVVSGNENKLDVNVGADLL-GTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 169 ~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~-G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
.+++|++..+.|++.++.|+|++-|.+.+ -++|.++..
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~----------------------------------------- 40 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE----------------------------------------- 40 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCc-----------------------------------------
Confidence 46799999999999999999999876543 333333221
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEE-CCeEEEEEC-CeEEEeec
Q 011538 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPK 325 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~-k~G~fV~I~-Gi~gFVP~ 325 (483)
...+++||+|.++++ .|.++++.+|.+.+.. ..|+.-.++|+.++ +-|+||++| .-+.+||.
T Consensus 41 ----~~e~evGdev~vFiY-~D~~~rl~aTt~~p~~-----------tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~ 104 (287)
T COG2996 41 ----EDELEVGDEVTVFIY-VDSEDRLIATTREPKA-----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPL 104 (287)
T ss_pred ----CCccccCcEEEEEEE-ECCCCceeheeecceE-----------eecceeEEEEEEEcCCcceEEecCCCcceeeeh
Confidence 123679999999999 6889999999987753 68999999999999 679999996 46799999
Q ss_pred cccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh--Hhhh--cCCC---CCcEEEEEEEEEeCceEEEEECCC
Q 011538 326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--AWAT--LNLR---EGTLLEGTVKKIYPYGAQIRIGDS 398 (483)
Q Consensus 326 Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~--~~e~--~~l~---vG~iv~G~V~~I~~~GaFV~I~~~ 398 (483)
+++.. .++++..+|+++.|+ +.+|++ +|+....+. .++. .... .|+.+.|+|+++...|.||-+.+
T Consensus 105 ~elp~----~~~~wpq~Gd~l~v~-l~~Dkk-~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~- 177 (287)
T COG2996 105 DELPT----LKSLWPQKGDKLLVY-LYVDKK-GRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN- 177 (287)
T ss_pred hhccc----ccccCCCCCCEEEEE-EEEccC-CcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-
Confidence 99842 223455799999999 588865 477776653 2221 1223 49999999999999999999977
Q ss_pred ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCcC
Q 011538 399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPG 452 (483)
Q Consensus 399 gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dPw 452 (483)
++-||||.||.. ..++.|+++++||+.+.++++|.||++....+-.
T Consensus 178 ~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~p~~~E~l 223 (287)
T COG2996 178 GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLRPRAHEML 223 (287)
T ss_pred CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccccccHHhh
Confidence 899999999975 5689999999999999999999999998766543
No 20
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.72 E-value=2.3e-17 Score=187.30 Aligned_cols=196 Identities=20% Similarity=0.248 Sum_probs=168.6
Q ss_pred CCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE--CCeEEEeecccc
Q 011538 252 RPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAEL 328 (483)
Q Consensus 252 ~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel 328 (483)
-+.+++|.++.+++... +-+..+++|.++......+.++.+ ++.|+.|.|+|.++.+.|+.|.+ +.+.|++|.+|+
T Consensus 465 v~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hl 543 (1710)
T KOG1070|consen 465 VPIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHL 543 (1710)
T ss_pred CCceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccceeeeEEEEecCCcEEEEEecCceeeecChHhh
Confidence 35689999999999885 345556899988876666666655 79999999999999999999998 459999999999
Q ss_pred ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh---------hcCCCCCcEEEEEEEEEeCceEEEEECCCc
Q 011538 329 LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---------TLNLREGTLLEGTVKKIYPYGAQIRIGDSN 399 (483)
Q Consensus 329 ~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e---------~~~l~vG~iv~G~V~~I~~~GaFV~I~~~g 399 (483)
.+....+....+.+|..+++||+.++...+++.+++|..+- ..++++|.++.|+|.++.++||||++.+ |
T Consensus 544 sd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g-~ 622 (1710)
T KOG1070|consen 544 SDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTG-G 622 (1710)
T ss_pred hhcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecC-c
Confidence 54333333344589999999999999999999999998642 2478899999999999999999999998 8
Q ss_pred eEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538 400 RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (483)
Q Consensus 400 i~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~ 449 (483)
++||.|.++|+++++.++++.|.+||+|.|+|+++| +++||.|++|+...
T Consensus 623 lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~ 673 (1710)
T KOG1070|consen 623 LSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC 673 (1710)
T ss_pred cccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence 999999999999999999999999999999999997 88999999997653
No 21
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=6.2e-18 Score=148.50 Aligned_cols=82 Identities=38% Similarity=0.576 Sum_probs=78.4
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP 451 (483)
.+++|++++|+|++|++|||||+|++ |-.||+|+||+++.+++++.+.+++||.|+|+|+++|++++|+||+|++++.|
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 SMKVGSKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEP 80 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCc
Confidence 47899999999999999999999998 79999999999999999999999999999999999999999999999999988
Q ss_pred Ccc
Q 011538 452 GLF 454 (483)
Q Consensus 452 w~~ 454 (483)
-..
T Consensus 81 e~~ 83 (129)
T COG1098 81 EKQ 83 (129)
T ss_pred ccc
Confidence 654
No 22
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.70 E-value=2.2e-16 Score=179.55 Aligned_cols=247 Identities=22% Similarity=0.287 Sum_probs=196.6
Q ss_pred ccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeec-ccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538 163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLT-KEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (483)
Q Consensus 163 ~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~-sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~ 241 (483)
+....+...+|++..|+|..+++.++.|+.+.+.-|-++. .++.+.+ + .+|
T Consensus 1058 ~~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~--~---------~~P----------------- 1109 (1710)
T KOG1070|consen 1058 FSKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY--S---------MTP----------------- 1109 (1710)
T ss_pred cccCCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc--c---------CCh-----------------
Confidence 3344556669999999999999999999999888874332 2443321 0 011
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEeh-------HHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEE
Q 011538 242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTR-------RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313 (483)
Q Consensus 242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~-~G~iiLS~k-------~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~f 313 (483)
...+..++.+.+.++..+. ++.+.||.+ .+.....--...+.++.|+++.|.|..+.+.|+|
T Consensus 1110 ----------~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glf 1179 (1710)
T KOG1070|consen 1110 ----------VEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLF 1179 (1710)
T ss_pred ----------HHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEE
Confidence 1235677888888888653 344899988 3332222222356779999999999999999999
Q ss_pred EEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH---------hhhcCCCCCcEEEEE
Q 011538 314 TRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA---------WATLNLREGTLLEGT 382 (483)
Q Consensus 314 V~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~---------~e~~~l~vG~iv~G~ 382 (483)
+.+. ++.||+|.+++ +...+.|+..+ .+|+.+.++|+.++...+|+.+|.|.. .....+++|+...|+
T Consensus 1180 i~ls~~v~a~v~is~~~ds~~k~w~k~~-~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~ 1258 (1710)
T KOG1070|consen 1180 IALSRKVEAFVPISGLSDSFEKEWEKHL-PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGT 1258 (1710)
T ss_pred EEEccceEEEEEccccccchhhhhhccC-CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccce
Confidence 9996 79999999999 45555666554 899999999999999999999999852 123579999999999
Q ss_pred EEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538 383 VKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (483)
Q Consensus 383 V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~ 448 (483)
|..+.++|.||+++.+ ++.|++|+++..+++..+....+..|+.|+|.+++++ +++||.|++|..-
T Consensus 1259 v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~ 1326 (1710)
T KOG1070|consen 1259 VEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSY 1326 (1710)
T ss_pred EEEecCCceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhc
Confidence 9999999999999875 4699999999999999999999999999999999998 8899999988653
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.66 E-value=3e-16 Score=159.68 Aligned_cols=98 Identities=20% Similarity=0.255 Sum_probs=90.9
Q ss_pred CCC-CCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538 372 NLR-EGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (483)
Q Consensus 372 ~l~-vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~ 448 (483)
.+. +|++|.|+|++|.+||+||+|.++ |++||||+|++||.++.++++.+++||.|.|+|+++| ++++|.||+|++.
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~ 92 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS 92 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence 455 899999999999999999999733 7999999999999999999999999999999999998 8899999999999
Q ss_pred CCcCcccccccccceeeEEEE
Q 011538 449 SEPGLFVSDKEVHIIFLFILL 469 (483)
Q Consensus 449 ~dPw~~l~~k~~V~~~~~~~~ 469 (483)
++||..+.++|+.+..+.-++
T Consensus 93 ~~pw~~~~e~~~~g~~v~~~V 113 (319)
T PTZ00248 93 PEDIEACEEKFSKSKKVHSIM 113 (319)
T ss_pred cchHHHHHHhCcCCCEEEEEE
Confidence 999999999999999884443
No 24
>PRK08582 hypothetical protein; Provisional
Probab=99.57 E-value=1.3e-14 Score=132.04 Aligned_cols=82 Identities=30% Similarity=0.497 Sum_probs=77.8
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP 451 (483)
.+++|++|.|+|++|+++|+||+|++ +++||||+++++|.++.++.+.|++||.|+|+|++++.+++|.||+|++.++|
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~ 80 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCc
Confidence 37899999999999999999999998 79999999999999999999999999999999999986799999999999999
Q ss_pred Ccc
Q 011538 452 GLF 454 (483)
Q Consensus 452 w~~ 454 (483)
|..
T Consensus 81 ~~~ 83 (139)
T PRK08582 81 KRQ 83 (139)
T ss_pred hhh
Confidence 964
No 25
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.53 E-value=2.2e-15 Score=153.40 Aligned_cols=138 Identities=16% Similarity=0.257 Sum_probs=121.2
Q ss_pred hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE---- 366 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~---- 366 (483)
+.|++|.|+|+++.++|+||++ +|++||||.|++ |.++.+++++. ++|+++.|+|+++|+++++|.||.|+
T Consensus 16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v-kvGd~v~vkVl~VD~ekg~IdLS~K~v~~~ 94 (319)
T PTZ00248 16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI-RVGRHEVVVVLRVDKEKGYIDLSKKRVSPE 94 (319)
T ss_pred CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence 4799999999999999999999 489999999999 88999999986 89999999999999999999999996
Q ss_pred Hhhh--cCCCCCcEEEEEEEEEeC-ceEEEE------ECCCceEEEEeccCcCcccccCcccccC---CCCEEEEEEEEE
Q 011538 367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIR------IGDSNRSGLLHISNMSRTRVTSVSDLLN---EGERVKVLVVKS 434 (483)
Q Consensus 367 ~~e~--~~l~vG~iv~G~V~~I~~-~GaFV~------I~~~gi~GLlhiSels~~~i~~~~~~~k---vGd~VkVkVi~v 434 (483)
+|.. ..++.|++++|+|..+.. +|++++ ... .+.++.|..++....+.++.+.|. +++.++..++.+
T Consensus 95 pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~p-l~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~~ 173 (319)
T PTZ00248 95 DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWP-LYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQD 173 (319)
T ss_pred hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHH-HHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHHH
Confidence 4643 478999999999999955 999998 344 689999999998888888877777 888887777654
No 26
>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=99.52 E-value=4.5e-14 Score=115.10 Aligned_cols=70 Identities=24% Similarity=0.367 Sum_probs=64.6
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCc---ccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV---SDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~---~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
+++|+++.|+|++|+++|+||++++ +++|++|+++++|.++.++ .+.|++||.|+|+|+++| ++++|.||
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 IKEGQLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 5799999999999999999999988 8999999999999987775 588999999999999998 77899886
No 27
>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=99.48 E-value=2.1e-13 Score=109.63 Aligned_cols=73 Identities=30% Similarity=0.562 Sum_probs=68.9
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
++++|+++.|+|+++.++|+||++++ +++|+||.+++++.+..++...+++||+|+|+|++++ +++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGN-GIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEEST-SSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECC-cEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 37899999999999999999999996 7999999999999999999999999999999999998 7889999986
No 28
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.48 E-value=1.3e-13 Score=111.49 Aligned_cols=71 Identities=24% Similarity=0.386 Sum_probs=66.6
Q ss_pred CCCCcEEEEEEEEEeC-ceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538 373 LREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~-~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK 445 (483)
+++|+++.|+|++|.+ +|+||++.+ +.+|++|+++++|++..++.+.|++||.|+|+|+++++ +|+.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCC-CCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence 5789999999999986 899999988 79999999999999999999999999999999999865 89999986
No 29
>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=99.46 E-value=3.3e-13 Score=109.23 Aligned_cols=71 Identities=34% Similarity=0.534 Sum_probs=65.1
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL 444 (483)
+.|+++.|+|++|++||+||++.+.+.+||+|+++++|.++.++.+.|++||+|+|+|++++..+|+.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 58999999999999999999996534799999999999999999999999999999999998555999987
No 30
>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=99.45 E-value=5.5e-13 Score=108.80 Aligned_cols=72 Identities=25% Similarity=0.285 Sum_probs=65.4
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~ 449 (483)
++++|+++.|+|++|+++|+||+++..|++||+|.++++|. +.+++||.+.|+|++++ +++++.||+|++.+
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 47899999999999999999999972279999999999976 77999999999999998 78999999998765
No 31
>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=99.43 E-value=5.5e-13 Score=108.32 Aligned_cols=70 Identities=17% Similarity=0.161 Sum_probs=65.6
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD 446 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~ 446 (483)
|+++.|+|+++.++|+||++.+ +++|+||.++++|.+ ..++.+.|++||.|+|+|+++| +++||.||+|.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k~ 73 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEecC
Confidence 7899999999999999999988 799999999999874 8899999999999999999998 78999999973
No 32
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.42 E-value=4.9e-13 Score=110.55 Aligned_cols=73 Identities=27% Similarity=0.346 Sum_probs=69.1
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
.++++|+++.|+|++|.++|+||++++ +++||+|.++++++++.++.+.|++||.|+|+|++++ ++++|.|||
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HhCCCCCEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 368999999999999999999999988 7999999999999999999999999999999999998 689999986
No 33
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.42 E-value=6.7e-13 Score=105.75 Aligned_cols=69 Identities=26% Similarity=0.352 Sum_probs=65.5
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
|+++.|+|+++.++|+||++++ +++||+|.+++++++..++.+.|++||.++|+|++++ +++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 7899999999999999999988 7999999999999999999999999999999999998 6789999986
No 34
>PRK07252 hypothetical protein; Provisional
Probab=99.42 E-value=1.1e-12 Score=116.75 Aligned_cols=77 Identities=38% Similarity=0.592 Sum_probs=72.6
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP 451 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP 451 (483)
++|+++.|+|++|+++|+||+|.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +++++.||+|++.+++
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~ 79 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK 79 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 589999999999999999999988 7999999999999999999999999999999999998 6899999999998843
No 35
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.42 E-value=2.7e-13 Score=153.10 Aligned_cols=85 Identities=28% Similarity=0.392 Sum_probs=80.5
Q ss_pred CCCCCcEEE-EEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCC
Q 011538 372 NLREGTLLE-GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE 450 (483)
Q Consensus 372 ~l~vG~iv~-G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~d 450 (483)
..++|+++. |+|++|++||+||+|.+ |++||||+|+|+|+++.++.+.|++||.|+|+|+++|.++||.||+|++.+|
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~~~ 828 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPE 828 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEeccccC
Confidence 578999995 69999999999999988 7999999999999999999999999999999999998889999999999999
Q ss_pred cCccccc
Q 011538 451 PGLFVSD 457 (483)
Q Consensus 451 Pw~~l~~ 457 (483)
||+....
T Consensus 829 Pw~~~~~ 835 (891)
T PLN00207 829 ANSEKSS 835 (891)
T ss_pred chhhhhh
Confidence 9997766
No 36
>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=99.41 E-value=1.7e-12 Score=104.37 Aligned_cols=72 Identities=21% Similarity=0.309 Sum_probs=67.5
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
+++|+++.|+|++++++|+||++++ +++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|
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 LKVGDILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 4789999999999999999999998 7999999999999988888899999999999999998 6789999985
No 37
>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=99.40 E-value=1.7e-12 Score=106.23 Aligned_cols=75 Identities=32% Similarity=0.573 Sum_probs=69.5
Q ss_pred CcEEEEEEEEEeCceEEEEECCC--ceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~--gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP 451 (483)
|+++.|+|++|+++|+||++++. +.+||+|.++++|.++ .++.+.|++||.|+|+|++++ ++++.+|+|+++++.
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 78999999999999999999842 5899999999999986 899999999999999999999 999999999998864
No 38
>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=99.39 E-value=1.4e-12 Score=103.93 Aligned_cols=68 Identities=22% Similarity=0.449 Sum_probs=64.5
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
|+++.|+|++|.++|+||++++ +++|++|.++++|.+..++.+.|++||.++|+|+++| +++++.|||
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 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 7899999999999999999987 7999999999999999999999999999999999998 689999985
No 39
>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=99.39 E-value=2.4e-12 Score=103.91 Aligned_cols=74 Identities=31% Similarity=0.395 Sum_probs=68.1
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD 446 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~ 446 (483)
+++|+++.|+|.++.++|+||++.+. +++||+|.++++++++.++.+.|++||.|+|+|++++ +++++.||+|+
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 36899999999999999999999743 5899999999999999999999999999999999998 67899999985
No 40
>PRK05807 hypothetical protein; Provisional
Probab=99.38 E-value=2.7e-12 Score=116.55 Aligned_cols=75 Identities=39% Similarity=0.582 Sum_probs=70.8
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE 448 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~ 448 (483)
.+++|+++.|+|+.|+++|+||++. +..||||++++++.++.++.+.|++||.|+|+|++++++++|.||+|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 3679999999999999999999994 58999999999999999999999999999999999987799999999987
No 41
>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=99.38 E-value=1.7e-12 Score=104.73 Aligned_cols=68 Identities=25% Similarity=0.403 Sum_probs=64.0
Q ss_pred CcEEE-EEEEEE-eCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 376 GTLLE-GTVKKI-YPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 376 G~iv~-G~V~~I-~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
|++++ |+|+++ .++|+||++.+ |++||+|.|++++.+..++.+.|++||.++|+|+++| .+++|.||+
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 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 69999999988 7999999999999999999999999999999999998 778999985
No 42
>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=99.37 E-value=3.5e-12 Score=102.79 Aligned_cols=74 Identities=35% Similarity=0.542 Sum_probs=68.5
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL 447 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~ 447 (483)
++|+++.|+|++++++|+||++.+.+++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|+.
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 46999999999999999999998546899999999999999899999999999999999998 689999999974
No 43
>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=99.36 E-value=3.6e-12 Score=101.78 Aligned_cols=72 Identities=31% Similarity=0.527 Sum_probs=67.7
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~ 448 (483)
|+++.|+|+++.++|+||++.+ +++|++|.++++++++.++.+.|++||.++|+|++++ +++++.||+|+++
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 GSIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 7899999999999999999988 7999999999999999999999999999999999998 5689999999864
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=99.35 E-value=2.9e-12 Score=101.79 Aligned_cols=67 Identities=21% Similarity=0.311 Sum_probs=63.4
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
|+++.|+|++|.++|+||++.+ +++||+|.+++++++..++.+.|++||.|+|+|+++| ++++|.||
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 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 7899999999999999999998 7999999999999999999999999999999999998 67898876
No 45
>PRK08059 general stress protein 13; Validated
Probab=99.34 E-value=6.1e-12 Score=112.20 Aligned_cols=79 Identities=37% Similarity=0.586 Sum_probs=75.3
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d 450 (483)
++++|+++.|+|++|+++|+||++.+ ++.|++|.++++++++.++.+.|++||.|+|+|++++ +++++.||+|.+..+
T Consensus 4 ~~k~G~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~ 82 (123)
T PRK08059 4 QYEVGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA 82 (123)
T ss_pred cCCCCCEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence 58899999999999999999999998 7999999999999999999999999999999999997 789999999999998
Q ss_pred c
Q 011538 451 P 451 (483)
Q Consensus 451 P 451 (483)
|
T Consensus 83 ~ 83 (123)
T PRK08059 83 P 83 (123)
T ss_pred c
Confidence 8
No 46
>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=99.33 E-value=3.6e-12 Score=100.98 Aligned_cols=67 Identities=31% Similarity=0.560 Sum_probs=62.0
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
|+++.|+|++|+++|+||++.+ +++||+|.++++| .+..++.+.|++||+|+|+|+++| ++++|.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 7899999999999999999988 7999999999997 577888899999999999999998 77898875
No 47
>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=99.31 E-value=1e-11 Score=97.28 Aligned_cols=69 Identities=45% Similarity=0.755 Sum_probs=65.1
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK 445 (483)
|+++.|+|++++++|+||++++ ++.||+|.++++++++.++.+.|++||.|+|+|++++.++++.||+|
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 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 7899999999999999999987 79999999999999999999999999999999999977789999986
No 48
>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=99.28 E-value=1.8e-11 Score=97.53 Aligned_cols=69 Identities=25% Similarity=0.379 Sum_probs=65.3
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
|+++.|+|.++.++|+||+++. +.+|++|.+++++.+..++.+.|++||.++|+|++++ +++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGY-KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC-CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 7899999999999999999987 7999999999999999999999999999999999998 6789999986
No 49
>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=99.25 E-value=2.7e-11 Score=97.12 Aligned_cols=70 Identities=31% Similarity=0.488 Sum_probs=62.6
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
+.+|+++.|+|++|+++|+||++.+ +++||+|.++++|. +..++.+.|++||.|+|+|+++| +++++.||
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 4689999999999999999999988 79999999999975 55577788999999999999998 77888764
No 50
>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=99.25 E-value=3.7e-11 Score=96.57 Aligned_cols=71 Identities=23% Similarity=0.450 Sum_probs=63.2
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
++.|++++|+|+++.++|+||+++ |+.||||.+++ +.+..++.... .+||++.|+|+++|++++++.+|+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVY-KIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTC-ETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCcccccccccc-CCCCEEEEEEEEEECCCCeEEEEEC
Confidence 478999999999999999999998 89999999999 45455555544 8999999999999999999999986
No 51
>PHA02945 interferon resistance protein; Provisional
Probab=99.23 E-value=4.8e-11 Score=99.56 Aligned_cols=75 Identities=23% Similarity=0.227 Sum_probs=68.9
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCc--CcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNM--SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSel--s~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~ 448 (483)
.++|+++.|+|+. .+||+||.+.++ |.+||+|.|+. +..++++ ++.+ +||+|.|+|+++| .++.|.||||+..
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 4689999999999 999999999776 89999999955 9999999 9999 9999999999998 7899999999986
Q ss_pred CC
Q 011538 449 SE 450 (483)
Q Consensus 449 ~d 450 (483)
++
T Consensus 86 ~~ 87 (88)
T PHA02945 86 RH 87 (88)
T ss_pred cC
Confidence 54
No 52
>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=99.21 E-value=2.4e-11 Score=104.76 Aligned_cols=74 Identities=30% Similarity=0.405 Sum_probs=66.6
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-------------------cCcccccCCCCEEEEEEEE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-------------------~~~~~~~kvGd~VkVkVi~ 433 (483)
|++|++|.|+|++|.++|+||.+.+ ++.|++|.++++|.+. .++.+.|++||.|+|+|++
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 LSEGMLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 5789999999999999999999988 8999999999998752 3477899999999999999
Q ss_pred EeC----CCeEEEEEecC
Q 011538 434 SMF----PDKISLSIADL 447 (483)
Q Consensus 434 vde----k~rI~LSLK~~ 447 (483)
++. +++|.||+|..
T Consensus 80 ~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 80 LDKSKSGKKRIELSLEPE 97 (100)
T ss_pred ccCCcCCCcEEEEEecHH
Confidence 984 68999999864
No 53
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.21 E-value=2.6e-11 Score=107.06 Aligned_cols=75 Identities=21% Similarity=0.297 Sum_probs=69.2
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWAT 370 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~ 370 (483)
++.|.+++|+|+++.++|+||.++ |-+||||+|++ ...++++.++. .+||+|.|+|+.+|. ++++.||.|.+.+.
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L-~vG~eV~vKVl~ide-~GKisLSIr~~~e~ 79 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL-KVGQEVKVKVLDIDE-NGKISLSIRKLEEE 79 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh-cCCCEEEEEEEeecc-CCCcceehHHhhhC
Confidence 578999999999999999999995 69999999999 78899999987 899999999999997 89999999987653
No 54
>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=99.20 E-value=5.6e-11 Score=98.70 Aligned_cols=74 Identities=18% Similarity=0.199 Sum_probs=67.1
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc----ccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR----TRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~----~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
+++|++|.|+|+++.++|++|+++. +++|++|.+++++ .+..++.+.+++||.|+|+|+++++++++.||+|+.
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 PEVGDVVIGRVTEVGFKRWKVDINS-PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCC-CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 5799999999999999999999987 7999999999996 455677888999999999999997669999999975
No 55
>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=99.20 E-value=9.6e-11 Score=92.90 Aligned_cols=66 Identities=41% Similarity=0.700 Sum_probs=59.0
Q ss_pred CCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
|++++|+|+++.++|++|+++|++||||.+++ +.+..++.+ .+|+.+.|+|+++|++++++.+|+|
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 78999999999999999999999999999999 455555444 4899999999999999999999985
No 56
>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=99.20 E-value=4.9e-11 Score=93.24 Aligned_cols=67 Identities=39% Similarity=0.583 Sum_probs=62.6
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
|+++.|+|++++++|+||++.. +..|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 7899999999999999999987 7999999999999988899999999999999999998 67888876
No 57
>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=99.20 E-value=6.8e-11 Score=94.15 Aligned_cols=65 Identities=18% Similarity=0.328 Sum_probs=58.7
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
|+++.|+|+++.++|+||++.+ +++|++|.++++..+.. .+.|++||+|+|+|+.+| ++++|.||
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 GMLVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 7899999999999999999987 79999999999866544 778999999999999998 67888876
No 58
>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=99.17 E-value=1.1e-10 Score=91.75 Aligned_cols=68 Identities=43% Similarity=0.605 Sum_probs=63.4
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL 444 (483)
|+++.|+|.++.++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++.++++.||+
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 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 6899999999999999999987 6999999999999999888999999999999999997777998884
No 59
>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=99.15 E-value=1.9e-10 Score=91.26 Aligned_cols=66 Identities=21% Similarity=0.302 Sum_probs=60.0
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
|+++.|+|+++.++|++|++ + |++||||.+++++.+..++.+ .+||.++|+|+++| ++++|.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-E-GVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 5 799999999999988777766 38999999999998 6789999976
No 60
>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=99.15 E-value=1.7e-10 Score=94.00 Aligned_cols=69 Identities=12% Similarity=0.124 Sum_probs=60.1
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChh---hhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFT---ELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~---~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
++.|+++.|+|+++.++|+||+++ +++||+|.+++ +.++.+++ +. +++|+.++|+|+++|++++++.||
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 368999999999999999999995 89999999999 66655543 44 389999999999999999999886
No 61
>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=99.14 E-value=1.7e-10 Score=90.39 Aligned_cols=67 Identities=46% Similarity=0.671 Sum_probs=62.3
Q ss_pred CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
+|+++.|+|.++.++|+||+++ +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999997 5899999999999999899999999999999999998 67888876
No 62
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.14 E-value=2.6e-10 Score=89.00 Aligned_cols=71 Identities=37% Similarity=0.597 Sum_probs=65.6
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
++|+++.|+|.+++++|+||++++ ++.|++|.+++++.+..++.+.|++||.|+|+|++++ +++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 479999999999999999999997 7999999999999888888889999999999999998 5699999985
No 63
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.14 E-value=1.7e-10 Score=115.46 Aligned_cols=79 Identities=28% Similarity=0.507 Sum_probs=73.3
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d 450 (483)
.++|+++.|+|++|.++|+||++.++ |++||+|.|+++++++.++.+.|++||.|.|+|+++| ++++|.||+|++.++
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 57899999999999999999999754 7999999999999999999999999999999999998 678999999988865
Q ss_pred c
Q 011538 451 P 451 (483)
Q Consensus 451 P 451 (483)
-
T Consensus 86 e 86 (262)
T PRK03987 86 Q 86 (262)
T ss_pred h
Confidence 4
No 64
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=4.2e-11 Score=117.76 Aligned_cols=79 Identities=28% Similarity=0.517 Sum_probs=74.0
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d 450 (483)
.++|++|-|+|.+|.+||+||.|..+ |++||+|+||++.++++++++.+++||.+-|+||++| .++.|.||||...++
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 46899999999999999999999655 7999999999999999999999999999999999998 789999999999876
Q ss_pred c
Q 011538 451 P 451 (483)
Q Consensus 451 P 451 (483)
-
T Consensus 89 q 89 (269)
T COG1093 89 Q 89 (269)
T ss_pred H
Confidence 3
No 65
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.13 E-value=1.1e-09 Score=108.51 Aligned_cols=145 Identities=17% Similarity=0.141 Sum_probs=114.0
Q ss_pred cCCCCCcEEEEEEEEEe-CCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538 168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~-~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~ 246 (483)
..+.+|+.-.++|+.++ +.|+|||.|...+-++|.+|+... +++
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~--~~~--------------------------------- 113 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL--KSL--------------------------------- 113 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc--ccc---------------------------------
Confidence 55678999999999999 789999999988999999987532 111
Q ss_pred CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhh--CCCeEEEEEEEEECCeEEEEE-CCeEEEe
Q 011538 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRI-EGLRAFL 323 (483)
Q Consensus 247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k--~GeiV~GkV~~v~k~G~fV~I-~Gi~gFV 323 (483)
=+++||.+-+.++ .|+.||+..+++.... .++....+.. .|+.+.|+|.+....|.||-+ ++..|||
T Consensus 114 -------wpq~Gd~l~v~l~-~Dkk~Ri~g~~a~~~~--l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI 183 (287)
T COG2996 114 -------WPQKGDKLLVYLY-VDKKGRIWGTLAIEKI--LENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI 183 (287)
T ss_pred -------CCCCCCEEEEEEE-EccCCcEEEEecchhH--HHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence 1679999999887 7888899777654321 1111111222 589999999999999999999 4799999
Q ss_pred eccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 324 PKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 324 P~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
|.||....+ .+|++++++|+.+.. .++|.||.+.
T Consensus 184 h~sEr~~~p--------rlG~~l~~rVi~~re-Dg~lnLSl~p 217 (287)
T COG2996 184 HKSERFAEP--------RLGERLTARVIGVRE-DGKLNLSLRP 217 (287)
T ss_pred cchhhcccc--------cCCceEEEEEEEEcc-CCeeeccccc
Confidence 999985332 589999999999965 8999999985
No 66
>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=99.12 E-value=2.6e-10 Score=96.13 Aligned_cols=73 Identities=32% Similarity=0.442 Sum_probs=62.7
Q ss_pred CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCc---ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSR---TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~---~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
.+++|+++.|+|++|.++ ||||++++ +.+||||.++++| .++.++.+.+++||.|.|+|++.. ..+-..|+.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 468999999999999997 99999998 7999999999999 678888999999999999999875 3343444443
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=99.11 E-value=3.7e-10 Score=91.75 Aligned_cols=68 Identities=12% Similarity=0.170 Sum_probs=60.6
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc--ccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS--RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~--rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
|++++|+|+++.++|+||.++ +++||||.+++ +. +.+++.+.+ ++|+.++|+|+++|+++++|.||.|
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKF-PIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhC-CCCCEEEEEEEEEeCCCCEEEEEec
Confidence 789999999999999999995 89999999999 43 366666654 8999999999999999999999975
No 68
>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=99.11 E-value=1.1e-10 Score=129.71 Aligned_cols=71 Identities=32% Similarity=0.456 Sum_probs=66.3
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcC----cccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels----~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LS 443 (483)
.+++|++|.|+|++|++||+||+|.+ |++||||+|+++ |.++.++.+.+++||+|+|+|+++|+++||+|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~-G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecC-CceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 47899999999999999999999987 799999999996 468999999999999999999999988899886
No 69
>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=99.10 E-value=3.5e-10 Score=90.02 Aligned_cols=68 Identities=21% Similarity=0.328 Sum_probs=60.6
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
|+++.|+|+++.++|+||+++ ++.||+|.+++ +.+..++.+.. ++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHF-RVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcc-cCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999995 79999999999 55666666643 8999999999999999999999975
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=99.09 E-value=6.4e-10 Score=90.94 Aligned_cols=71 Identities=21% Similarity=0.416 Sum_probs=61.9
Q ss_pred CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKISL 442 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek~rI~L 442 (483)
+|+++.|+|++|+++|+||+++..+++|++|.++++++++. +....|++||.|+|+|++++ +++++.+
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 48999999999999999999987569999999999876432 44578999999999999998 6889999
Q ss_pred EEe
Q 011538 443 SIA 445 (483)
Q Consensus 443 SLK 445 (483)
++.
T Consensus 81 ~l~ 83 (83)
T cd04471 81 ELV 83 (83)
T ss_pred EEC
Confidence 863
No 71
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.07 E-value=6.6e-10 Score=124.82 Aligned_cols=76 Identities=36% Similarity=0.533 Sum_probs=71.9
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
..+++|+++.|+|++|.+||+||+|.+ +.+||+|+|+++|.++.++.+.|++||.|+|+|+++|..++|.||+|.+
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~ 692 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 368999999999999999999999988 7999999999999999999999999999999999998559999999976
No 72
>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=99.05 E-value=9e-10 Score=87.71 Aligned_cols=67 Identities=12% Similarity=0.325 Sum_probs=59.0
Q ss_pred CCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
|++++|+|+++.++|++|++ +|++||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKF-KPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcC-CCCCEEEEEEEEEECCCCEEEEEC
Confidence 78999999999999999999 479999999999 55566665543 899999999999999999999874
No 73
>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=99.04 E-value=8.5e-10 Score=90.02 Aligned_cols=68 Identities=21% Similarity=0.290 Sum_probs=59.4
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
++.|+++.|+|+++.++|+||+++ |++||||.+++... ..+ ++||.+.|+|+++|++++++.||.|+.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----~~~--~~Gq~v~~~V~~vd~~~~~v~ls~k~~ 71 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----SKL--KVGQLLLCVVEKVKDDGRVVSLSADPS 71 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----ccc--CCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 468999999999999999999996 89999999999422 122 699999999999999999999998753
No 74
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=99.04 E-value=7.7e-10 Score=118.87 Aligned_cols=108 Identities=20% Similarity=0.281 Sum_probs=85.7
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHHHH-----HhhhHHHHHHhh--CCCeEEEEEEEEECCeEEEEECCeEEEeec
Q 011538 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFR-----KMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK 325 (483)
Q Consensus 253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~-----~~~w~~L~~~~k--~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~ 325 (483)
+.+++||.+.+.|...+ -||+.++..+... +..++.+.+.++ .|++|+|+|.++.++|++|+++|+.||||.
T Consensus 85 ~~~~vGD~ie~~I~~~~-fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~ 163 (470)
T PRK09202 85 PDAEVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPR 163 (470)
T ss_pred ccccCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEECCeEEEecH
Confidence 34789999999987655 5556544443332 334447777776 999999999999999999999999999999
Q ss_pred cccccccCChhhhhhhcCCEEEEEEEEEECCCC--ceeechhhH
Q 011538 326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA 367 (483)
Q Consensus 326 Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~--rLiLS~K~~ 367 (483)
+++.. .+. +++|++++|+|++++++++ +|+|||+.+
T Consensus 164 sE~ip-----~E~-~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 164 KEQIP-----REN-FRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred HHcCC-----Ccc-CCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 99941 122 2799999999999998777 999999975
No 75
>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=99.03 E-value=1.1e-09 Score=90.46 Aligned_cols=70 Identities=17% Similarity=0.210 Sum_probs=63.2
Q ss_pred hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
++.|+++.|+|+++.++|+||++ +|+.||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.+|+
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~-~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGF-KKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEeC
Confidence 58999999999999999999999 479999999999 66677777654 899999999999999999999884
No 76
>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=99.03 E-value=1.3e-09 Score=89.93 Aligned_cols=73 Identities=16% Similarity=0.145 Sum_probs=68.0
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD 446 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~ 446 (483)
.++|++|.|+|+++.+.|++|+++. ..+|++|.++++..+..++.+.|++||.+.|+|+++++.+++.||++.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILS-RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCC-CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 4799999999999999999999987 799999999999888888899999999999999999755899999987
No 77
>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=99.00 E-value=1.5e-09 Score=87.62 Aligned_cols=67 Identities=24% Similarity=0.204 Sum_probs=58.1
Q ss_pred CCeEE-EEEEEE-ECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 297 NEPIE-VKFTEW-NTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 297 GeiV~-GkV~~v-~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
|++++ |+|+++ .++|+||++ +|++||+|.|++ +.+..++.+.. ++|+.++++|+.+|+.++++.||.
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPF-KAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCccccc-CCCCEEEEEEEEEeCCCCEEEEeC
Confidence 68889 999999 699999999 489999999999 56665555543 799999999999999999999984
No 78
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.99 E-value=6.3e-10 Score=123.37 Aligned_cols=80 Identities=35% Similarity=0.545 Sum_probs=75.2
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~ 449 (483)
.+|++|+++.|+|+++.+||+||+|+- ..+|++|+|+++..++.+|.+++++||.|+|+|+++| .++||.|||+....
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv-~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~ 732 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGV-HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEE 732 (780)
T ss_pred hhccCCCEEEEEEEEeeeccceEEecc-ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence 489999999999999999999999998 6999999999999999999999999999999999999 78999999997765
Q ss_pred Cc
Q 011538 450 EP 451 (483)
Q Consensus 450 dP 451 (483)
.+
T Consensus 733 ~~ 734 (780)
T COG2183 733 EG 734 (780)
T ss_pred cc
Confidence 43
No 79
>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=98.98 E-value=3.9e-09 Score=86.39 Aligned_cols=65 Identities=29% Similarity=0.394 Sum_probs=59.5
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL 444 (483)
.+++.|+.+.|+|++++++|+||++.+ +..||+|.+++. +.+++||+++++|+++.+++++.+|+
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 EDLEVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECC-CcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 468899999999999999999999998 699999999974 56999999999999997789999986
No 80
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.97 E-value=2.6e-09 Score=84.80 Aligned_cols=66 Identities=18% Similarity=0.282 Sum_probs=58.6
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
|+++.|+|+++.++|+||++. ++.||+|.+++ +.+..++.+.. .+||.++++|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRF-KVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhcc-CCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999995 79999999999 56666666654 89999999999999999999876
No 81
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.97 E-value=3.1e-09 Score=84.62 Aligned_cols=68 Identities=19% Similarity=0.339 Sum_probs=61.2
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
|+++.|+|.++.++|++|+++ +.+|++|.+++ +.+..++.+.. ++|+.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~-~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEV-KVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcC-CCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999996 69999999999 66677776654 8999999999999988889999985
No 82
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.96 E-value=3e-09 Score=84.70 Aligned_cols=64 Identities=14% Similarity=0.173 Sum_probs=54.9
Q ss_pred CCeEEEEEEEEECCeEEEEE-CCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
|++++|+|+++.++|++|++ ++++||+|.+|+. .+.. .+. +++|++++|+|+.+|++++++.||
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 78999999999999999999 5799999999994 2322 222 379999999999999999998887
No 83
>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=98.96 E-value=2.2e-09 Score=85.92 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=57.0
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--ccCcccccCCCCEEEEEEEEEeCCC
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSMFPD 438 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i~~~~~~~kvGd~VkVkVi~vdek~ 438 (483)
|+++.|+|+++.++|+||++++ +++|++|.+++++++ ..++.+.|++||.|+|+|++++..+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 7899999999999999999988 799999999999884 7888899999999999999997443
No 84
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.95 E-value=3.5e-09 Score=101.12 Aligned_cols=90 Identities=23% Similarity=0.352 Sum_probs=75.6
Q ss_pred EEECCCCceeechhhHhhh--cCCCCCcEEEEEEEEEeCceEEEEECC---------CceEEEEeccCcCcccccCcccc
Q 011538 352 RINEDTNDLILSEREAWAT--LNLREGTLLEGTVKKIYPYGAQIRIGD---------SNRSGLLHISNMSRTRVTSVSDL 420 (483)
Q Consensus 352 ~ID~e~~rLiLS~K~~~e~--~~l~vG~iv~G~V~~I~~~GaFV~I~~---------~gi~GLlhiSels~~~i~~~~~~ 420 (483)
++|.+++++.+. +|.. ..+++|++|.|+|++|.++|+||+|++ .++.|++|.+++++.+..++.+.
T Consensus 42 ~id~~~~~Isv~---P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~ 118 (189)
T PRK09521 42 FIDDINRKISVI---PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA 118 (189)
T ss_pred EEcCCCCEEEEe---cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc
Confidence 346556666664 4432 357899999999999999999999952 15789999999999988899999
Q ss_pred cCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538 421 LNEGERVKVLVVKSMFPDKISLSIAD 446 (483)
Q Consensus 421 ~kvGd~VkVkVi~vdek~rI~LSLK~ 446 (483)
|++||.|.|+|++++ +++.||+|+
T Consensus 119 ~~~GD~V~akV~~i~--~~i~LS~k~ 142 (189)
T PRK09521 119 FKIGDIVRAKVISYT--DPLQLSTKG 142 (189)
T ss_pred cCCCCEEEEEEEecC--CcEEEEEec
Confidence 999999999999987 899999996
No 85
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.95 E-value=3.4e-09 Score=85.70 Aligned_cols=68 Identities=19% Similarity=0.324 Sum_probs=60.4
Q ss_pred hCCCeEEEEEEEEECCeEEEEECC--eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
+.|++++|+|+++.++|+||++.| .+||+|.+++ +.++.++.+.. .+||+++++|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~-~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVV-DVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEE-CCCCEEEEEEEEECCCC-cEEEEe
Confidence 479999999999999999999977 5999999999 77777777764 89999999999999865 888875
No 86
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.95 E-value=3.6e-09 Score=84.96 Aligned_cols=70 Identities=10% Similarity=0.037 Sum_probs=60.8
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
+.|+++.|+|+++.++|++|+++ +++||+|.+++ +++..++.+.. ++||.++++|+++|++++++.||.|
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~-~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKF-KKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccccccccc-CCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 58999999999999999999996 79999999999 55444444543 8999999999999998999999864
No 87
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.94 E-value=1.7e-09 Score=118.45 Aligned_cols=77 Identities=36% Similarity=0.578 Sum_probs=73.8
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCC
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE 448 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~ 448 (483)
..+++|+++.|+|++|.+||+||.+.+ |-+||+|+|++++.|+.+..+.+++||.|.|||+.+|+++|+.||+|...
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL 691 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecC-CcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehhcc
Confidence 479999999999999999999999998 89999999999999999999999999999999999999999999999764
No 88
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.93 E-value=5.3e-09 Score=84.32 Aligned_cols=71 Identities=21% Similarity=0.353 Sum_probs=63.0
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
+.|+++.|+|+++.++|+||++. |+.||+|.+++ +.+..++.+.. .+||.++++|+++|..++++.+|+|+
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLV-KVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHee-CCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 47999999999999999999994 59999999999 66677776654 89999999999999988999999863
No 89
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.90 E-value=4e-09 Score=80.74 Aligned_cols=64 Identities=33% Similarity=0.497 Sum_probs=58.4
Q ss_pred EEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538 379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (483)
Q Consensus 379 v~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS 443 (483)
+.|+|.++.++|+||+++. ++.|++|.+++++.+..++.+.|++||.|+|+|++++ +++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~-~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecC-CCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 4799999999999999997 7999999999999888888899999999999999997 57788775
No 90
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.89 E-value=7.4e-09 Score=83.31 Aligned_cols=71 Identities=17% Similarity=0.354 Sum_probs=62.3
Q ss_pred CCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538 296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 296 ~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
.|+++.|+|+++.++|+||++. ++.|++|.+++ +.+..++.+.. .+||.|+|+|+++|.+++++.+|+|++
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~-~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLF-RVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHee-cCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 6899999999999999999996 59999999999 55655555543 899999999999999999999998754
No 91
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.89 E-value=6.4e-09 Score=84.13 Aligned_cols=68 Identities=21% Similarity=0.095 Sum_probs=60.2
Q ss_pred hCCCeEEEEEEEEEC-CeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 295 QLNEPIEVKFTEWNT-GGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 295 k~GeiV~GkV~~v~k-~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
+.|+++.|+|+++.+ +|+||++. |.+|++|.+++ +++..++.+.. .+||.++|+|+++|. +++.||+|
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~-~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGF-KPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhC-CCCCEEEEEEEEecC--CEEEEEeC
Confidence 589999999999986 89999994 89999999999 67777777754 899999999999984 88999875
No 92
>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=98.89 E-value=6.7e-09 Score=88.85 Aligned_cols=80 Identities=26% Similarity=0.433 Sum_probs=69.5
Q ss_pred cEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccC-----------cccccCCCCEEEEEEEEEe-C-----CCe
Q 011538 377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-----------VSDLLNEGERVKVLVVKSM-F-----PDK 439 (483)
Q Consensus 377 ~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~-----------~~~~~kvGd~VkVkVi~vd-e-----k~r 439 (483)
+++.|+|++|.++|+||++. +++|++|.++++++++.. ....|++||.|+|+|++++ + ..+
T Consensus 1 ~vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence 47899999999999999997 489999999999887653 3478999999999999998 3 258
Q ss_pred EEEEEecCCCCcCcccccc
Q 011538 440 ISLSIADLESEPGLFVSDK 458 (483)
Q Consensus 440 I~LSLK~~~~dPw~~l~~k 458 (483)
+.||+|+....||+.+++.
T Consensus 79 i~ls~k~~~~g~~~~~~~~ 97 (99)
T cd04460 79 IGLTMRQPGLGKLEWIEEE 97 (99)
T ss_pred EEEEEecCCCCcHHHhhhh
Confidence 9999999999999887653
No 93
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.89 E-value=7.7e-09 Score=82.48 Aligned_cols=69 Identities=30% Similarity=0.439 Sum_probs=61.2
Q ss_pred CCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
|+++.|+|+++.++|++|++ ++++||+|.+++ +.+..++.+.. .+|+.++|+|+++|++++++.+|+|.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~-~~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERF-KVGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHcc-CCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 78999999999999999999 479999999999 56666666654 89999999999999988999999875
No 94
>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=98.85 E-value=1.3e-08 Score=80.53 Aligned_cols=66 Identities=15% Similarity=0.318 Sum_probs=57.4
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-c-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
|+++.|+|+++.++|+||+++ ++.||+|.+++ | .+..++.+.. .+||.++++|+++|.+++++.+|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~-~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIY-KKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEE-CCCCEEEEEEEEEECCcCEEeCC
Confidence 689999999999999999995 79999999999 4 4555665543 89999999999999999988775
No 95
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.83 E-value=1.7e-08 Score=78.86 Aligned_cols=67 Identities=18% Similarity=0.337 Sum_probs=59.1
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+|+.+.++|+++|+ ++++.+|+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVL-KEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHcc-CCCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999996 79999999999 56666666554 899999999999998 889999865
No 96
>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=98.83 E-value=2e-08 Score=78.61 Aligned_cols=67 Identities=18% Similarity=0.346 Sum_probs=59.0
Q ss_pred CCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
.|+++.|+|+++.++|++|+++++.||+|.+++ +.+..++.+.. .+||.++|+|+++|+.++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVV-NVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEE-CCCCEEEEEEEEEECCCCEEecC
Confidence 488999999999999999999999999999999 55565555543 89999999999999988888876
No 97
>PRK07252 hypothetical protein; Provisional
Probab=98.83 E-value=1.3e-08 Score=90.66 Aligned_cols=73 Identities=23% Similarity=0.339 Sum_probs=64.4
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~ 368 (483)
+.|+++.|+|+++.++|+||+++ ++.||+|.+++ +.++.++.+.. .+||.|.|+|+++|.+++++.+|++..-
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~-~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLL-KVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhcc-CCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 57999999999999999999995 79999999999 66666665543 8999999999999999999999998653
No 98
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.83 E-value=2.8e-08 Score=81.94 Aligned_cols=76 Identities=24% Similarity=0.296 Sum_probs=62.5
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
|-+++||+|.|+|+++.+++++|+++.+.+|++|.+++...+.+ +.
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~-----------~~----------------------- 47 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKK-----------EI----------------------- 47 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchH-----------HH-----------------------
Confidence 45789999999999999999999999999999999998643100 01
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~ 281 (483)
...+++||.+.|+|++.+.++++.||++..
T Consensus 48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~ 77 (82)
T cd04454 48 ----RKSLQPGDLILAKVISLGDDMNVLLTTADN 77 (82)
T ss_pred ----HhcCCCCCEEEEEEEEeCCCCCEEEEECCC
Confidence 234789999999999977668999998753
No 99
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.81 E-value=2.7e-08 Score=82.59 Aligned_cols=80 Identities=28% Similarity=0.337 Sum_probs=62.9
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
|.+++|++|.|+|+++.+++++|+++.+.+|++|.+|+.... . .....+
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~-------~~~~~~--------------------- 50 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---T-------DEDELN--------------------- 50 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---C-------ccchHH---------------------
Confidence 457899999999999999999999999999999999985210 0 000000
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~ 281 (483)
....+++||.+.|+|++.+.++++.||++..
T Consensus 51 ---~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 51 ---MRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred ---HHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 0234789999999999987779999999875
No 100
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.81 E-value=2.6e-08 Score=77.60 Aligned_cols=70 Identities=27% Similarity=0.464 Sum_probs=59.8
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
+.|+++.|+|+++.++|++|+++ ++.||+|.+++. .+..+..+. +.+|+.+.++|+++++.++++.+|++
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 36999999999999999999997 899999999994 434444443 38999999999999998899999864
No 101
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.79 E-value=9e-09 Score=115.55 Aligned_cols=70 Identities=37% Similarity=0.593 Sum_probs=65.7
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L 442 (483)
.+++|+++.|+|++|.+||+||++.+ +.+||+|+|+++|.++.++.+.|++||.|+|+|++++.++||.|
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki~L 684 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCccC
Confidence 57899999999999999999999988 79999999999999999999999999999999999987777754
No 102
>PRK08582 hypothetical protein; Provisional
Probab=98.79 E-value=1.5e-08 Score=92.51 Aligned_cols=72 Identities=18% Similarity=0.280 Sum_probs=63.5
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
++.|+++.|+|+++.++|+||+++ ++.||||.+++ +.++.++.+.. .+||.|+|+|+++|. .++|.||++++
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l-~vGD~VkvkV~~id~-~gkI~LSlk~~ 76 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHL-KVGDEVEVKVLNVED-DGKIGLSIKKA 76 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCccccccccccc-CCCCEEEEEEEEECC-CCcEEEEEEec
Confidence 468999999999999999999995 79999999999 66666665554 899999999999996 48999999875
No 103
>PRK05807 hypothetical protein; Provisional
Probab=98.76 E-value=2.5e-08 Score=90.69 Aligned_cols=73 Identities=18% Similarity=0.245 Sum_probs=64.9
Q ss_pred hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~ 368 (483)
++.|++++|+|+++.++|+||++++..||||.+++ +.++.++.+.. .+||.|+|+|+++|. +++|.||+|...
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~-kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHL-KEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccC-CCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 46899999999999999999999989999999999 66676666654 899999999999997 789999998753
No 104
>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=98.76 E-value=3.2e-08 Score=102.57 Aligned_cols=108 Identities=23% Similarity=0.280 Sum_probs=83.8
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHH-----HHHhhhHHHHHHh--hCCCeEEEEEEEEECCe-EEEEECCeEEEee
Q 011538 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLP 324 (483)
Q Consensus 253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~-----~~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G-~fV~I~Gi~gFVP 324 (483)
+.+++||.+.+.+... .-|++.++..+. ..+..++.+.+.+ +.|++|+|+|.++.++| ++|+++|+.||||
T Consensus 82 ~~~~vGD~I~~~I~~~-~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP 160 (341)
T TIGR01953 82 PDVQIGDEVKKEIPPE-NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILP 160 (341)
T ss_pred cccccCCEEEEEeccc-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEec
Confidence 4578999999887533 345555444433 3466777787777 49999999999999988 6999999999999
Q ss_pred ccccccccCChhhhhhhcCCEEEEEEEEEECC--CCceeechhhH
Q 011538 325 KAELLSRVNNFTELKEKVGRRMYVQITRINED--TNDLILSEREA 367 (483)
Q Consensus 325 ~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e--~~rLiLS~K~~ 367 (483)
.+++... +. +.+|++++|.|++++.. +..++|||+.+
T Consensus 161 ~~E~ip~-----E~-~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 161 KKEQIPG-----EK-FRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred HHHcCCC-----cC-CCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 9999421 11 26999999999999954 45899999975
No 105
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.76 E-value=4.4e-08 Score=96.78 Aligned_cols=75 Identities=19% Similarity=0.225 Sum_probs=68.7
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
..++||+|.|+|++++++|+||+|+. ...|+||.++++|.++ .++++.|++||.|.|+|++++..+++.||+|+.
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~ 138 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK 138 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence 35899999999999999999999987 6899999999999987 888999999999999999998666799999864
No 106
>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=98.73 E-value=5.9e-08 Score=75.65 Aligned_cols=66 Identities=18% Similarity=0.206 Sum_probs=57.4
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
|+.+.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+||.+.|+|+++|++++++.+|
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~-~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVV-SVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhc-CCCCEEEEEEEEEECCCCEEecC
Confidence 678999999999999999995 68999999999 55565665543 89999999999999988888876
No 107
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.72 E-value=3.6e-08 Score=85.05 Aligned_cols=72 Identities=14% Similarity=0.248 Sum_probs=61.4
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccc-------------------cCChhhhhhhcCCEEEEEEEEE
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-------------------VNNFTELKEKVGRRMYVQITRI 353 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~r-------------------v~~~~~l~~~VGq~V~vkVl~I 353 (483)
+.|++|.|+|+++.+.|++|.+. |+.||+|.+++ +.+ ..++.+.+ ++||.|+|+|+++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f-~vGd~V~~kVi~~ 80 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLF-SVGQLVRCKVVSL 80 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhc-cCCCEEEEEEEEc
Confidence 68999999999999999999995 89999999999 432 12344554 8999999999999
Q ss_pred ECC---CCceeechhhH
Q 011538 354 NED---TNDLILSEREA 367 (483)
Q Consensus 354 D~e---~~rLiLS~K~~ 367 (483)
|++ +++|.||.|..
T Consensus 81 d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 81 DKSKSGKKRIELSLEPE 97 (100)
T ss_pred cCCcCCCcEEEEEecHH
Confidence 987 78999999865
No 108
>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=98.71 E-value=5.1e-08 Score=79.72 Aligned_cols=68 Identities=18% Similarity=0.256 Sum_probs=59.3
Q ss_pred CCeEEEEEEEEECCeEEEEEC----CeEEEeecccc-cccc-CChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-LSRV-NNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~----Gi~gFVP~Sel-~~rv-~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.+. .++.+.. .+||.|+++|+++| ++++.+|+|..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~-~~Gd~v~v~v~~vd--~~~i~~s~k~~ 74 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVV-KRGQKVKVKVISIQ--NGKISLSMKDV 74 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhee-CCCCEEEEEEEEEe--CCEEEEEEEec
Confidence 689999999999999999997 68999999999 6654 6666553 89999999999999 78999998763
No 109
>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=98.69 E-value=7.4e-08 Score=77.08 Aligned_cols=68 Identities=16% Similarity=0.265 Sum_probs=56.6
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
..|+++.|+|+++.++|+||+++ |+.||+|.+++ +. +..++... +.+||.++|+|+++|.+++++.+|
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence 57999999999999999999994 79999999999 43 32233333 379999999999999988888764
No 110
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.66 E-value=3.5e-08 Score=105.51 Aligned_cols=84 Identities=26% Similarity=0.362 Sum_probs=79.8
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP 451 (483)
++..|-++.|+|+.+.++|+||++.+ +..||+|+|+++..++.+|++.+.+||.|.|+.+..|.++.+.+|.|.+.++|
T Consensus 665 ~l~~g~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~p 743 (760)
T KOG1067|consen 665 DLEFGGVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPDP 743 (760)
T ss_pred ceEeeeEEEEEEeeecccceEEEecC-CchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhhhhcCCc
Confidence 78899999999999999999999999 89999999999999999999999999999999999999999999999999999
Q ss_pred Ccccc
Q 011538 452 GLFVS 456 (483)
Q Consensus 452 w~~l~ 456 (483)
-....
T Consensus 744 ~~~~~ 748 (760)
T KOG1067|consen 744 ATKES 748 (760)
T ss_pred ccCCc
Confidence 76544
No 111
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.65 E-value=5.1e-08 Score=96.27 Aligned_cols=71 Identities=17% Similarity=0.272 Sum_probs=66.8
Q ss_pred hhCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
-..|++|-|+|.++.++|+||.+ +|++||+|.||+ ..++++++++. ++||++-|+|+++|++++.|-||+|
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~v-kegqkvV~kVlrVd~~rg~IDLSlk 83 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYV-KEGQKVVAKVLRVDPKRGHIDLSLK 83 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHh-hcCCeEEEEEEEEcCCCCeEeeehh
Confidence 36899999999999999999998 689999999999 67889999987 9999999999999999999999997
No 112
>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=98.65 E-value=1.4e-07 Score=73.89 Aligned_cols=66 Identities=23% Similarity=0.327 Sum_probs=57.2
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+||.+.++|+++|+ ++++.+|+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVL-KVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHcc-CCCCEEEEEEEEECC-CCcEEeeC
Confidence 678999999999999999995 69999999999 55555555543 899999999999998 88998885
No 113
>PRK08059 general stress protein 13; Validated
Probab=98.64 E-value=1e-07 Score=85.03 Aligned_cols=74 Identities=16% Similarity=0.270 Sum_probs=65.0
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~ 368 (483)
++.|+++.|+|+++.++|++|+++ ++.|++|.+++ +.+..++.+.. .+|+.|.|+|+++|++++++.+|++..-
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~-~vGD~I~vkI~~id~~~~~i~lslk~~~ 80 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFL-SVGDEVKVKVLSVDEEKGKISLSIRATE 80 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcC-CCCCEEEEEEEEEECCCCeEEEEEEEcc
Confidence 578999999999999999999995 79999999999 55666655543 7999999999999999999999998763
No 114
>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=98.63 E-value=1.7e-07 Score=74.60 Aligned_cols=62 Identities=24% Similarity=0.391 Sum_probs=53.6
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeC-C--CeEEEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF-P--DKISLS 443 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vde-k--~rI~LS 443 (483)
..|+++.|+|.++.++|+||+++ +.+|+||.++++. .+.|++||.|+|.|+++++ + ..|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 47999999999999999999996 4899999999873 4678999999999999972 2 467777
No 115
>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=98.62 E-value=1.5e-07 Score=74.93 Aligned_cols=64 Identities=20% Similarity=0.341 Sum_probs=54.1
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCC--Cceeech
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSE 364 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~--~rLiLS~ 364 (483)
..|++++|+|.++.++|++|++++++||||.+++.. .+. +.+|+++++.|++++..+ .+|.|||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~-----~~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP-----GES-YRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC-----CCc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 479999999999999999999988999999999942 111 279999999999998643 4688886
No 116
>PHA02945 interferon resistance protein; Provisional
Probab=98.62 E-value=9.4e-08 Score=80.00 Aligned_cols=69 Identities=14% Similarity=0.176 Sum_probs=60.9
Q ss_pred hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc---ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL---LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel---~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
+.|+++-|+|.. .++|+||.+ +|.+||+|.|+. ..++++ ++.. +||++-|+|+++|+.++.|-||+|..
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l--~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL--VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe--cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 689999999999 999999999 589999999955 456666 6664 99999999999999999999998853
No 117
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.61 E-value=2.7e-07 Score=103.18 Aligned_cols=95 Identities=18% Similarity=0.246 Sum_probs=74.7
Q ss_pred EEcCCCcEEEEehH-HHHHhhhHHHHHH-----hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc----c-cccCC
Q 011538 267 GRTLSGRPLLSTRR-LFRKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL----L-SRVNN 334 (483)
Q Consensus 267 ~~d~~G~iiLS~k~-~~~~~~w~~L~~~-----~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel----~-~rv~~ 334 (483)
.++.+|.+.++... ....++...+... .+.|++++|+|+++.++|+||++ .|++||||.|++ | .++.+
T Consensus 612 di~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~ 691 (719)
T TIGR02696 612 SIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN 691 (719)
T ss_pred EEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCC
Confidence 34568888766533 3334444444433 46999999999999999999999 489999999998 3 57888
Q ss_pred hhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 335 FTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 335 ~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
+.++. ++||+|+|+|+++|+ ++|+.|+
T Consensus 692 ~~dv~-kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 692 VEDVL-SVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred HHHcC-CCCCEEEEEEEEECC-CCCeeec
Confidence 88865 899999999999995 6788775
No 118
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.56 E-value=2.3e-07 Score=96.97 Aligned_cols=109 Identities=17% Similarity=0.258 Sum_probs=79.3
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHHH----HHhhhHHHHHHh--hCCCeEEEEEEEEECCeEEEEECCeEEEeecc
Q 011538 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLF----RKMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA 326 (483)
Q Consensus 253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~----~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~S 326 (483)
+..++||.+...+...+.++....+.|+.. .+...+.+.+.+ +.|++++|+|.++.++|++|+++|++||||.+
T Consensus 85 ~~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~ 164 (362)
T PRK12327 85 PAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPA 164 (362)
T ss_pred ccccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHH
Confidence 347899999888754333333333333332 233444555555 79999999999999999999999999999988
Q ss_pred ccccccCChhhhhhhcCCEEEEEEEEEECCCC--ceeechhhH
Q 011538 327 ELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA 367 (483)
Q Consensus 327 el~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~--rLiLS~K~~ 367 (483)
++... +. +.+|++++|+|++++...+ .|+|||..+
T Consensus 165 E~ip~-----e~-~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p 201 (362)
T PRK12327 165 EQIPG-----ET-YKHGDRIKVYVVKVEKTTKGPQIFVSRTHP 201 (362)
T ss_pred HcCCC-----CC-CCCCCEEEEEEEEEecCCCCCeEEEEeCCH
Confidence 88321 11 2699999999999995443 799999864
No 119
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.55 E-value=2.2e-07 Score=100.17 Aligned_cols=112 Identities=15% Similarity=0.207 Sum_probs=85.0
Q ss_pred EEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeec-hhhH----hh-------hcCCC--CCcEEEEEEEE
Q 011538 320 RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS-EREA----WA-------TLNLR--EGTLLEGTVKK 385 (483)
Q Consensus 320 ~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS-~K~~----~e-------~~~l~--vG~iv~G~V~~ 385 (483)
.++||.++.-.. ++. ..+|+.+.+.|...+ .+|+.++ .|+. |. ...++ .|+++.|+|++
T Consensus 72 ~~eI~L~eAk~~--~~~---~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~r 144 (470)
T PRK09202 72 TKEISLEEARKI--DPD---AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKR 144 (470)
T ss_pred cceeeHHHHhhh--Ccc---ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEE
Confidence 467787777321 221 259999999998876 3444333 3332 22 13454 99999999999
Q ss_pred EeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEec
Q 011538 386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIAD 446 (483)
Q Consensus 386 I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~--rI~LSLK~ 446 (483)
+.++|+||+++ +++||||.++++ |++.|++||+|+|+|++++ +++ +|.||.+.
T Consensus 145 i~~~giiVDLg--gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 145 VERGNIIVDLG--RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred EecCCEEEEEC--CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 99999999996 689999999985 6788999999999999997 444 78888774
No 120
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.54 E-value=2.8e-07 Score=105.11 Aligned_cols=71 Identities=21% Similarity=0.300 Sum_probs=64.7
Q ss_pred hhCCCeEE-EEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 294 KQLNEPIE-VKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 294 ~k~GeiV~-GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
.+.|++++ |+|+++.++|+||++. |++||||.|++ +.++.++++.. ++||.|+|+|+++|+ +++|.||+|.
T Consensus 751 ~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~-kvGD~V~VkVi~ID~-~grI~LSlK~ 824 (891)
T PLN00207 751 PTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAF-KVGDRIDVKLIEVND-KGQLRLSRRA 824 (891)
T ss_pred cCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhc-CCCCEEEEEEEEECC-CCcEEEEEec
Confidence 57999996 6999999999999995 89999999999 78888888765 899999999999997 7899999986
No 121
>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=98.53 E-value=5e-07 Score=85.59 Aligned_cols=81 Identities=25% Similarity=0.415 Sum_probs=68.9
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe------C
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM------F 436 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd------e 436 (483)
.+|++++|+|++++++|+||+++ .++|++|.+++.+++.. +....++.||.|++||++++ +
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 47999999999999999999996 48999999999866432 23467999999999999996 2
Q ss_pred CCeEEEEEecCCCCcCcccc
Q 011538 437 PDKISLSIADLESEPGLFVS 456 (483)
Q Consensus 437 k~rI~LSLK~~~~dPw~~l~ 456 (483)
..+|.||+|+....|++.++
T Consensus 158 ~~~I~lt~k~~~LG~~~w~~ 177 (179)
T TIGR00448 158 GSKIGLTMRQPLLGKLEWIE 177 (179)
T ss_pred cceEEEEeccCcCCcccccc
Confidence 46999999998888887764
No 122
>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=98.50 E-value=4.2e-07 Score=77.32 Aligned_cols=74 Identities=19% Similarity=0.259 Sum_probs=65.5
Q ss_pred CCCCcEEEEEEEEEeCceEEEEE--------CCCceEEEEeccCcCccccc--CcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRI--------GDSNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMFPDKISL 442 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I--------~~~gi~GLlhiSels~~~i~--~~~~~~kvGd~VkVkVi~vdek~rI~L 442 (483)
.++|++|.|+|++++...+.|+| .. ...|++|++++...+.. ++.+.|++||.|+|+|+++.+...+.|
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~L 82 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYL 82 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEE
Confidence 47999999999999999999999 55 58999999999877666 788999999999999999876677999
Q ss_pred EEecC
Q 011538 443 SIADL 447 (483)
Q Consensus 443 SLK~~ 447 (483)
|+++-
T Consensus 83 st~~~ 87 (92)
T cd05791 83 STAEN 87 (92)
T ss_pred EecCC
Confidence 99863
No 123
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.49 E-value=4.4e-07 Score=69.29 Aligned_cols=63 Identities=22% Similarity=0.350 Sum_probs=52.9
Q ss_pred EEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 300 V~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
+.|+|+++.++|++|+++ +++||+|.+++ +.+..++.+.. .+|+.+.++|+++|++++++.+|
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~-~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVF-KVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEe-CCCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999997 89999999999 44444444443 79999999999999988888776
No 124
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.48 E-value=4.3e-07 Score=91.13 Aligned_cols=71 Identities=18% Similarity=0.295 Sum_probs=64.3
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
.+.|+++.|+|+++.++|+||++. |+.||+|.+++ +.++.++.+.. .+||.+.|+|+++|++++++.||+|
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~-kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHV-KEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhC-CCCCEEEEEEEEEecccCeEEEEEE
Confidence 468999999999999999999994 79999999999 66777777664 8999999999999999999999987
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=98.48 E-value=5.4e-07 Score=75.96 Aligned_cols=70 Identities=17% Similarity=0.234 Sum_probs=58.0
Q ss_pred hhCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccc-c---cccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 294 KQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-L---SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel-~---~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
.+.|+++.|+|+++.++ |+||+++ |.+||||.+++ + .++.++.+.. ++||.|.|+|++.....+-..+|.
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~-~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL-KEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC-CCCCEEEEEEEEecCCCCCceEEE
Confidence 46899999999999996 9999996 79999999999 5 4566666654 899999999999876665555554
No 126
>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=98.46 E-value=5.7e-07 Score=101.70 Aligned_cols=73 Identities=26% Similarity=0.446 Sum_probs=63.9
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK 439 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~r 439 (483)
.-++|++++|+|++|+++|+||++.+.+++||+|+++++++++ .+....|++||+|+|+|+++| ++++
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 4578999999999999999999998656999999999997643 344578999999999999998 7899
Q ss_pred EEEEE
Q 011538 440 ISLSI 444 (483)
Q Consensus 440 I~LSL 444 (483)
|.+++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99986
No 127
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.39 E-value=1.2e-06 Score=98.86 Aligned_cols=97 Identities=19% Similarity=0.217 Sum_probs=75.9
Q ss_pred cCCCcEEEEehH-HHHHhhhHHHH---HHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhc
Q 011538 269 TLSGRPLLSTRR-LFRKMAWHRVR---QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKV 342 (483)
Q Consensus 269 d~~G~iiLS~k~-~~~~~~w~~L~---~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~V 342 (483)
+.+|.+.++... ...+++...+. ...+.|+++.|+|+++.++|+||++. |.+||+|.|++ +.++.++.+.. ++
T Consensus 590 ~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~-kv 668 (693)
T PRK11824 590 EDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL-KE 668 (693)
T ss_pred CCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee-CC
Confidence 457888655432 22222333332 33579999999999999999999995 79999999999 67787777764 89
Q ss_pred CCEEEEEEEEEECCCCceeechhhH
Q 011538 343 GRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 343 Gq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
||.|+|+|+++|++ +++.||+|..
T Consensus 669 GD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 669 GDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CCEEEEEEEEECCC-CcEEEEEEec
Confidence 99999999999987 9999998753
No 128
>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=98.35 E-value=1.5e-06 Score=70.87 Aligned_cols=67 Identities=12% Similarity=0.234 Sum_probs=54.4
Q ss_pred CCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccC-----------ChhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-----------NFTELKEKVGRRMYVQITRINEDTNDLIL 362 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~-----------~~~~l~~~VGq~V~vkVl~ID~e~~rLiL 362 (483)
|++++|+|+++.++|+||+++ |+.|++|.+++ +.++. +.... ..+||.|+++|+++|.+++++.+
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEEE
Confidence 889999999999999999997 69999999998 33211 11122 27899999999999988888887
Q ss_pred ch
Q 011538 363 SE 364 (483)
Q Consensus 363 S~ 364 (483)
+.
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 64
No 129
>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=98.35 E-value=2.3e-06 Score=68.50 Aligned_cols=61 Identities=10% Similarity=0.134 Sum_probs=51.6
Q ss_pred CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc--ccCChhhhhhhcCCEEEEEEEEEECCCC
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS--RVNNFTELKEKVGRRMYVQITRINEDTN 358 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~--rv~~~~~l~~~VGq~V~vkVl~ID~e~~ 358 (483)
|+++.|+|+++.+.|++|.++ |++|++|.+++ +. ...++.+.. .+||.+.|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~-~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKF-KIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhC-CCCCEEEEEEEEEeCccc
Confidence 789999999999999999995 89999999999 44 255555543 799999999999987543
No 130
>PRK11642 exoribonuclease R; Provisional
Probab=98.34 E-value=1.6e-06 Score=99.23 Aligned_cols=76 Identities=25% Similarity=0.388 Sum_probs=65.5
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKIS 441 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek~rI~ 441 (483)
++|+++.|+|++|+++|+||+|.+.+++||+|++++.++++. +....|++||.|+|+|+++| ++++|.
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 689999999999999999999987569999999999977432 33577999999999999998 789999
Q ss_pred EEEecCCC
Q 011538 442 LSIADLES 449 (483)
Q Consensus 442 LSLK~~~~ 449 (483)
|++-....
T Consensus 722 f~l~~~~~ 729 (813)
T PRK11642 722 FSLISSER 729 (813)
T ss_pred EEEecccc
Confidence 99864443
No 131
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.32 E-value=1.7e-06 Score=81.94 Aligned_cols=79 Identities=25% Similarity=0.407 Sum_probs=64.8
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc----------C-cccccCCCCEEEEEEEEEe--CC--
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT----------S-VSDLLNEGERVKVLVVKSM--FP-- 437 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~----------~-~~~~~kvGd~VkVkVi~vd--ek-- 437 (483)
...|++|.|.|+++.++|+||.|+. .+||+|++++.++++. + -...+++||.|+|||+... +.
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~igp--~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~ 156 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIGP--LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP 156 (183)
T ss_pred eccccEEEEEEEEEeecceEEEecc--ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence 3469999999999999999999996 7999999999988431 2 3347999999999999885 32
Q ss_pred --CeEEEEEecCCCCcCc
Q 011538 438 --DKISLSIADLESEPGL 453 (483)
Q Consensus 438 --~rI~LSLK~~~~dPw~ 453 (483)
.+|.|+||+.-..+.+
T Consensus 157 ~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 157 RESKIGLTMRQPGLGKLE 174 (183)
T ss_pred ccceEEEEeccccCCcch
Confidence 6899999987655443
No 132
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.32 E-value=2e-06 Score=82.25 Aligned_cols=104 Identities=15% Similarity=0.234 Sum_probs=78.8
Q ss_pred CCCcccCCCEEEEEEEEE---cCCC-cEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC---------
Q 011538 251 GRPVVETGTVLFAEVLGR---TLSG-RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE--------- 317 (483)
Q Consensus 251 ~~~~~kVGd~V~v~Vi~~---d~~G-~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~--------- 317 (483)
+...+..+..+.+.+.+. |.++ ++.+. +|.......+.|++|.|+|+++.+.|++|+++
T Consensus 23 G~Gty~~~~~i~as~~G~~~id~~~~~Isv~--------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l 94 (189)
T PRK09521 23 GEGTYEDNGEVYASVVGKVFIDDINRKISVI--------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSEREL 94 (189)
T ss_pred CCCEEeeCCEEEEEeeEEEEEcCCCCEEEEe--------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEeccccccc
Confidence 345577788888888873 4333 34342 45443345679999999999999999999994
Q ss_pred --CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 318 --GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 318 --Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
++.||+|.+++ +.+..+..+.. ++||.|.|+|++++ +++.||.|.
T Consensus 95 ~~~~~G~l~~s~i~~~~~~~~~~~~-~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 95 ATSKLAYIHISQVSDGYVESLTDAF-KIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred CCCceeeEEhhHcChhhhhhHHhcc-CCCCEEEEEEEecC---CcEEEEEec
Confidence 57899999999 55555555544 89999999999997 689999874
No 133
>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=98.28 E-value=2.7e-06 Score=95.51 Aligned_cols=72 Identities=22% Similarity=0.405 Sum_probs=63.1
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCeE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDKI 440 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~rI 440 (483)
-++|++++|+|++|+++|+||++.+.+++||+|++++.|+++ .+....|++||+|+|+|+++| ++++|
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I 649 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSI 649 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence 367999999999999999999998558999999999998742 234577999999999999998 88899
Q ss_pred EEEE
Q 011538 441 SLSI 444 (483)
Q Consensus 441 ~LSL 444 (483)
.+++
T Consensus 650 ~f~l 653 (654)
T TIGR00358 650 IFEL 653 (654)
T ss_pred EEEE
Confidence 9886
No 134
>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=98.26 E-value=6e-06 Score=67.52 Aligned_cols=62 Identities=19% Similarity=0.326 Sum_probs=54.3
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
++.|+.+.|+|+++.++|+||+++ ++.||+|.+++... .++||.++++|.++ .+++++.+|.
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~~~--------~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD--------YEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCc--------CCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 578999999999999999999995 59999999997432 26999999999999 7888888763
No 135
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.23 E-value=2.8e-06 Score=70.58 Aligned_cols=70 Identities=13% Similarity=0.149 Sum_probs=65.7
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEe-ccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLH-ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlh-iSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
.++|+++. .|+.|.+.|++|.+.++|++|++. .+|++.+++.++++.+ +|..+.|+|+.+| +++.|.||.
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 56899999 899999999999998888999999 9999999999999999 9999999999998 889999984
No 136
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.21 E-value=2.8e-06 Score=94.91 Aligned_cols=82 Identities=16% Similarity=0.097 Sum_probs=71.7
Q ss_pred hhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538 285 MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLIL 362 (483)
Q Consensus 285 ~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiL 362 (483)
.....+. .++.|+++.|+|.++..+|+||+|| ..+|+||+|++ ...+++|.++. .+|+.|+++|+++|..+++|.|
T Consensus 648 ~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv-~vGdiV~v~V~~vD~~r~rI~L 725 (780)
T COG2183 648 EGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVV-KVGDIVKVKVIEVDTARKRIAL 725 (780)
T ss_pred hhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhc-ccCCEEEEEEEEEecccCeeee
Confidence 3344443 5689999999999999999999997 58999999999 56788888876 8999999999999999999999
Q ss_pred chhhHh
Q 011538 363 SEREAW 368 (483)
Q Consensus 363 S~K~~~ 368 (483)
|++..-
T Consensus 726 smr~~~ 731 (780)
T COG2183 726 SMRLDE 731 (780)
T ss_pred EeeccC
Confidence 998753
No 137
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.20 E-value=5.7e-06 Score=78.72 Aligned_cols=83 Identities=25% Similarity=0.396 Sum_probs=67.0
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CC---
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP--- 437 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek--- 437 (483)
..+|+++.|+|++++++|+||+++. ++|++|.+++.+++.. +....+++||.|+++|++++ +.
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg~--~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~ 156 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEeC--ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence 3479999999999999999999974 8999999999876432 34567999999999999997 32
Q ss_pred --CeEEEEEecCCCCcCccccc
Q 011538 438 --DKISLSIADLESEPGLFVSD 457 (483)
Q Consensus 438 --~rI~LSLK~~~~dPw~~l~~ 457 (483)
.+|.+|+++..--+.+.+.+
T Consensus 157 ~~~~I~ls~~~~~LG~~~w~~~ 178 (187)
T PRK08563 157 RGSKIGLTMRQPGLGKLEWIEE 178 (187)
T ss_pred CCCEEEEEecCCCCCcHHHHHH
Confidence 48999999866555444443
No 138
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.19 E-value=9.1e-06 Score=91.66 Aligned_cols=92 Identities=15% Similarity=0.173 Sum_probs=70.4
Q ss_pred EcCCCcEEEEeh-HHHHHhhhH---HHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538 268 RTLSGRPLLSTR-RLFRKMAWH---RVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK 341 (483)
Q Consensus 268 ~d~~G~iiLS~k-~~~~~~~w~---~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~ 341 (483)
++.+|++.++.. ....+++.. .+....+.|+++.|+|+++.++|+||++ +|.+||+|.|++ +.++.++.+.. +
T Consensus 586 i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~-k 664 (684)
T TIGR03591 586 IEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVL-K 664 (684)
T ss_pred EecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhcc-C
Confidence 445788865542 222222322 2333457899999999999999999999 579999999999 77788887765 8
Q ss_pred cCCEEEEEEEEEECCCCcee
Q 011538 342 VGRRMYVQITRINEDTNDLI 361 (483)
Q Consensus 342 VGq~V~vkVl~ID~e~~rLi 361 (483)
+||.|.|+|+++|+ ++++.
T Consensus 665 vGD~V~VkVi~id~-~gki~ 683 (684)
T TIGR03591 665 EGDEVKVKVLEIDK-QGRIK 683 (684)
T ss_pred CCCEEEEEEEEECC-CCCcc
Confidence 99999999999997 56654
No 139
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.11 E-value=1.3e-05 Score=79.34 Aligned_cols=79 Identities=23% Similarity=0.274 Sum_probs=63.0
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
|.+++||+|.|+|+++.+++++||++....|+||.+++...+. + .|.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~-~--------------------------~d~------ 105 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPV-N--------------------------VEG------ 105 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcc-c--------------------------cch------
Confidence 7789999999999999999999999988999999999864310 0 000
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~ 280 (483)
.+..+.+++||.|.|+|+..+.++.+.||++.
T Consensus 106 -~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~ 137 (235)
T PRK04163 106 -TDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG 137 (235)
T ss_pred -hhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence 01134589999999999998877789999864
No 140
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.11 E-value=1.1e-05 Score=89.09 Aligned_cols=98 Identities=16% Similarity=0.178 Sum_probs=78.0
Q ss_pred EcCCCcEEEEehHH-HHHhhh---HHHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538 268 RTLSGRPLLSTRRL-FRKMAW---HRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK 341 (483)
Q Consensus 268 ~d~~G~iiLS~k~~-~~~~~w---~~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~ 341 (483)
++.+|++.++.... ....+. ..+....+.|+++.|+|+++.++|+||.+ +|-.|++|.|++ +.++....+.. +
T Consensus 587 ieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvl-k 665 (692)
T COG1185 587 IEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVL-K 665 (692)
T ss_pred ecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhccccee-e
Confidence 45789886665443 223333 33445578999999999999999999999 689999999999 66777777766 8
Q ss_pred cCCEEEEEEEEEECCCCceeechhhH
Q 011538 342 VGRRMYVQITRINEDTNDLILSEREA 367 (483)
Q Consensus 342 VGq~V~vkVl~ID~e~~rLiLS~K~~ 367 (483)
+||.+.++|+.+|+ ++++.+|++..
T Consensus 666 ~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 666 EGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred cCceEEEEEeeecc-cCCccceehhc
Confidence 99999999999984 68899998754
No 141
>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=98.04 E-value=1.1e-05 Score=68.99 Aligned_cols=69 Identities=19% Similarity=0.213 Sum_probs=55.6
Q ss_pred CeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCCh-----------hhhhhhcCCEEEEEEEEEECCC-----Cce
Q 011538 298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNF-----------TELKEKVGRRMYVQITRINEDT-----NDL 360 (483)
Q Consensus 298 eiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~-----------~~l~~~VGq~V~vkVl~ID~e~-----~rL 360 (483)
+++.|+|+++.++|+||+++++.||+|.+++ +++.... ... +.+|+.+.++|.++|.+. +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRV-LKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCE-ECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 4789999999999999999889999999999 4433211 122 379999999999999764 478
Q ss_pred eechhhH
Q 011538 361 ILSEREA 367 (483)
Q Consensus 361 iLS~K~~ 367 (483)
.||.|..
T Consensus 80 ~ls~k~~ 86 (99)
T cd04460 80 GLTMRQP 86 (99)
T ss_pred EEEEecC
Confidence 9999864
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=98.01 E-value=2.9e-05 Score=80.82 Aligned_cols=97 Identities=20% Similarity=0.324 Sum_probs=73.3
Q ss_pred hcCCEEEEEEEEEECCCCceeech-hhHh----h-------hcCC--CCCcEEEEEEEEEeCce-EEEEECCCceEEEEe
Q 011538 341 KVGRRMYVQITRINEDTNDLILSE-REAW----A-------TLNL--REGTLLEGTVKKIYPYG-AQIRIGDSNRSGLLH 405 (483)
Q Consensus 341 ~VGq~V~vkVl~ID~e~~rLiLS~-K~~~----e-------~~~l--~vG~iv~G~V~~I~~~G-aFV~I~~~gi~GLlh 405 (483)
.+|+.+++.|..- +.+|+.++. |+.+ . ...+ +.|+++.|+|.++.+.| ++|+++ +++|+||
T Consensus 85 ~vGD~I~~~I~~~--~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP 160 (341)
T TIGR01953 85 QIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILP 160 (341)
T ss_pred ccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEec
Confidence 6999999987543 234444443 3321 0 0234 69999999999999988 699996 6899999
Q ss_pred ccCcCcccccCcccccCCCCEEEEEEEEEeC---CCeEEEEEecC
Q 011538 406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSMF---PDKISLSIADL 447 (483)
Q Consensus 406 iSels~~~i~~~~~~~kvGd~VkVkVi~vde---k~rI~LSLK~~ 447 (483)
.+++. +.+.|++||+++|.|++++. ...|.||.+..
T Consensus 161 ~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 161 KKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred HHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 99987 45679999999999999972 24788888753
No 143
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.99 E-value=1.4e-05 Score=83.63 Aligned_cols=96 Identities=19% Similarity=0.262 Sum_probs=70.9
Q ss_pred hcCCEEEEEEEEEECCCCceeechhhHhh-----------hcCC--CCCcEEEEEEEEEeCceEEEEECCCceEEEEecc
Q 011538 341 KVGRRMYVQITRINEDTNDLILSEREAWA-----------TLNL--REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS 407 (483)
Q Consensus 341 ~VGq~V~vkVl~ID~e~~rLiLS~K~~~e-----------~~~l--~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiS 407 (483)
.+|+.+.+.+...+-.+. ...+.|+.+. ...+ +.|+++.|+|.++.+.|+||+++ +++|+||.+
T Consensus 88 ~vGD~i~~~I~~~~fgR~-aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg--~vEa~LP~~ 164 (362)
T PRK12327 88 ELGDVIEIEVTPKDFGRI-AAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPA 164 (362)
T ss_pred cCCCEEEEecCcCCCChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHH
Confidence 589999998765443222 2222222210 1244 89999999999999999999997 589999998
Q ss_pred CcCcccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEe
Q 011538 408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIA 445 (483)
Q Consensus 408 els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~--rI~LSLK 445 (483)
++. +++.|++||+++|.|++++ +++ .|.||..
T Consensus 165 E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 165 EQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred HcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 875 3688999999999999997 332 5776654
No 144
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.91 E-value=4.2e-05 Score=80.09 Aligned_cols=108 Identities=20% Similarity=0.243 Sum_probs=74.8
Q ss_pred CcccCCCEEEEEEEEEcCCCcE-EEEehHHH----HHhhhHHHHHH--hhCCCeEEEEEEEEEC-CeEEEEECCeEEEee
Q 011538 253 PVVETGTVLFAEVLGRTLSGRP-LLSTRRLF----RKMAWHRVRQI--KQLNEPIEVKFTEWNT-GGLLTRIEGLRAFLP 324 (483)
Q Consensus 253 ~~~kVGd~V~v~Vi~~d~~G~i-iLS~k~~~----~~~~w~~L~~~--~k~GeiV~GkV~~v~k-~G~fV~I~Gi~gFVP 324 (483)
+.+++||.+...+--.+ =||+ .-+.++.. .+...+.+.+. -+.|+++.|+|.++.. ++++|++++..|+||
T Consensus 89 ~~~~vGd~i~~~i~~~~-fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP 167 (374)
T PRK12328 89 PSVEIGDELTYELSLEN-MGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLP 167 (374)
T ss_pred CCCCCCCEEEEecChhh-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeC
Confidence 45789999987654322 2333 22333332 11222223332 2699999999999996 569999999999999
Q ss_pred ccccccccCChhhhhhhcCCEEEEEEEEEECCCC---ceeechhhH
Q 011538 325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDTN---DLILSEREA 367 (483)
Q Consensus 325 ~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~---rLiLS~K~~ 367 (483)
.+++... +. +.+|+.++|.|.+|+...+ .++|||..+
T Consensus 168 ~~eqip~----E~--~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p 207 (374)
T PRK12328 168 MKNRIKG----EK--FKVGDVVKAVLKRVKIDKNNGILIELSRTSP 207 (374)
T ss_pred HHHcCCC----Cc--CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence 9998421 11 2699999999999987654 899999864
No 145
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.91 E-value=5.2e-05 Score=59.66 Aligned_cols=61 Identities=21% Similarity=0.115 Sum_probs=37.8
Q ss_pred CCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCCC
Q 011538 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG 251 (483)
Q Consensus 172 ~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~~ 251 (483)
+|++...+|+++++.|+|++.|...+-+||.+|+.
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~--------------------------------------------- 35 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP--------------------------------------------- 35 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-----------------------------------------------
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC---------------------------------------------
Confidence 48999999999999999999988788888888863
Q ss_pred CCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 011538 252 RPVVETGTVLFAEVLGRTLSGRPLLSTR 279 (483)
Q Consensus 252 ~~~~kVGd~V~v~Vi~~d~~G~iiLS~k 279 (483)
..+++||.|.++|+ .|.++++++|++
T Consensus 36 -~~~~~Gd~v~VFvY-~D~~~rl~AT~k 61 (61)
T PF13509_consen 36 -EPLKVGDEVEVFVY-LDKEGRLVATTK 61 (61)
T ss_dssp -----TTSEEEEEEE-E-TTS-EEEE--
T ss_pred -CCCCCCCEEEEEEE-ECCCCCEEEecC
Confidence 12679999999999 578889999864
No 146
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.89 E-value=9.4e-06 Score=76.88 Aligned_cols=74 Identities=19% Similarity=0.212 Sum_probs=58.7
Q ss_pred hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccC----------ChhhhhhhcCCEEEEEEEEEECCC-----
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN----------NFTELKEKVGRRMYVQITRINEDT----- 357 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~----------~~~~l~~~VGq~V~vkVl~ID~e~----- 357 (483)
...|++|.|.|+++.++|+||.++..+||+|.+++ ++++. .-.+....+|+.|++||+.+....
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 45899999999999999999999999999999999 43221 011222368999999999997554
Q ss_pred CceeechhhH
Q 011538 358 NDLILSEREA 367 (483)
Q Consensus 358 ~rLiLS~K~~ 367 (483)
.++.+++|++
T Consensus 159 ~~I~lTmrq~ 168 (183)
T COG1095 159 SKIGLTMRQP 168 (183)
T ss_pred ceEEEEeccc
Confidence 4788888876
No 147
>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=97.86 E-value=8.6e-05 Score=63.16 Aligned_cols=78 Identities=21% Similarity=0.241 Sum_probs=59.6
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEe--------CCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~Vdi--------G~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~ 239 (483)
+-+++||+|.|+|+++....+.|+| .....|++|.+++.+.+-.+
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~--------------------------- 54 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDK--------------------------- 54 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccch---------------------------
Confidence 4568999999999999999999999 67778999998886431000
Q ss_pred ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (483)
Q Consensus 240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~ 281 (483)
..+ ...|++||.|.|+|++.+....+.||++..
T Consensus 55 --~~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~~ 87 (92)
T cd05791 55 --VEM-------YKCFRPGDIVRAKVISLGDASSYYLSTAEN 87 (92)
T ss_pred --HHH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecCC
Confidence 001 234899999999999866556788998653
No 148
>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=97.82 E-value=4.5e-05 Score=72.34 Aligned_cols=73 Identities=14% Similarity=0.183 Sum_probs=59.0
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccc-cccC-Ch---------hhhhhhcCCEEEEEEEEEE-----CCCC
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NF---------TELKEKVGRRMYVQITRIN-----EDTN 358 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~-~rv~-~~---------~~l~~~VGq~V~vkVl~ID-----~e~~ 358 (483)
..|++++|+|++++++|+||+++.++|++|.+++. +... +. ......+|+.|+++|.++| ++..
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 159 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGS 159 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcc
Confidence 47999999999999999999998899999999983 3221 11 1123479999999999998 5567
Q ss_pred ceeechhhH
Q 011538 359 DLILSEREA 367 (483)
Q Consensus 359 rLiLS~K~~ 367 (483)
++.+|+|++
T Consensus 160 ~I~lt~k~~ 168 (179)
T TIGR00448 160 KIGLTMRQP 168 (179)
T ss_pred eEEEEeccC
Confidence 899999976
No 149
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.82 E-value=5.8e-06 Score=81.83 Aligned_cols=88 Identities=22% Similarity=0.283 Sum_probs=78.6
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~ 449 (483)
-.+++++|-+.|.+|.+.|+||.+..+ +++|++-.||||..|+.++....++|..=.|.|+.+| +++.|.||.+...+
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 457899999999999999999999543 7999999999999999999999999999999999998 89999999999988
Q ss_pred CcCccccccc
Q 011538 450 EPGLFVSDKE 459 (483)
Q Consensus 450 dPw~~l~~k~ 459 (483)
+--...++++
T Consensus 93 ed~~kC~Er~ 102 (304)
T KOG2916|consen 93 EDKEKCEERF 102 (304)
T ss_pred HHHHHHHHHH
Confidence 7665555443
No 150
>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=97.64 E-value=0.00037 Score=58.77 Aligned_cols=74 Identities=26% Similarity=0.409 Sum_probs=59.1
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
|.+++||+|-|+|+.+..+...|||+....|+||..++...
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga--------------------------------------- 42 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA--------------------------------------- 42 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc---------------------------------------
Confidence 56789999999999999999999999888999887654211
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~ 280 (483)
..+.++.+++||.|.|+|...+.+..+.||...
T Consensus 43 tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~ 75 (86)
T cd05790 43 TKRNRPNLNVGDLVYARVVKANRDMEPELSCVD 75 (86)
T ss_pred cccccccCCCCCEEEEEEEecCCCCCeEEEEeC
Confidence 011246789999999999987777778888754
No 151
>PRK05054 exoribonuclease II; Provisional
Probab=97.60 E-value=0.00024 Score=79.88 Aligned_cols=71 Identities=14% Similarity=0.202 Sum_probs=58.3
Q ss_pred CCC--cEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--c--c--------CcccccCCCCEEEEEEEEEe-CCC
Q 011538 374 REG--TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--V--T--------SVSDLLNEGERVKVLVVKSM-FPD 438 (483)
Q Consensus 374 ~vG--~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i--~--------~~~~~~kvGd~VkVkVi~vd-ek~ 438 (483)
++| +.+.|.|++|+++|+||+|.+.+++||||.+.+..++ + . .-...|+.||+|+|+|.++| +++
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 455 5999999999999999999877899999999996531 1 0 11247999999999999998 788
Q ss_pred eEEEEE
Q 011538 439 KISLSI 444 (483)
Q Consensus 439 rI~LSL 444 (483)
+|.+++
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 888764
No 152
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.57 E-value=0.00042 Score=65.95 Aligned_cols=73 Identities=25% Similarity=0.331 Sum_probs=62.0
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCC---------ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~---------gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L 442 (483)
-++.|++|-|+|+++....+.|++.+. -..|-+|+|+.+..++.++++.|++||.|+|+|++.- ..+.|
T Consensus 61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~L 138 (188)
T COG1096 61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQL 138 (188)
T ss_pred CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEE
Confidence 578899999999999999999998431 1467899999999999999999999999999999853 45667
Q ss_pred EEec
Q 011538 443 SIAD 446 (483)
Q Consensus 443 SLK~ 446 (483)
|++.
T Consensus 139 st~~ 142 (188)
T COG1096 139 STKG 142 (188)
T ss_pred EecC
Confidence 7653
No 153
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.55 E-value=0.00022 Score=76.16 Aligned_cols=62 Identities=35% Similarity=0.568 Sum_probs=53.3
Q ss_pred CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCcc------------cccCcccccCCCCEEEEEEEEE
Q 011538 372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~~------------~i~~~~~~~kvGd~VkVkVi~v 434 (483)
...+|++|.|+|.+|.+. ||||+|+. +..||||.+++.+. +..++.+.+++||.|.|.|++-
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence 356899999999999998 99999998 79999999998753 2345567899999999999974
No 154
>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=97.53 E-value=0.00059 Score=57.63 Aligned_cols=59 Identities=10% Similarity=0.182 Sum_probs=48.0
Q ss_pred CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe
Q 011538 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd 435 (483)
+|++++|+|++++++|+||.+++ +++|+|.+.+..+..- +-...+..|+.|++||+.+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gp--l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~ 70 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGP--LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcC--ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence 58999999999999999999986 7899988877544221 22455899999999999885
No 155
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.52 E-value=0.00046 Score=54.26 Aligned_cols=61 Identities=20% Similarity=0.235 Sum_probs=37.6
Q ss_pred CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK 445 (483)
+|++...+|.+++++|+|++.+. +-+-+||.+++. ..+++||.|.|-|- .|.++|+..++|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~-~~~vlLp~~e~~--------~~~~~Gd~v~VFvY-~D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGE-GKEVLLPKSEVP--------EPLKVGDEVEVFVY-LDKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT--EEEEEEGGG--------------TTSEEEEEEE-E-TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCC-CCEEEechHHcC--------CCCCCCCEEEEEEE-ECCCCCEEEecC
Confidence 48899999999999999999887 689999999985 45999999999886 577789988876
No 156
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.49 E-value=0.0004 Score=68.53 Aligned_cols=76 Identities=24% Similarity=0.360 Sum_probs=67.4
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
..++||+|-|+|..+...+..|+|+. -+.+++|.|++.+..+ .+++..|++||.|.|+|.+++......|++|+.
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~s-p~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~ 139 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGS-PYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDE 139 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCC-ccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecC
Confidence 35789999999999999999999997 4899999999966653 577889999999999999999999999999764
Q ss_pred C
Q 011538 448 E 448 (483)
Q Consensus 448 ~ 448 (483)
.
T Consensus 140 ~ 140 (239)
T COG1097 140 G 140 (239)
T ss_pred C
Confidence 3
No 157
>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=97.48 E-value=0.00038 Score=79.07 Aligned_cols=70 Identities=16% Similarity=0.265 Sum_probs=56.8
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccc-ccc-----------CChhhhhhhcCCEEEEEEEEEECCCCc
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRV-----------NNFTELKEKVGRRMYVQITRINEDTND 359 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~-~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e~~r 359 (483)
.+.|++++|+|+++.++|+||++. |+.|++|.+++. +++ ++.... +.+||+|+|+|.++|..+++
T Consensus 625 ~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~-~~lGd~V~Vkv~~vd~~~~~ 703 (709)
T TIGR02063 625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-FRLGDRVKVRVVKADLDTGK 703 (709)
T ss_pred ccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcE-ECCCCEEEEEEEEEecccCe
Confidence 368999999999999999999996 699999999993 322 111122 37999999999999998899
Q ss_pred eeech
Q 011538 360 LILSE 364 (483)
Q Consensus 360 LiLS~ 364 (483)
+.++.
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 88763
No 158
>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=97.45 E-value=0.0008 Score=56.79 Aligned_cols=73 Identities=22% Similarity=0.116 Sum_probs=62.3
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
.++||.|-|+|+.+...+.+|+|+. -..|+||..++... .++.+..+++||-|-|||.+++......||+.+.
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 4689999999999999999999988 48999999886432 4455678999999999999988767889999873
No 159
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.44 E-value=0.00049 Score=56.09 Aligned_cols=67 Identities=21% Similarity=0.341 Sum_probs=56.5
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc---CcccccCCCCEE-EEEEEEEe-CCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT---SVSDLLNEGERV-KVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~---~~~~~~kvGd~V-kVkVi~vd-ek~rI~LSLK 445 (483)
|++|+|+|..-++.+++|++.+.|+.|++|..++|+ +.. ..-..+++||++ .+.|+ + ..+.|.||.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 789999999999999999999889999999999998 443 234559999999 89998 4 5567778765
No 160
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.44 E-value=0.00048 Score=56.16 Aligned_cols=65 Identities=23% Similarity=0.390 Sum_probs=53.4
Q ss_pred CCeEEEEEEEEECCeEEEEEC--CeEEEeeccccccccCC----hhhhhhhcCCEE-EEEEEEEECCCCceeechh
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNN----FTELKEKVGRRM-YVQITRINEDTNDLILSER 365 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~rv~~----~~~l~~~VGq~V-~vkVl~ID~e~~rLiLS~K 365 (483)
|++|+|+|....+.+++|+++ |++|++|..|+.+++.+ ++.+ .+|+++ .+-|+ +...+.+.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~kl--rvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCL--QEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhh--hcCCCccceEEE--eccccEEEEecC
Confidence 689999999999999999994 69999999999544432 2334 599999 88888 777888888865
No 161
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.43 E-value=0.00072 Score=66.73 Aligned_cols=80 Identities=21% Similarity=0.383 Sum_probs=64.8
Q ss_pred ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (483)
Q Consensus 167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~ 246 (483)
-|.++.||+|-|+|+.+...+..||||+...+++|++++..+. + ..
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~---~-------------------------------~~ 104 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRK---F-------------------------------EN 104 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccc---c-------------------------------cc
Confidence 4788999999999999999999999999999999999984321 0 00
Q ss_pred CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (483)
Q Consensus 247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~ 280 (483)
...+.++.+.+||.|.|+|...+.++.+.|++|.
T Consensus 105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~ 138 (239)
T COG1097 105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD 138 (239)
T ss_pred cccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence 0112356799999999999999999999998844
No 162
>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=97.40 E-value=0.00035 Score=58.41 Aligned_cols=61 Identities=18% Similarity=0.310 Sum_probs=42.2
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCC-----------------ceEEEEeccCcCccccc--CcccccCCCCEEEEEEEEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDS-----------------NRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~-----------------gi~GLlhiSels~~~i~--~~~~~~kvGd~VkVkVi~v 434 (483)
++|++|.|+|++|++.-|+++|-.. ...|++|.+++...... ++.+.|++||.|+|+|+++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 5899999999999998888887422 46899999998766544 4588899999999999974
No 163
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.40 E-value=0.00024 Score=67.61 Aligned_cols=72 Identities=19% Similarity=0.252 Sum_probs=57.1
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccc-cccC-----------ChhhhhhhcCCEEEEEEEEEECCCC----
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-----------NFTELKEKVGRRMYVQITRINEDTN---- 358 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~-~rv~-----------~~~~l~~~VGq~V~vkVl~ID~e~~---- 358 (483)
..|+++.|+|+++++.|++|+++.+.||++.+++. ++.. +.. ....+|+.|+++|.+++...+
T Consensus 80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~-~~i~~Gd~VrvrV~~v~~~~~~~~~ 158 (187)
T PRK08563 80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESK-RVLKVGDVVRARIVAVSLKERRPRG 158 (187)
T ss_pred cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCC-eEEcCCCEEEEEEEEEEcccCCCCC
Confidence 58999999999999999999998899999999983 3221 111 123789999999999986543
Q ss_pred -ceeechhhH
Q 011538 359 -DLILSEREA 367 (483)
Q Consensus 359 -rLiLS~K~~ 367 (483)
++.+|++.+
T Consensus 159 ~~I~ls~~~~ 168 (187)
T PRK08563 159 SKIGLTMRQP 168 (187)
T ss_pred CEEEEEecCC
Confidence 678888863
No 164
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.37 E-value=0.00075 Score=72.02 Aligned_cols=109 Identities=16% Similarity=0.241 Sum_probs=74.4
Q ss_pred CcccCCCEEEEEEEEE-cCCCcEE-EEehHH----HHHhhhHHHHHHh--hCCCeEEEEEEEEECCeEEEEE----CC--
Q 011538 253 PVVETGTVLFAEVLGR-TLSGRPL-LSTRRL----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRI----EG-- 318 (483)
Q Consensus 253 ~~~kVGd~V~v~Vi~~-d~~G~ii-LS~k~~----~~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G~fV~I----~G-- 318 (483)
+.+++||.+...+.-. ..=||+. .+.|+. ..+...+.+.+.+ +.|+++.|+|.++.+++++|++ |.
T Consensus 101 ~~~~iGD~v~~~v~~~~~~fgRiAAq~aKQvi~Qkire~ER~~i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~ 180 (449)
T PRK12329 101 DEAQLGDTVVLDVTPEQEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPE 180 (449)
T ss_pred CCCcCCCEEEEecCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcc
Confidence 4478999998766421 1235553 223332 1222233333333 6999999999999999999998 42
Q ss_pred eEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCC---CceeechhhH
Q 011538 319 LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT---NDLILSEREA 367 (483)
Q Consensus 319 i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~---~rLiLS~K~~ 367 (483)
+.|+||.+++... +. +.+|+.++|.|.+|.... -+|+|||..+
T Consensus 181 ~EaiLP~~Eqip~-----E~-y~~Gdrika~i~~V~~~~~kGpqIilSRt~p 226 (449)
T PRK12329 181 VEAELPKREQLPN-----DN-YRANATFKVFLKEVSEGPRRGPQLFVSRANA 226 (449)
T ss_pred eEEEecHHHcCCC-----Cc-CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence 8999999998321 11 269999999999997652 3799999864
No 165
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.34 E-value=0.0011 Score=63.12 Aligned_cols=73 Identities=10% Similarity=0.041 Sum_probs=56.3
Q ss_pred CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-----------cc-cCcccccCCCCEEEEEEEEEe--C-C
Q 011538 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-----------RV-TSVSDLLNEGERVKVLVVKSM--F-P 437 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-----------~i-~~~~~~~kvGd~VkVkVi~vd--e-k 437 (483)
.-.|++++|+|++++++|+||.++. .++|+|.+.|... +. .+-...+..|+.|++||+.+. + +
T Consensus 79 Pf~gEVv~g~V~~v~~~G~~v~~Gp--~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 156 (176)
T PTZ00162 79 PFKDEVLDAIVTDVNKLGFFAQAGP--LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN 156 (176)
T ss_pred cCCCCEEEEEEEEEecceEEEEeeC--eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence 4579999999999999999999986 6799999998733 11 122456999999999999885 2 2
Q ss_pred CeEEEEEecC
Q 011538 438 DKISLSIADL 447 (483)
Q Consensus 438 ~rI~LSLK~~ 447 (483)
.+...|||+-
T Consensus 157 ~~~i~T~~~~ 166 (176)
T PTZ00162 157 LFAIATINSD 166 (176)
T ss_pred cEEEEEecCC
Confidence 3455677753
No 166
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.23 E-value=0.0014 Score=55.39 Aligned_cols=34 Identities=18% Similarity=0.315 Sum_probs=31.7
Q ss_pred CCCeEEEEEEEEECCeEEEEECCeEEEeeccccc
Q 011538 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL 329 (483)
Q Consensus 296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~ 329 (483)
.|++++|+|+++++.|++|.+|.+++|++.+++.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip 34 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIP 34 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecC
Confidence 4899999999999999999999999999998883
No 167
>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=97.14 E-value=0.0019 Score=72.82 Aligned_cols=68 Identities=16% Similarity=0.352 Sum_probs=55.7
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-cccc-----------CChhhhhhhcCCEEEEEEEEEECCCCce
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL 360 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e~~rL 360 (483)
+.|+.++|+|+++.++|+||++. |++|++|.+++ ++++ ++... .+.+|++|+|+|.++|..+++|
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~-~~~lGD~V~Vki~~vd~~~~~I 649 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGK-VYRIGDRVTVKLTEVNMETRSI 649 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCc-EECCCCEEEEEEEEEecccCeE
Confidence 57999999999999999999995 69999999999 4321 11111 2379999999999999999988
Q ss_pred eec
Q 011538 361 ILS 363 (483)
Q Consensus 361 iLS 363 (483)
.++
T Consensus 650 ~f~ 652 (654)
T TIGR00358 650 IFE 652 (654)
T ss_pred EEE
Confidence 776
No 168
>PRK11642 exoribonuclease R; Provisional
Probab=97.13 E-value=0.0014 Score=75.45 Aligned_cols=70 Identities=14% Similarity=0.205 Sum_probs=57.4
Q ss_pred hCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccC-C----------hhhhhhhcCCEEEEEEEEEECCCCce
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-N----------FTELKEKVGRRMYVQITRINEDTNDL 360 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~-~----------~~~l~~~VGq~V~vkVl~ID~e~~rL 360 (483)
+.|++++|+|+++.++|+||++. +++|+||.+++ ++++. + ... .+.+||.|+|+|.++|..+++|
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 58999999999999999999995 49999999999 33211 1 011 2379999999999999999999
Q ss_pred eechh
Q 011538 361 ILSER 365 (483)
Q Consensus 361 iLS~K 365 (483)
.++.-
T Consensus 721 ~f~l~ 725 (813)
T PRK11642 721 DFSLI 725 (813)
T ss_pred EEEEe
Confidence 98874
No 169
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.09 E-value=0.0022 Score=69.67 Aligned_cols=73 Identities=16% Similarity=0.306 Sum_probs=61.7
Q ss_pred hCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA 369 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e 369 (483)
..|-+.+++|+++.+.|+||.+ .+..|++|.+|+ .+++.++.++. .+||+|.++.++.|+.. .+.+|.|+.+.
T Consensus 667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~l-evGq~I~vk~ie~d~~g-~~~ls~ralLp 741 (760)
T KOG1067|consen 667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLL-EVGQEIQVKYIERDPRG-GIMLSSRALLP 741 (760)
T ss_pred EeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHH-hhcceeEEEEEeecCcc-ceeehhhhhcC
Confidence 4677889999999999999999 468899999999 57788999885 89999999999999765 46666666543
No 170
>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=97.07 E-value=0.0016 Score=73.25 Aligned_cols=68 Identities=10% Similarity=0.198 Sum_probs=55.0
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--TRV-----T---SV--SDLLNEGERVKVLVVKSM-FPDKISL 442 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~--~~i-----~---~~--~~~~kvGd~VkVkVi~vd-ek~rI~L 442 (483)
|+.+.|+|+.++++|+||++...+++||+|.+.+.. +++ . .+ ...|+.||+|+|+|.++| ++++|.+
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 459999999999999999997668999999999965 221 1 11 126999999999999998 7778765
Q ss_pred E
Q 011538 443 S 443 (483)
Q Consensus 443 S 443 (483)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 171
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.06 E-value=0.0018 Score=54.09 Aligned_cols=67 Identities=16% Similarity=0.255 Sum_probs=58.1
Q ss_pred hCCCeEEEEEEEEECCeEEEEE--CCeEEEee-cccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLP-KAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP-~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~ 364 (483)
+.|+.+. .|+.+.+.|++|.+ -|++|+|+ .+++ .++++...++. +|....++|+++|+.+|-|-||.
T Consensus 15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll--VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL--VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh--cCCeeEEEEEEECCCCCEEEeEc
Confidence 6889998 89999999999998 25999988 9999 56777777764 99999999999999999887763
No 172
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.03 E-value=0.0019 Score=73.54 Aligned_cols=74 Identities=23% Similarity=0.363 Sum_probs=63.1
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK 439 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~r 439 (483)
.-++|+...|+|++++.+|+||.+.+.+++|++|.+.+..+++ .+....++.||.|+|++++++ ..++
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 5578999999999999999999998877999999999986432 234557999999999999997 7788
Q ss_pred EEEEEe
Q 011538 440 ISLSIA 445 (483)
Q Consensus 440 I~LSLK 445 (483)
|.+++-
T Consensus 699 i~~~~v 704 (706)
T COG0557 699 IDFELV 704 (706)
T ss_pred eEEEec
Confidence 887764
No 173
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.01 E-value=0.0038 Score=65.60 Aligned_cols=88 Identities=16% Similarity=0.114 Sum_probs=64.1
Q ss_pred cCCCCCcEEEEEEEEEeC-CeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538 168 YEPKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~-~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~ 246 (483)
+.-+.|++|.|+|.+++. +.++|++| +.+|+||.+|..|.
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip~-------------------------------------- 174 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIKG-------------------------------------- 174 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCCC--------------------------------------
Confidence 455689999999999996 46999998 69999999887653
Q ss_pred CCCCCCCcccCCCEEEEEEEEEc--CC--CcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEE
Q 011538 247 GSGPGRPVVETGTVLFAEVLGRT--LS--GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKF 304 (483)
Q Consensus 247 ~~~~~~~~~kVGd~V~v~Vi~~d--~~--G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV 304 (483)
..|++||.+.|.|.... .. -.++||+..+..- .+|.+ .+.=++.+|.|
T Consensus 175 ------E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v---~~Lfe-~EVPEI~dG~V 226 (374)
T PRK12328 175 ------EKFKVGDVVKAVLKRVKIDKNNGILIELSRTSPKFL---EALLE-LEVPEIKDGEV 226 (374)
T ss_pred ------CcCCCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH---HHHHH-HhCccccCCeE
Confidence 24789999999999843 22 3678998877532 22222 24556666654
No 174
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.84 E-value=0.0037 Score=59.38 Aligned_cols=73 Identities=14% Similarity=0.233 Sum_probs=50.2
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccC-C-------h----hhhhhhcCCEEEEEEEEEECCC--Cce
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVN-N-------F----TELKEKVGRRMYVQITRINEDT--NDL 360 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~-~-------~----~~l~~~VGq~V~vkVl~ID~e~--~rL 360 (483)
-.|++++|+|+++++.|++|.+|-+++|+|.++|.+... + + .+.....|+.|++||..+..+. ...
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~ 159 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFA 159 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEE
Confidence 489999999999999999999988999999999942210 0 0 1122256777777776664332 234
Q ss_pred eechhhH
Q 011538 361 ILSEREA 367 (483)
Q Consensus 361 iLS~K~~ 367 (483)
+.|+|++
T Consensus 160 i~T~~~~ 166 (176)
T PTZ00162 160 IATINSD 166 (176)
T ss_pred EEEecCC
Confidence 5555543
No 175
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.68 E-value=0.0022 Score=74.39 Aligned_cols=76 Identities=21% Similarity=0.256 Sum_probs=66.6
Q ss_pred CCCCCcEEEEEEEEEeCce---EEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 011538 372 NLREGTLLEGTVKKIYPYG---AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL 447 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~G---aFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~ 447 (483)
.+.+|.+|.++|++|+..- +-|.+.+ |+.|+|+.+++|...+.+|...+++||+|.+||++++ ++=.+.||+|..
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~-G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRLDC-GVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEecC-CCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 5889999999999998754 4567777 8999999999999999999999999999999999998 666777888765
Q ss_pred C
Q 011538 448 E 448 (483)
Q Consensus 448 ~ 448 (483)
.
T Consensus 1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred H
Confidence 3
No 176
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.65 E-value=0.0082 Score=64.29 Aligned_cols=89 Identities=10% Similarity=0.034 Sum_probs=64.0
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEe----CC-ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccc
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI 242 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~Vdi----G~-k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~ 242 (483)
+.-+.|++|.|+|.+++.++++|++ |. +.+|+||.+|..|.
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~---------------------------------- 193 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPN---------------------------------- 193 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCC----------------------------------
Confidence 4556899999999999999999998 33 48999998887653
Q ss_pred cccCCCCCCCCcccCCCEEEEEEEEEcC---C-CcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEE
Q 011538 243 AMSGGSGPGRPVVETGTVLFAEVLGRTL---S-GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKF 304 (483)
Q Consensus 243 ~~~~~~~~~~~~~kVGd~V~v~Vi~~d~---~-G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV 304 (483)
..|++|+.+.|.|..... . -.++||+..+..- .+|.+ .+.=++..|.|
T Consensus 194 ----------E~y~~Gdrika~i~~V~~~~~kGpqIilSRt~p~lv---~~Lfe-~EVPEI~dG~V 245 (449)
T PRK12329 194 ----------DNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLV---VYLFE-NEVPEIEEGVV 245 (449)
T ss_pred ----------CcCCCCCEEEEEEEEeecCCCCCCEEEEEcCCHHHH---HHHHH-hhCcccccCeE
Confidence 248899999999998532 2 3678998776532 22222 24555555543
No 177
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.63 E-value=0.0045 Score=71.31 Aligned_cols=92 Identities=18% Similarity=0.281 Sum_probs=64.4
Q ss_pred CCCcEEEEEEEEEeC--ceEEEEECCCceEEEEeccCcCccccc---------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538 374 REGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVT---------SVSDLLNEGERVKVLVVKSM-FPDKIS 441 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~--~GaFV~I~~~gi~GLlhiSels~~~i~---------~~~~~~kvGd~VkVkVi~vd-ek~rI~ 441 (483)
.+|.||.|+|.+|.+ .++||+|+. +..||||.+++....+. +..+.++.||.|-|.|.+-. ..+-..
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~ 115 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA 115 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCc
Confidence 489999999999987 589999998 89999999998643322 23456999999999999743 333333
Q ss_pred EEEecCCCCcCcccccccccceee--EEEEeecc
Q 011538 442 LSIADLESEPGLFVSDKEVHIIFL--FILLFNKQ 473 (483)
Q Consensus 442 LSLK~~~~dPw~~l~~k~~V~~~~--~~~~~~~~ 473 (483)
||.+- .|..+|-||+-- .++.||++
T Consensus 116 LTt~I-------SLpGRYLVLtP~~~~~IgISRK 142 (1068)
T PRK10811 116 LTTFI-------SLAGSYLVLMPNNPRAGGISRR 142 (1068)
T ss_pred eeeeE-------EecceeEEEeCCCCCcceecCC
Confidence 33332 244566666555 25566654
No 178
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.61 E-value=0.0018 Score=70.69 Aligned_cols=71 Identities=18% Similarity=0.351 Sum_probs=61.4
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~ 448 (483)
.+++.|.+++|+|.++..||+||++.. .+.||+|.++++.. ..+.+|+.+-|.+..+. +++.|.+....+.
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hhcccceeeeccccchhhhcceeecCh-hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 479999999999999999999999998 69999999999852 34899999999999986 5578777666555
No 179
>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=96.04 E-value=0.023 Score=47.53 Aligned_cols=23 Identities=39% Similarity=0.564 Sum_probs=17.9
Q ss_pred CCCCcEEEEEEEEEeCCeEEEEe
Q 011538 170 PKPGDFVIGVVVSGNENKLDVNV 192 (483)
Q Consensus 170 ik~GdiV~G~Vv~V~~~gv~Vdi 192 (483)
+++|++|.|+|+++++..++++|
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~I 24 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEI 24 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEE
Confidence 57899999999999999998877
No 180
>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=95.82 E-value=0.025 Score=60.58 Aligned_cols=57 Identities=16% Similarity=0.202 Sum_probs=46.2
Q ss_pred hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccccc-------------ccCChhhhhhhcCCEEEEEEEE
Q 011538 295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-------------RVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~-------------rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
..|.++.|+|.++.++ |+||+|+ |-.||+|.+++.. +..++.+.. .+||.|.|.|++
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l-~~G~~IlVQV~K 96 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELL-RPGQSVLVQVVK 96 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhC-cCCCEEEEEEee
Confidence 5899999999999998 9999996 5899999999831 122333433 689999999988
No 181
>PRK11712 ribonuclease G; Provisional
Probab=95.67 E-value=0.027 Score=61.48 Aligned_cols=61 Identities=30% Similarity=0.523 Sum_probs=49.5
Q ss_pred CCCCcEEEEEEEEEeC--ceEEEEECCCceEEEEeccCcCcc------------cccCcccccCCCCEEEEEEEEE
Q 011538 373 LREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~--~GaFV~I~~~gi~GLlhiSels~~------------~i~~~~~~~kvGd~VkVkVi~v 434 (483)
..+|.++.|+|.+|.| .+|||+|+. +..||+|.+++... ....+.+.++.||.|-|.|++-
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 4589999999999988 579999998 89999999997321 1123456699999999999874
No 182
>PRK05054 exoribonuclease II; Provisional
Probab=95.56 E-value=0.052 Score=61.30 Aligned_cols=67 Identities=21% Similarity=0.346 Sum_probs=51.5
Q ss_pred CCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-cc--ccC---C------hhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LS--RVN---N------FTELKEKVGRRMYVQITRINEDTNDLIL 362 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~--rv~---~------~~~l~~~VGq~V~vkVl~ID~e~~rLiL 362 (483)
|+.+.|.|+++.++|+||++. |+.||||.+.+ .. .+. + .....+.+||+|+|+|.++|..+++|.+
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 459999999999999999994 79999999988 21 110 0 0011247899999999999988888765
Q ss_pred c
Q 011538 363 S 363 (483)
Q Consensus 363 S 363 (483)
+
T Consensus 642 ~ 642 (644)
T PRK05054 642 R 642 (644)
T ss_pred E
Confidence 4
No 183
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.54 E-value=0.016 Score=57.90 Aligned_cols=71 Identities=21% Similarity=0.372 Sum_probs=64.3
Q ss_pred hhCCCeEEEEEEEEECCeEEEEE---CCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
-+.+++|-+.|..+..-|++|.+ +.+.|+|-.|+|+ +|++++..+- +||..=.|.|+++|+++|-|-||.|
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kli-rVGr~E~vvVlrVDkekGYIDLSkr 88 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLI-RVGRNEPVVVLRVDKEKGYIDLSKR 88 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHH-hcCCcceEEEEEEcCCCCceechhc
Confidence 36899999999999999999988 7899999999994 6788887776 8999999999999999999999987
No 184
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.37 E-value=0.031 Score=65.28 Aligned_cols=72 Identities=21% Similarity=0.236 Sum_probs=58.6
Q ss_pred hhCCCeEEEEEEEEECC--eE-EEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538 294 KQLNEPIEVKFTEWNTG--GL-LTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~--G~-fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~ 366 (483)
+..|.+|.++|+++..+ +| -|.+ +|++||||.+.+ +..+.+|.... .+|+.|.|+|+++|.++=.+-||.|.
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v-~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRV-KVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhh-ccCceEEEEeeeeeHhhhhhhhhhhh
Confidence 56899999999999754 44 3455 599999999999 45677777766 79999999999999887777788763
No 185
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.96 E-value=0.12 Score=49.51 Aligned_cols=105 Identities=15% Similarity=0.173 Sum_probs=68.1
Q ss_pred CCCcccCCCEEEEEEEEE--cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEECC----------
Q 011538 251 GRPVVETGTVLFAEVLGR--TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG---------- 318 (483)
Q Consensus 251 ~~~~~kVGd~V~v~Vi~~--d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~G---------- 318 (483)
+...+..|..|.+.+.+. -.+.+...|.+.... .-...+.|++|-|+|+++....+.|++-+
T Consensus 23 G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~------~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~ 96 (188)
T COG1096 23 GEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKK------TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELAT 96 (188)
T ss_pred CCCeEeECCEEEEeecccEEEcccceEEEeccCCC------CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCC
Confidence 455677788888777662 123445555554432 22446899999999999999999999833
Q ss_pred -eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 319 -LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 319 -i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
..|-+|.|+. ....++.++.+ .+|+-|+++|++.- ..+.||.+
T Consensus 97 ~~~~~ihvs~~~~~~~~~~~d~f-~~GDivrA~Vis~~---~~~~Lst~ 141 (188)
T COG1096 97 SGAADIHVSQVRDGYVEKLSDAF-RIGDIVRARVISTG---DPIQLSTK 141 (188)
T ss_pred CceeeEEEEeccccccccccccc-ccccEEEEEEEecC---CCeEEEec
Confidence 3466777777 44455555443 67777777777652 33555544
No 186
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=94.95 E-value=0.15 Score=56.32 Aligned_cols=150 Identities=14% Similarity=0.187 Sum_probs=96.9
Q ss_pred ccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccc
Q 011538 165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM 244 (483)
Q Consensus 165 ~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~ 244 (483)
-+++++..|.+-.|+|.++...|+||++...+.|+|+.+.+..
T Consensus 115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~------------------------------------- 157 (715)
T COG1107 115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG------------------------------------- 157 (715)
T ss_pred cchhhcccceeeeccccchhhhcceeecChhhhccccccccCC-------------------------------------
Confidence 3678899999999999999999999999999999888777642
Q ss_pred cCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHH------HH-----hhhHHHHHHhhCCCe--EEEEEEEEEC-
Q 011538 245 SGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLF------RK-----MAWHRVRQIKQLNEP--IEVKFTEWNT- 309 (483)
Q Consensus 245 ~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~------~~-----~~w~~L~~~~k~Gei--V~GkV~~v~k- 309 (483)
.+.+.+|+++.+.|... ...|.+-+....+. .+ .....|.+ ..|+. |+|+|+.+..
T Consensus 158 -------~~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~~~~~~ke~~r~~i~~id~--~ig~tV~I~GeV~qikqT 228 (715)
T COG1107 158 -------DPDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYREVQVEKELPRTLIDDLDE--MIGKTVRIEGEVTQIKQT 228 (715)
T ss_pred -------CCCCCCCCeEEEEeeccCCCCCccceeecCCccchhhhhhhhcccccHHHHHh--hcCceEEEEEEEEEEEEc
Confidence 12367888888888774 34465543322221 11 12233333 35554 7889998853
Q ss_pred Ce-EEEEECCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538 310 GG-LLTRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (483)
Q Consensus 310 ~G-~fV~I~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS 363 (483)
.| -+..+-.-+|++|..-+. .-++.--++ .+|+.|.+. =.++...+++.+-
T Consensus 229 ~GPTVFtltDetg~i~aAAFe~aGvRAyP~I--evGdiV~Vi-G~V~~r~g~lQiE 281 (715)
T COG1107 229 SGPTVFTLTDETGAIWAAAFEEAGVRAYPEI--EVGDIVEVI-GEVTRRDGRLQIE 281 (715)
T ss_pred CCCEEEEEecCCCceehhhhccCCcccCCCC--CCCceEEEE-EEEeecCCcEEEe
Confidence 44 334444457888877762 111111123 489988875 5667777877554
No 187
>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=94.78 E-value=0.12 Score=58.53 Aligned_cols=66 Identities=27% Similarity=0.422 Sum_probs=50.5
Q ss_pred CCeEEEEEEEEECCeEEEEE--CCeEEEeecccccc---cc-CCh--------hhhhhhcCCEEEEEEEEEECCCCceee
Q 011538 297 NEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELLS---RV-NNF--------TELKEKVGRRMYVQITRINEDTNDLIL 362 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel~~---rv-~~~--------~~l~~~VGq~V~vkVl~ID~e~~rLiL 362 (483)
|+...|.|+++.++|+||++ .|+.||||.+.+.+ .. -+. ..-.+.+|++|+++|.++|..+++|.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 45899999999999999999 47999999998822 11 010 010247899999999999988887764
No 188
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=94.58 E-value=0.058 Score=53.89 Aligned_cols=87 Identities=24% Similarity=0.376 Sum_probs=64.4
Q ss_pred ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (483)
Q Consensus 167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~ 246 (483)
-|..++||+|.|+|+.|.....-||++.+.++.++++-+.-. +|..+.-.+.|+..++
T Consensus 80 rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLP---------------------Gg~~RRk~~~DEl~MR- 137 (301)
T KOG3013|consen 80 RYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLP---------------------GGIQRRKSEEDELQMR- 137 (301)
T ss_pred hcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCC---------------------chhhhccchhhHHHHH-
Confidence 377899999999999999999999999999999988776311 1222222223444454
Q ss_pred CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (483)
Q Consensus 247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~ 281 (483)
..++.||.|.++|-..-.+|.+.|-.|..
T Consensus 138 ------~fl~egDLi~AEVQ~v~~dGs~sLhTRS~ 166 (301)
T KOG3013|consen 138 ------SFLKEGDLIVAEVQNVFHDGSLSLHTRSL 166 (301)
T ss_pred ------HHhhccCeehHHHHHhccCCeEEEEecch
Confidence 34899999999987766788888776654
No 189
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.51 E-value=0.58 Score=43.95 Aligned_cols=60 Identities=15% Similarity=0.268 Sum_probs=43.0
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEec----cCcCcccccC-------cccccCCCCEEEEEEEEEe
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHI----SNMSRTRVTS-------VSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhi----Sels~~~i~~-------~~~~~kvGd~VkVkVi~vd 435 (483)
=.|++++|+|+++...|+|+++++ ++.++.. .++....-++ -...+++|..|+++|+...
T Consensus 80 fKGEVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 80 FKGEVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred cCCcEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 369999999999999999999997 4555432 2332222222 1236899999999999874
No 190
>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=93.32 E-value=0.37 Score=41.98 Aligned_cols=32 Identities=19% Similarity=0.327 Sum_probs=28.9
Q ss_pred CCCcEEEEEEEEEeCCeEEEEeCCceeeEeec
Q 011538 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLT 202 (483)
Q Consensus 171 k~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~ 202 (483)
..|.+|.|+|.++-++-+|+|+|.|..++++.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~r 53 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKR 53 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEec
Confidence 36999999999999999999999999998653
No 191
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=93.14 E-value=0.42 Score=45.35 Aligned_cols=71 Identities=20% Similarity=0.165 Sum_probs=49.6
Q ss_pred CCCcEEEEEEEEEeCceEEEEEC--------CCceEEEEeccCcCcc--cccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIG--------DSNRSGLLHISNMSRT--RVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~--------~~gi~GLlhiSels~~--~i~~~~~~~kvGd~VkVkVi~vdek~rI~LS 443 (483)
..|+||.++|..|...-|-|+|. . ...|+||..++... .--++-+.|++||.|.|+|++..+.....|+
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~-~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LT 145 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKK-SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLT 145 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhh-hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEE
Confidence 46777777777776655555552 2 47899999988643 2235567799999999999996555566666
Q ss_pred Ee
Q 011538 444 IA 445 (483)
Q Consensus 444 LK 445 (483)
..
T Consensus 146 tA 147 (193)
T KOG3409|consen 146 TA 147 (193)
T ss_pred Ee
Confidence 54
No 192
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=91.95 E-value=0.57 Score=53.63 Aligned_cols=70 Identities=16% Similarity=0.261 Sum_probs=53.6
Q ss_pred hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccccc-ccC-Ch---------hhhhhhcCCEEEEEEEEEECCCCce
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS-RVN-NF---------TELKEKVGRRMYVQITRINEDTNDL 360 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~-rv~-~~---------~~l~~~VGq~V~vkVl~ID~e~~rL 360 (483)
...|+..+|.|+++.++|+||.+. |++|++|.+.+.. ++. +. ....+.+|+.|+++|.+++...+++
T Consensus 620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i 699 (706)
T COG0557 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKI 699 (706)
T ss_pred HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccce
Confidence 368999999999999999999995 5899999999942 211 00 0012368999999999998877776
Q ss_pred eec
Q 011538 361 ILS 363 (483)
Q Consensus 361 iLS 363 (483)
.++
T Consensus 700 ~~~ 702 (706)
T COG0557 700 DFE 702 (706)
T ss_pred EEE
Confidence 654
No 193
>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=91.65 E-value=0.79 Score=41.20 Aligned_cols=60 Identities=18% Similarity=0.222 Sum_probs=43.0
Q ss_pred CCCeEEEEEEEEECCeEEEEECCe-EEEeeccccc--cccC-----------ChhhhhhhcCCEEEEEEEEEEC
Q 011538 296 LNEPIEVKFTEWNTGGLLTRIEGL-RAFLPKAELL--SRVN-----------NFTELKEKVGRRMYVQITRINE 355 (483)
Q Consensus 296 ~GeiV~GkV~~v~k~G~fV~I~Gi-~gFVP~Sel~--~rv~-----------~~~~l~~~VGq~V~vkVl~ID~ 355 (483)
.|+++.|+|.+.++.|+.|.++-. +.|||.+.|. .... .-.++....|+.|+|||.++.-
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 699999999999999999999653 6899988882 1111 2233444689999999988853
No 194
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=91.02 E-value=0.3 Score=53.55 Aligned_cols=62 Identities=31% Similarity=0.458 Sum_probs=51.9
Q ss_pred CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCcccccCc-----ccccCCCCEEEEEEEEEe
Q 011538 372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRTRVTSV-----SDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~~~i~~~-----~~~~kvGd~VkVkVi~vd 435 (483)
...+|.++.|+|++|.|. .+||+|+. +-.||+|.+++.+ ++..+ ...++.||.+-|.|++-.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~-~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGL-ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccC-CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 345899999999999884 68999998 7999999999988 44333 458999999999998753
No 195
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=90.81 E-value=1.1 Score=42.68 Aligned_cols=76 Identities=24% Similarity=0.293 Sum_probs=52.2
Q ss_pred CCCCcEEEEEEEEEeCCeEEEEe---CC-----ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538 170 PKPGDFVIGVVVSGNENKLDVNV---GA-----DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (483)
Q Consensus 170 ik~GdiV~G~Vv~V~~~gv~Vdi---G~-----k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~ 241 (483)
+..|+||.++|.+++...+-|+| |. ...|+|+..++.+. | +|. +.+
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t---E---------kdr--------v~v------ 119 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT---E---------KDR--------VKV------ 119 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc---c---------cch--------hhh------
Confidence 56799999999999998877665 43 35687777776432 0 111 111
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538 242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (483)
Q Consensus 242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~ 281 (483)
-.-|++||.|.|.|++.....+..||..+.
T Consensus 120 ----------~ksFrPgDiVlAkVis~~~~~~y~LTtAen 149 (193)
T KOG3409|consen 120 ----------YKSFRPGDIVLAKVISLGDGSNYLLTTAEN 149 (193)
T ss_pred ----------hhccCCCcEEEEEEeecCCCCcEEEEEecc
Confidence 134889999999999855556677876543
No 196
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=90.60 E-value=1 Score=42.35 Aligned_cols=34 Identities=21% Similarity=0.176 Sum_probs=29.5
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCeEEEeecccc
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel 328 (483)
-.|++++|+|+++++.|+|+++|.++.|+-...+
T Consensus 80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ 113 (170)
T KOG3298|consen 80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLK 113 (170)
T ss_pred cCCcEEEEEEEEEeeeeEEEeccceEeeeecccC
Confidence 3799999999999999999999999988764443
No 197
>PRK11712 ribonuclease G; Provisional
Probab=89.99 E-value=0.8 Score=50.25 Aligned_cols=58 Identities=19% Similarity=0.336 Sum_probs=44.4
Q ss_pred hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeeccccccc-------------cCChhhhhhhcCCEEEEEEEEE
Q 011538 295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSR-------------VNNFTELKEKVGRRMYVQITRI 353 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~r-------------v~~~~~l~~~VGq~V~vkVl~I 353 (483)
..|.++.|+|.++.++ ++||+|| +-.||+|.+++... ..+..++. ..||.|-|.|.+-
T Consensus 37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l-~~Gq~iLVQV~Ke 110 (489)
T PRK11712 37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELV-RQGQDIMVQVVKD 110 (489)
T ss_pred ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhc-cCCCEEEEEEEeC
Confidence 4899999999999996 8999997 68999999987210 11122333 6799999998874
No 198
>PRK10811 rne ribonuclease E; Reviewed
Probab=89.93 E-value=0.6 Score=54.57 Aligned_cols=61 Identities=18% Similarity=0.255 Sum_probs=45.5
Q ss_pred hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccccc-ccC---------ChhhhhhhcCCEEEEEEEEEECC
Q 011538 295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-RVN---------NFTELKEKVGRRMYVQITRINED 356 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~-rv~---------~~~~l~~~VGq~V~vkVl~ID~e 356 (483)
..|.|+.|+|.++.++ ++||+|| |..||||.++... .+. +..... ..||.|-|.|.+-...
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~L-k~GqeILVQV~KEa~g 110 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVL-REGQEVIVQIDKEERG 110 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccccccccccccc-CCCCEEEEEEeecccC
Confidence 3799999999999985 9999997 6899999998832 111 112212 5799999999885433
No 199
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=89.05 E-value=1.7 Score=37.95 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=45.9
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
..|.+|.|+|..|...-+||++++ ...+.|+..... .+.|..|.+|.+++.+.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~-KFhcVc~rp~~~-------~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGG-KFHCVCKRPAVN-------GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCC-ceeEEEeccccc-------ccccccCCEEEEEECCH
Confidence 579999999999999999999998 799999987754 35689999999998754
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=88.06 E-value=3.2 Score=37.30 Aligned_cols=60 Identities=17% Similarity=0.231 Sum_probs=43.8
Q ss_pred CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-------------cccCcccccCCCCEEEEEEEEEe
Q 011538 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-------------RVTSVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-------------~i~~~~~~~kvGd~VkVkVi~vd 435 (483)
+|+++.|+|++-++.|+.|.++= --+-+||.+.|... +-..-.-.+..|+.|++||.++.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgF-FddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGF-FDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECC-EEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecc-cccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 69999999999999999999963 46778888887621 11333445799999999999875
No 201
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=87.02 E-value=4.2 Score=34.53 Aligned_cols=64 Identities=17% Similarity=0.160 Sum_probs=50.1
Q ss_pred EEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD 446 (483)
Q Consensus 378 iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~ 446 (483)
.++|+|+.+.+.+.| |.+.+ |..-+.|++---.. -.-.+.+||.|+|.+-..| .++||..-.|.
T Consensus 8 e~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR~----~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMRK----HRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceee----eeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 478999999999987 68887 77888888753211 1223789999999998777 88999998885
No 202
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=85.42 E-value=4.8 Score=39.53 Aligned_cols=63 Identities=27% Similarity=0.513 Sum_probs=46.8
Q ss_pred cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (483)
Q Consensus 168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~ 247 (483)
|-+.+||.|-|.|+....+...||||....+.||.--+. +.
T Consensus 61 YiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe---------------------------------------~A 101 (230)
T KOG1004|consen 61 YIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE---------------------------------------GA 101 (230)
T ss_pred ecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeecccc---------------------------------------Cc
Confidence 667889999999999999999999998666755432221 11
Q ss_pred CCCCCCcccCCCEEEEEEEEEc
Q 011538 248 SGPGRPVVETGTVLFAEVLGRT 269 (483)
Q Consensus 248 ~~~~~~~~kVGd~V~v~Vi~~d 269 (483)
..+.++.+++||.|-|+|...+
T Consensus 102 tkrNrPnl~vGdliyakv~~a~ 123 (230)
T KOG1004|consen 102 TKRNRPNLQVGDLIYAKVVDAN 123 (230)
T ss_pred cccCCCccccccEEEEEEEecC
Confidence 1223577999999999998644
No 203
>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=84.68 E-value=5.4 Score=32.36 Aligned_cols=59 Identities=24% Similarity=0.266 Sum_probs=44.3
Q ss_pred EEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKIS 441 (483)
Q Consensus 378 iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~ 441 (483)
.+.|+|+...+.+.| |.+.+ |..-+.|++---. .-.-.+.+||.|.|.+-..+ ++++|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr----~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC-CCEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEE
Confidence 478999999999987 68887 7888888875321 11234889999999887666 666764
No 204
>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=80.42 E-value=19 Score=28.07 Aligned_cols=55 Identities=33% Similarity=0.389 Sum_probs=38.4
Q ss_pred EEEEEEEEeC---ceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCe
Q 011538 379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK 439 (483)
Q Consensus 379 v~G~V~~I~~---~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~r 439 (483)
..|+|+...+ || ||.-.+.+-+-|+|.+++.... -..+..|+.|...+.. .+++-
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g~ 58 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKGP 58 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTSE
T ss_pred CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCCC
Confidence 4799999976 44 5555553569999999998553 2568999999999986 44443
No 205
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=75.99 E-value=24 Score=36.62 Aligned_cols=113 Identities=19% Similarity=0.247 Sum_probs=73.2
Q ss_pred hCCCeEEEEEEEEEC-CeEE-EEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhhcC
Q 011538 295 QLNEPIEVKFTEWNT-GGLL-TRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLN 372 (483)
Q Consensus 295 k~GeiV~GkV~~v~k-~G~f-V~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~~~ 372 (483)
+.|.+++|+|.+-.+ +|+. +.++...-.+|.-.+ .+|..+.++|-.-| +.+.++++- .
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~~~a------------~~g~~~R~~I~a~D-----Vslal~~P~---~ 289 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKLDA------------PVGARLRIRIQARD-----VSLALQKPE---Q 289 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecCceEEEeeccCC------------CCCCcEEEEEEccc-----eEEEecCcc---c
Confidence 568899999988875 5655 344434444443222 48999999975543 666666553 2
Q ss_pred CCCCcEEEEEEEEEeCceE----EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 373 LREGTLLEGTVKKIYPYGA----QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 373 l~vG~iv~G~V~~I~~~Ga----FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
...--++.|+|+.|.+-+- +++++ |-.-+..++.++.+. -.+++||.|-|.|..+
T Consensus 290 ~SirNiLp~~v~~i~~~~~~V~v~ld~~--g~~l~Arit~~srd~-----L~l~~G~~v~AqIKsV 348 (352)
T COG4148 290 TSIRNILPGKVVGIEDDDGQVDVQLDCG--GKTLWARITPWARDE-----LALKPGQWVYAQIKSV 348 (352)
T ss_pred cchhhccceeEEEEEcCCCcEEEEEEcC--CcEEEEEccHhhHHh-----hcCCCCCeEEEEEEEE
Confidence 3344567889999876543 34444 345566677766543 2399999999999876
No 206
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=75.74 E-value=23 Score=29.00 Aligned_cols=63 Identities=21% Similarity=0.126 Sum_probs=44.6
Q ss_pred EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (483)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~ 447 (483)
.|+|+-... .|. ||...+.+-+-|+|++.+.... ...+..||.|...+.. +++++-...+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~-~~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQ-GPKGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEE-CCCCceeeEEEEC
Confidence 488888755 454 6666554689999999996432 2458999999998864 4666666665554
No 207
>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=74.07 E-value=13 Score=36.64 Aligned_cols=97 Identities=18% Similarity=0.246 Sum_probs=61.8
Q ss_pred hhccccccccCCCC--CcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538 159 GEDKVSVEYYEPKP--GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (483)
Q Consensus 159 ~~~~~~~~~~~ik~--GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv 236 (483)
-...|+...+++.. |+...|++.+..+.|..|+++ +...-+|.++|.+.+. ..++++.
T Consensus 59 l~eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~-----------g~~~Qi~-------- 118 (225)
T PF09883_consen 59 LREEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGP-----------GSPRQIR-------- 118 (225)
T ss_pred HHHHhCCCCchhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCC-----------CCHHHHH--------
Confidence 44555655566666 999999999999999999987 6777788899877641 1222221
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHH
Q 011538 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR 289 (483)
Q Consensus 237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~ 289 (483)
...+ +=.--.|+++|+..+......+|-++......|.+
T Consensus 119 ------~rFG--------~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~ 157 (225)
T PF09883_consen 119 ------RRFG--------LVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTR 157 (225)
T ss_pred ------HHhC--------cccCCceEEEEEEcccCcccccCHHHHHHHHHHhh
Confidence 0011 01123456677764444556777777776666664
No 208
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=73.49 E-value=4.4 Score=44.55 Aligned_cols=44 Identities=20% Similarity=0.205 Sum_probs=37.6
Q ss_pred cccccCCCCCcEEEEEEEEEeCC--eEEEEeCCceeeEeecccccc
Q 011538 164 SVEYYEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP 207 (483)
Q Consensus 164 ~~~~~~ik~GdiV~G~Vv~V~~~--gv~VdiG~k~~G~lp~sEl~~ 207 (483)
+.......+|++..|+|.+|.++ .+|||+|....||+|++++.+
T Consensus 29 e~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~ 74 (487)
T COG1530 29 ERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP 74 (487)
T ss_pred ecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccch
Confidence 33445566899999999999996 589999999999999999975
No 209
>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=73.17 E-value=10 Score=30.18 Aligned_cols=64 Identities=19% Similarity=0.282 Sum_probs=42.6
Q ss_pred CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
|+.++-+|..+++.|--+--++ .+.|+. +.-.|+..-...+.+||++++.|+.+| -+-.+.+||
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 GDQLKLVVQDVTEDGSVMFSGG-QVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecC-CcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 5677778888877775544444 356652 222333334566889999999999998 555666664
No 210
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=72.66 E-value=25 Score=29.13 Aligned_cols=65 Identities=23% Similarity=0.249 Sum_probs=48.4
Q ss_pred CcEEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538 376 GTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (483)
Q Consensus 376 G~iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK 445 (483)
...+.|+|....+.+-| |.+.+ |..-+.|++---.. -.-.+.+||.|.|.....+ ++++|..-.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 45678999999998876 88887 78888888763322 1234889999999998876 6778776554
No 211
>PRK15464 cold shock-like protein CspH; Provisional
Probab=70.44 E-value=33 Score=27.80 Aligned_cols=56 Identities=25% Similarity=0.299 Sum_probs=40.4
Q ss_pred EEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCe
Q 011538 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK 439 (483)
Q Consensus 379 v~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~r 439 (483)
+.|+|+.... .|. ||.-.+.+-+-|+|++.+.... ...+.+||.|...|.. +.++.
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~-~~kG~ 62 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVN-GLRGP 62 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC----CCCCCCCCEEEEEEEE-CCCCc
Confidence 4799999865 554 7777654679999999996432 2358999999998864 34443
No 212
>PRK15463 cold shock-like protein CspF; Provisional
Probab=68.39 E-value=21 Score=28.87 Aligned_cols=51 Identities=25% Similarity=0.352 Sum_probs=38.2
Q ss_pred EEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 379 v~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
+.|+|+.... .|. ||.-.+.+-+-|+|++.+.... ...+.+||.|...+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g----~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD----AEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC----CCCCCCCCEEEEEEEE
Confidence 4799999865 554 7767554679999999997432 2358899999998764
No 213
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=67.88 E-value=18 Score=30.72 Aligned_cols=62 Identities=10% Similarity=0.198 Sum_probs=43.0
Q ss_pred CeEEEEEEEEECCeEE-EEE-CCeE--EEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538 298 EPIEVKFTEWNTGGLL-TRI-EGLR--AFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (483)
Q Consensus 298 eiV~GkV~~v~k~G~f-V~I-~Gi~--gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K 365 (483)
-.++|+|+...+++.| |.+ +|.. |.++-.--..++. + .+|+.|.+.+.-.|..+++|+.-.+
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIr----I--l~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIR----I--LAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEE----e--cCCCEEEEEECcccCCceeEEEEec
Confidence 3589999999999877 677 4644 4443221111221 1 5899999999999998888877655
No 214
>PRK14998 cold shock-like protein CspD; Provisional
Probab=66.20 E-value=46 Score=27.11 Aligned_cols=62 Identities=21% Similarity=0.118 Sum_probs=42.9
Q ss_pred EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD 446 (483)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~ 446 (483)
.|+|+-... .|. ||.-.+.+-+-|+|+|.+.... ...+..||.|...+.. +++++....+..
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~-~~~G~~A~~V~~ 66 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQ-GPKGNHASVIVP 66 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC----CCCCCCCCEEEEEEEE-CCCCceeEEEEE
Confidence 488888755 454 6766554689999999986432 2458999999998875 455655444443
No 215
>PRK09890 cold shock protein CspG; Provisional
Probab=66.01 E-value=54 Score=26.36 Aligned_cols=56 Identities=20% Similarity=0.274 Sum_probs=39.2
Q ss_pred EEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCe
Q 011538 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK 439 (483)
Q Consensus 379 v~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~r 439 (483)
+.|+|+...+ .|. ||.-.+.+-+-|+|++.+....+ ..+.+||.|...+.. .+++.
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~-~~~G~ 62 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ-GQRGP 62 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 4799999864 443 66665535799999999874422 358899999997754 34443
No 216
>PRK10943 cold shock-like protein CspC; Provisional
Probab=65.87 E-value=51 Score=26.44 Aligned_cols=52 Identities=23% Similarity=0.310 Sum_probs=38.2
Q ss_pred EEEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 378 LLEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 378 iv~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
.+.|+|+.... .|. ||.-.+.+-+-|+|++.+.... ...+..||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC----CCCCCCCCEEEEEEEE
Confidence 46799999865 454 6666543679999999996432 1458899999998764
No 217
>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=65.27 E-value=42 Score=26.00 Aligned_cols=56 Identities=27% Similarity=0.261 Sum_probs=38.9
Q ss_pred EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeE
Q 011538 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKI 440 (483)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI 440 (483)
.|+|+...+ .|. ||...+.+-+-|+|.+++...- ...+++||.|...+..- +++..
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~-~~g~~ 59 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG-DKGPQ 59 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC-CCCCe
Confidence 588888866 332 5555543679999999997431 35689999999988743 44433
No 218
>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=64.70 E-value=24 Score=28.62 Aligned_cols=57 Identities=14% Similarity=0.238 Sum_probs=39.3
Q ss_pred eEEEEEEEEECCeEE-EEE-CCeE--EEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCcee
Q 011538 299 PIEVKFTEWNTGGLL-TRI-EGLR--AFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLI 361 (483)
Q Consensus 299 iV~GkV~~v~k~G~f-V~I-~Gi~--gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLi 361 (483)
.+.|+|++..++|.| |.+ +|.. |.++-.--..++. + ..|+.|.+.+...|..+++|+
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 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIR----I--LPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEE----E--CCCCEEEEEECcccCCcEeEE
Confidence 578999999999877 677 4644 4444322111211 1 589999999988888887775
No 219
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=59.55 E-value=14 Score=34.23 Aligned_cols=54 Identities=17% Similarity=0.283 Sum_probs=46.4
Q ss_pred CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe
Q 011538 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd 435 (483)
-.|..|.|+|-.|...-+|+++++ ...+.+....+. .+.|..|-.|..|+++..
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~-KFhcVC~rP~~n-------~e~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGG-KFHCVCKRPALN-------GEAYQKGARVRLRLIDLE 134 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCC-eEEEEEcCcCcC-------HHHhhcCceEEEEEcChh
Confidence 468899999999999999999998 789999887764 466899999999998653
No 220
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=58.45 E-value=24 Score=32.68 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=35.2
Q ss_pred chhhhcccccc-cc--CCCCCcEEEEEEEEEeCCeEEEEeCCceeeEee
Q 011538 156 DKVGEDKVSVE-YY--EPKPGDFVIGVVVSGNENKLDVNVGADLLGTML 201 (483)
Q Consensus 156 ~~~~~~~~~~~-~~--~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp 201 (483)
+..|+.++--+ +- ..-.|.+|.|+|.++-.+-+|+|.|.+...+..
T Consensus 63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~ 111 (173)
T KOG4078|consen 63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCK 111 (173)
T ss_pred hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEc
Confidence 46788766433 21 233599999999999999999999999888654
No 221
>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=57.45 E-value=66 Score=24.92 Aligned_cols=48 Identities=21% Similarity=0.221 Sum_probs=36.4
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
-++|+|..+.+..+.++.++.|..-+++.+.+ ..+..++.+++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~---------~~l~~~~~v~l~t~~~ 51 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL---------SELPEGGEVKLYTYLI 51 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHH---------HTS-TTSEEEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchH---------HhCCCCCEEEEEEEEE
Confidence 47899999999999999998788888877765 3466677777766544
No 222
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=57.20 E-value=68 Score=27.37 Aligned_cols=69 Identities=19% Similarity=0.256 Sum_probs=49.4
Q ss_pred CCcEEEEEEEEEeC--ce-EEEEECCC--ceEEEEeccCcCcccccCcc-cccCCCCEEEEEEEEEe---CCCeEEEEEe
Q 011538 375 EGTLLEGTVKKIYP--YG-AQIRIGDS--NRSGLLHISNMSRTRVTSVS-DLLNEGERVKVLVVKSM---FPDKISLSIA 445 (483)
Q Consensus 375 vG~iv~G~V~~I~~--~G-aFV~I~~~--gi~GLlhiSels~~~i~~~~-~~~kvGd~VkVkVi~vd---ek~rI~LSLK 445 (483)
..-.|+|.|.+++. .| +|.+|-+. .+.+.+..+... .+. ..++.|++|.|+.- ++ ..++++|...
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~-----~i~~~~l~~G~~V~v~g~-~~~y~~~G~~sl~v~ 95 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRAR-----RIRGFDLKDGDKVLVRGR-VSFYEPRGSLSLIVE 95 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHh-----hCCCCCCCCCCEEEEEEE-EEEECCCcEEEEEEE
Confidence 57789999999976 44 68888542 356666555533 333 56899999998774 43 5688999988
Q ss_pred cCCC
Q 011538 446 DLES 449 (483)
Q Consensus 446 ~~~~ 449 (483)
++.|
T Consensus 96 ~i~P 99 (99)
T PF13742_consen 96 DIDP 99 (99)
T ss_pred EeEC
Confidence 8754
No 223
>PRK10943 cold shock-like protein CspC; Provisional
Probab=55.93 E-value=44 Score=26.83 Aligned_cols=49 Identities=16% Similarity=0.249 Sum_probs=34.9
Q ss_pred eEEEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 299 PIEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 299 iV~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
.++|+|+..+. +|++-.-+ |-+.|+|.+.+. ..... + ..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~---l--~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKT---L--AEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCC---C--CCCCEEEEEEEE
Confidence 56899999986 35554443 579999999994 22222 2 489999998655
No 224
>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=55.54 E-value=32 Score=26.28 Aligned_cols=49 Identities=20% Similarity=0.282 Sum_probs=31.8
Q ss_pred cEEEEEEEEEeCce----EEEEECCCc-eEEEEeccCcCcccccCcccccCCCCEEEEEEE
Q 011538 377 TLLEGTVKKIYPYG----AQIRIGDSN-RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (483)
Q Consensus 377 ~iv~G~V~~I~~~G----aFV~I~~~g-i~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi 432 (483)
-.+.|+|..|.+.| +.+++++.. +.+.++..... .-.+++||+|.+.+.
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 35789999999999 666667643 56666554432 123889999988764
No 225
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=54.01 E-value=57 Score=26.14 Aligned_cols=52 Identities=25% Similarity=0.350 Sum_probs=37.7
Q ss_pred EEEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 378 LLEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 378 iv~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
.+.|+|+.... .|. ||.-.+.+-+-|+|++.+.... ...+.+||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccC----CCCCCCCCEEEEEEEE
Confidence 36799999864 444 6666553679999999986432 1458899999997764
No 226
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=53.10 E-value=11 Score=38.11 Aligned_cols=75 Identities=17% Similarity=0.282 Sum_probs=58.3
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc--c--c------ccCcccccCCCCEEEEEEEEEeCCCeEE
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--T--R------VTSVSDLLNEGERVKVLVVKSMFPDKIS 441 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~--~--~------i~~~~~~~kvGd~VkVkVi~vdek~rI~ 441 (483)
.-++||+|-|+|..|...-.-|+++. ..++.+..+-+-- . | -...++.|+.||-|-|-|-++-.++.+.
T Consensus 82 ~pEvGDvVVgRV~eVq~KRWkvd~ns-k~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~s 160 (301)
T KOG3013|consen 82 APEVGDVVVGRVIEVQQKRWKVDLNS-KQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLS 160 (301)
T ss_pred CCccCCEEEEEeeeeecceeEEeccc-ccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEE
Confidence 45799999999999999999999987 6788877776531 1 1 1245678999999999998877788888
Q ss_pred EEEecC
Q 011538 442 LSIADL 447 (483)
Q Consensus 442 LSLK~~ 447 (483)
|-.+-+
T Consensus 161 LhTRS~ 166 (301)
T KOG3013|consen 161 LHTRSL 166 (301)
T ss_pred EEecch
Confidence 876643
No 227
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=49.79 E-value=63 Score=25.90 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=34.6
Q ss_pred eEEEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 299 PIEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 299 iV~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
.++|+|+..+. +|++-.-+ |-+.|+|.+.+. .... .+ ..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~---~l--~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFK---TL--AEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCC---CC--CCCCEEEEEEEE
Confidence 46799999985 46554444 479999999993 2222 22 489999998755
No 228
>CHL00010 infA translation initiation factor 1
Probab=48.43 E-value=1.3e+02 Score=24.83 Aligned_cols=67 Identities=25% Similarity=0.287 Sum_probs=39.8
Q ss_pred EEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (483)
Q Consensus 379 v~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d 450 (483)
+.|+|+++.+.|.| |.+.+ |..-.++..-- +..-.-.+.+||.|.+.+...+ .+++|..-.++...|
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGk----lr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~~~~ 77 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDN-GCQVLGYISGK----IRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNKDSN 77 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCC-CCEEEEEeccc----eecCCcccCCCCEEEEEEcccCCCeEEEEEEecCCCCC
Confidence 67999998875654 55544 33334443221 1111233789999999875443 457887777665543
No 229
>PRK15464 cold shock-like protein CspH; Provisional
Probab=48.31 E-value=58 Score=26.40 Aligned_cols=48 Identities=8% Similarity=0.032 Sum_probs=33.8
Q ss_pred EEEEEEEEEC-CeE-EEEE-C-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 300 IEVKFTEWNT-GGL-LTRI-E-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 300 V~GkV~~v~k-~G~-fV~I-~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
++|+|+-.+. .|+ |+.- + +-+.|+|++.+. ...+ .+ ..|+.|.+.|..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~---~l--~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAE---VL--IPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCC---CC--CCCCEEEEEEEE
Confidence 4799999985 343 4444 3 579999999993 2222 23 489999999755
No 230
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=48.29 E-value=91 Score=27.13 Aligned_cols=64 Identities=17% Similarity=0.083 Sum_probs=45.0
Q ss_pred CCcEEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 375 EGTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
....+.|+|+.....+.| |.+.+ |..-++|++--- .. .-.++.||.|.|.....+ .+++|..-+
T Consensus 19 ~e~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~----Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~ 84 (100)
T PRK04012 19 EEGEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGKM----KK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhh----cc-cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 445578999999999987 57776 778888876532 22 345889999999887665 445554443
No 231
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=48.26 E-value=30 Score=33.44 Aligned_cols=60 Identities=23% Similarity=0.248 Sum_probs=43.2
Q ss_pred hCCCeEEEEEEEEECCeEEEEECCe-EEEeecccccc--cc-------------C--ChhhhhhhcCCEEEEEEEEEE
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRIEGL-RAFLPKAELLS--RV-------------N--NFTELKEKVGRRMYVQITRIN 354 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I~Gi-~gFVP~Sel~~--rv-------------~--~~~~l~~~VGq~V~vkVl~ID 354 (483)
-.|+++.|+|.+-...|+-|.++-. +.|||.+-|.. +. + ...++.+-+|..|+|||.+..
T Consensus 80 F~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~ 157 (202)
T KOG3297|consen 80 FVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDES 157 (202)
T ss_pred ccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeec
Confidence 3799999999999999999988633 57888776621 11 0 124455677888888887763
No 232
>PRK15463 cold shock-like protein CspF; Provisional
Probab=47.24 E-value=64 Score=26.06 Aligned_cols=48 Identities=17% Similarity=0.172 Sum_probs=33.8
Q ss_pred EEEEEEEEEC-C--eEEEEEC-CeEEEeeccccccc-cCChhhhhhhcCCEEEEEEEE
Q 011538 300 IEVKFTEWNT-G--GLLTRIE-GLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 300 V~GkV~~v~k-~--G~fV~I~-Gi~gFVP~Sel~~r-v~~~~~l~~~VGq~V~vkVl~ 352 (483)
++|+|+..+. . |++-.-+ +-+.|+|.+.+... ... + ..|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~---l--~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEE---L--TTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCC---C--CCCCEEEEEEEE
Confidence 4799999986 3 5544433 57999999999422 222 3 489999998654
No 233
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=46.54 E-value=1.5e+02 Score=23.70 Aligned_cols=51 Identities=24% Similarity=0.355 Sum_probs=36.9
Q ss_pred EEEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 379 v~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
..|+|+...+ .|. ||.-.+.+-+-|+|++.+.... ...+.+||.|...+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence 3799998854 443 6666553579999999996432 2458999999998764
No 234
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=45.91 E-value=2.5e+02 Score=29.52 Aligned_cols=46 Identities=11% Similarity=0.045 Sum_probs=30.8
Q ss_pred ccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538 255 VETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (483)
Q Consensus 255 ~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV 314 (483)
..+|..+.++|... .+.++++++.... .--++.|+|+.+...+--|
T Consensus 265 a~~g~~~R~~I~a~----DVslal~~P~~~S----------irNiLp~~v~~i~~~~~~V 310 (352)
T COG4148 265 APVGARLRIRIQAR----DVSLALQKPEQTS----------IRNILPGKVVGIEDDDGQV 310 (352)
T ss_pred CCCCCcEEEEEEcc----ceEEEecCccccc----------hhhccceeEEEEEcCCCcE
Confidence 46899999888753 3677777664331 2236789999998765333
No 235
>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=45.74 E-value=1.5e+02 Score=29.52 Aligned_cols=81 Identities=12% Similarity=0.224 Sum_probs=55.2
Q ss_pred hhhHHHHHHhhC--CCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhh----hcCCEEEEEEEEEECCC
Q 011538 285 MAWHRVRQIKQL--NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKE----KVGRRMYVQITRINEDT 357 (483)
Q Consensus 285 ~~w~~L~~~~k~--GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~----~VGq~V~vkVl~ID~e~ 357 (483)
..|..+...++. |+++.|++.++.+-|+.++++|+..-+|.++| .-...+++.+.. -..-.|+++|++++..
T Consensus 61 eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~- 139 (225)
T PF09883_consen 61 EEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVDGIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDG- 139 (225)
T ss_pred HHhCCCCchhcccCCceEEEEEEeecccceEEEeecccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccC-
Confidence 455555444556 99999999999999999999899999999998 322233433321 1234567888888643
Q ss_pred Cceeechhh
Q 011538 358 NDLILSERE 366 (483)
Q Consensus 358 ~rLiLS~K~ 366 (483)
....+|-++
T Consensus 140 ~~~rltd~q 148 (225)
T PF09883_consen 140 IEARLTDEQ 148 (225)
T ss_pred cccccCHHH
Confidence 455666554
No 236
>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=45.66 E-value=51 Score=28.25 Aligned_cols=54 Identities=13% Similarity=0.189 Sum_probs=35.1
Q ss_pred EEEEEEEEEeCce--EEEEECCC--ceEEEEeccCcCcccccCcccccCCCCEEEEEE
Q 011538 378 LLEGTVKKIYPYG--AQIRIGDS--NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431 (483)
Q Consensus 378 iv~G~V~~I~~~G--aFV~I~~~--gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkV 431 (483)
.+.|.|.++...| +|+++-+. .+..++...+.....+.+....++.|+.|.|.=
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G 60 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTG 60 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEE
Confidence 4789999998766 89999542 356666555443232333333488999987654
No 237
>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=45.40 E-value=1.1e+02 Score=24.32 Aligned_cols=55 Identities=22% Similarity=0.140 Sum_probs=38.1
Q ss_pred EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCe
Q 011538 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK 439 (483)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~r 439 (483)
.|+|+-... .|. ||.-.+.+-+-|+|+|.+.... ...+..||.|...+.. ++++.
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~-~~~G~ 59 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQ-GPKGA 59 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEE-CCCCc
Confidence 488888754 454 6666543689999999986432 2458999999997764 34443
No 238
>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=43.58 E-value=1.5e+02 Score=22.86 Aligned_cols=48 Identities=21% Similarity=0.263 Sum_probs=33.7
Q ss_pred eEEEEEEEEECCeEEEEECC--eEEEeeccccccccCChhhhhhhcCCEEEEEEEEEEC
Q 011538 299 PIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINE 355 (483)
Q Consensus 299 iV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~ 355 (483)
.++|+|..+.+.-++++.+| .+.++|.+.+.. + ..+++++..+.-+-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~~-------l--~~~~~v~l~t~~~vr 53 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLSE-------L--PEGGEVKLYTYLIVR 53 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHHT-------S---TTSEEEEEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHHh-------C--CCCCEEEEEEEEEEe
Confidence 47999999999999999986 688999876632 1 245566666554433
No 239
>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=41.99 E-value=99 Score=25.51 Aligned_cols=58 Identities=24% Similarity=0.186 Sum_probs=40.4
Q ss_pred EEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (483)
Q Consensus 379 v~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~L 442 (483)
+.|+|+...+.+.| |.+.+ |..-++|++-=- .. .-.++.||.|.|.....+ .+++|.-
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~-g~~~la~i~gK~----rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~ 61 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD-GKKRLCRIRGKM----RK-RVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-CCEEEEEEchhh----cc-cEEEcCCCEEEEEeccccCCEEEEEE
Confidence 56899999998887 67776 677777776522 22 345889999999876554 3445543
No 240
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=41.30 E-value=83 Score=25.73 Aligned_cols=47 Identities=15% Similarity=0.216 Sum_probs=32.9
Q ss_pred EEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 301 ~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
+|+|+-.+. +|++..-+ |-+.|+|.+.+. ...+. + ..|+.|.+.+..
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~---l--~~G~~V~f~~~~ 54 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT---L--KAGQSVQFDVHQ 54 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCC---C--CCCCEEEEEEEE
Confidence 588998875 35554433 589999999994 22222 3 489999999765
No 241
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=41.02 E-value=1.2e+02 Score=25.03 Aligned_cols=47 Identities=32% Similarity=0.572 Sum_probs=32.4
Q ss_pred hCCCeEEEEEEEEECCe-EEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEEC
Q 011538 295 QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINE 355 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G-~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~ 355 (483)
+.|+..+.+|..+.+.| =...+.|+..|+|-. .+|++++++|.++-+
T Consensus 14 eeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a--------------~~Gd~V~vkI~~v~~ 61 (73)
T COG3269 14 EEGETYEVEIEDVGDQGDGIARVEGFVVFVPGA--------------EVGDEVKVKITKVKP 61 (73)
T ss_pred ccCCEEEEEEEEeccCCCceEEEEEEEEEeCCC--------------CCCCeeeEEEEEeec
Confidence 56777777777776543 122334888888843 379999999998854
No 242
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=40.55 E-value=1.6e+02 Score=26.97 Aligned_cols=53 Identities=23% Similarity=0.266 Sum_probs=32.4
Q ss_pred CCcEEEEEEEEEeCce---------EEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe
Q 011538 375 EGTLLEGTVKKIYPYG---------AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 375 vG~iv~G~V~~I~~~G---------aFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd 435 (483)
.|.+..-+|..+.+.| +.|++++ +-..+.|+.+ .+ .+.+++|++|++.+....
T Consensus 63 ~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~-~~~i~~~i~~------~~-p~~v~iGm~V~~v~~~~~ 124 (140)
T COG1545 63 EGKVETYTVVYVKPPGFSLEEPYVIAIVELEE-GGRILGQLVD------VD-PDDVEIGMKVEAVFRKRE 124 (140)
T ss_pred CeEEEEEEEEeeCCCCcccCCCEEEEEEEeCC-CCceEEEEEe------cC-cccccCCCEEEEEEEEcc
Confidence 4555555555555443 4666665 2355555554 11 245899999999998765
No 243
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=40.33 E-value=1e+02 Score=24.71 Aligned_cols=48 Identities=15% Similarity=0.201 Sum_probs=33.8
Q ss_pred EEEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 300 IEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 300 V~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
..|+|+..+. +|++-.-+ |-+.|+|.+.+. .... .+ ..|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~---~l--~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYK---SL--DEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCC---CC--CCCCEEEEEEEE
Confidence 4899999975 46654444 479999999994 2222 23 489999998655
No 244
>PRK09890 cold shock protein CspG; Provisional
Probab=38.34 E-value=1.3e+02 Score=24.24 Aligned_cols=48 Identities=13% Similarity=0.184 Sum_probs=33.8
Q ss_pred EEEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 300 IEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 300 V~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
.+|+|+..+. +|++-.-+ |-+.|+|.+.+. ..+.. + ..|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~---l--~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRT---L--NENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCC---C--CCCCEEEEEEEE
Confidence 4899999985 36555444 479999999993 22222 2 489999998644
No 245
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=37.51 E-value=2.1e+02 Score=28.89 Aligned_cols=113 Identities=14% Similarity=0.088 Sum_probs=64.0
Q ss_pred eEEEEEEEEECC--eEEEE--E--CC--eEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhh
Q 011538 299 PIEVKFTEWNTG--GLLTR--I--EG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWAT 370 (483)
Q Consensus 299 iV~GkV~~v~k~--G~fV~--I--~G--i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~ 370 (483)
.+.|+|+++..+ +..|. + ++ +.+.|...-+ +++.-.+|+.+.+.|... .+.++.-.+-
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~-------~~L~l~~G~~v~~~Ika~-----~V~l~~~~~~-- 194 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSA-------ERLGLDEGKEVLVLIKAP-----WVGITQDPAV-- 194 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHH-------hhcCCCCCCeEEEEEECC-----EEEEEcCCCC--
Confidence 689999999866 44444 3 22 4555554332 112225899999887443 3555532110
Q ss_pred cCCCCCcEEEEEEEEEeCceEEE----EECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 371 LNLREGTLLEGTVKKIYPYGAQI----RIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 371 ~~l~vG~iv~G~V~~I~~~GaFV----~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
....--.+.|+|.+|...|..+ ++++. -+...++.... . .-.+++|+.|.+.+..
T Consensus 195 -~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~-----~--~L~L~~G~~V~a~iKa 254 (263)
T PRK10676 195 -AQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEA-----A--RLSLQQGDAVTAYFNA 254 (263)
T ss_pred -CCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHH-----H--hcCCCCCCEEEEEEEc
Confidence 1233457899999998765433 33331 12333332221 1 1338999999998753
No 246
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=36.73 E-value=1e+02 Score=30.57 Aligned_cols=59 Identities=19% Similarity=0.151 Sum_probs=45.2
Q ss_pred hhCCCeEEEEEEEEECCeEEEEECC-eEEEeeccccc--cccCChhhhhhhcCCEEEEEEEEEEC
Q 011538 294 KQLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELL--SRVNNFTELKEKVGRRMYVQITRINE 355 (483)
Q Consensus 294 ~k~GeiV~GkV~~v~k~G~fV~I~G-i~gFVP~Sel~--~rv~~~~~l~~~VGq~V~vkVl~ID~ 355 (483)
-..|+.|-|.|+.....++-|+|+| -.|.+|.-... .+-+.| ++ .+|+-|.++|...++
T Consensus 63 P~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP-nl--~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP-NL--QVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC-cc--ccccEEEEEEEecCC
Confidence 3689999999999999999999988 66888876662 221222 23 599999999987754
No 247
>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=36.63 E-value=2e+02 Score=22.19 Aligned_cols=31 Identities=6% Similarity=-0.151 Sum_probs=22.5
Q ss_pred EEEEEEEEeC--CeEEEEeCC-ceeeEeeccccc
Q 011538 176 VIGVVVSGNE--NKLDVNVGA-DLLGTMLTKEVL 206 (483)
Q Consensus 176 V~G~Vv~V~~--~gv~VdiG~-k~~G~lp~sEl~ 206 (483)
++|+|...++ ..-|+.... +.+-|+|.+++.
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~ 34 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLS 34 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBC
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccc
Confidence 4799999987 445666643 347888888875
No 248
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=35.12 E-value=85 Score=26.31 Aligned_cols=34 Identities=26% Similarity=0.245 Sum_probs=26.7
Q ss_pred cccccCCCCCcEE------EEEEEEEeCCeEEEEeCCcee
Q 011538 164 SVEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLL 197 (483)
Q Consensus 164 ~~~~~~ik~GdiV------~G~Vv~V~~~gv~VdiG~k~~ 197 (483)
..-..++++||.| .|+|++++++.+.|.+..+..
T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~ 71 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTE 71 (84)
T ss_pred HHHHHhCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeE
Confidence 3445688899986 799999999999888865543
No 249
>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=34.20 E-value=1.7e+02 Score=22.10 Aligned_cols=45 Identities=22% Similarity=0.264 Sum_probs=30.0
Q ss_pred eEEEEEEEEECCe----EEEEECC---eEEEeeccccccccCChhhhhhhcCCEEEEEE
Q 011538 299 PIEVKFTEWNTGG----LLTRIEG---LRAFLPKAELLSRVNNFTELKEKVGRRMYVQI 350 (483)
Q Consensus 299 iV~GkV~~v~k~G----~fV~I~G---i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkV 350 (483)
.+.|+|..+...| +.+++++ +.+.++..... ++.-..|++|.+.|
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-------~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-------ELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-------HCT-STT-EEEEEE
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-------HcCCCCCCEEEEEE
Confidence 5789999999998 4455554 66777765542 12225899999875
No 250
>COG1278 CspC Cold shock proteins [Transcription]
Probab=34.07 E-value=1.5e+02 Score=24.09 Aligned_cols=50 Identities=32% Similarity=0.417 Sum_probs=34.3
Q ss_pred EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
.|+|+-..+ .|. |+.=.+.+-+-|+|+|.+....+ ..+..||+|...+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~----~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGF----RTLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCC----cccCCCCEEEEEEec
Confidence 467776644 343 56555524799999999864433 348899999998864
No 251
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=32.69 E-value=89 Score=27.40 Aligned_cols=35 Identities=23% Similarity=0.142 Sum_probs=28.1
Q ss_pred cccccCCCCCcEE------EEEEEEEeCCeEEEEeCCceee
Q 011538 164 SVEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLG 198 (483)
Q Consensus 164 ~~~~~~ik~GdiV------~G~Vv~V~~~gv~VdiG~k~~G 198 (483)
.....++++||.| .|+|++++++.+.|.++.+..-
T Consensus 47 ~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i 87 (106)
T PRK05585 47 KKMLSSLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEI 87 (106)
T ss_pred HHHHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEE
Confidence 4455688999998 7999999999999999766443
No 252
>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=32.65 E-value=1.3e+02 Score=28.99 Aligned_cols=48 Identities=15% Similarity=0.091 Sum_probs=39.0
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.|+.++.|+.-+++.+.++ .++.|+.|++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~---------~l~~g~~v~l~t~~~ 51 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAY---------ELNLEQKAQVFTHLV 51 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHH---------hcCCCCeEEEEEEEE
Confidence 478999999999999999987888888776653 245699999888765
No 253
>TIGR00187 ribE riboflavin synthase, alpha subunit. The name ribE was selected, from among alternatives including ribB and ribC, to match the usage in EcoCyc.
Probab=32.44 E-value=4.8e+02 Score=25.41 Aligned_cols=132 Identities=14% Similarity=0.105 Sum_probs=57.3
Q ss_pred EEEEEEECCCCceeechhhH-hhhcCCCCCcE-----EEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCccccc
Q 011538 348 VQITRINEDTNDLILSEREA-WATLNLREGTL-----LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLL 421 (483)
Q Consensus 348 vkVl~ID~e~~rLiLS~K~~-~e~~~l~vG~i-----v~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~ 421 (483)
++|.++++..+...+..+.+ .....+..|+- +-=+|.++.+....+++-+. .-..-....+.-...-|++..+
T Consensus 10 G~V~~i~~~~~~~~l~i~~~~~~~~~l~~G~SIAvnGvCLTV~~i~~~~f~vdvipE-Tl~~TtL~~l~~G~~VNLEral 88 (200)
T TIGR00187 10 AKLVSIKEKPLFISLVVNLADHMLDDLELGDSIAVNGVCLTVTEINKNHFSVDLSPE-TLKRTNLGDLKVGTWVNIERAL 88 (200)
T ss_pred EEEEEEEECCCcEEEEEEeChHHhcccccCCEEEECcEEEEEEEEcCCEEEEEEEHH-HhhhcchhhCcCCCEEEEcccC
Confidence 34455554444333333221 11235666655 23356666655555665321 0000001111122223455556
Q ss_pred CCCCEE-----------EEEEEEEe-CCC--eEEEEEecCCCCcCcccccccccceeeEEEEeecccceEEEEEe
Q 011538 422 NEGERV-----------KVLVVKSM-FPD--KISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHL 482 (483)
Q Consensus 422 kvGd~V-----------kVkVi~vd-ek~--rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~~~~~~~~~~~~~~~ 482 (483)
+.|+++ .++|+++. ... ++.+++. .++-...+..|..|.-.=-=|-++.-.++||-|.|
T Consensus 89 ~~g~rlgGH~V~GHVd~~~~i~~~~~~~~~~~~~~~~~--p~~~~~yiv~KGsIaidGvSLTV~~v~~~~f~v~l 161 (200)
T TIGR00187 89 KADGEIGGHFVSGHIDTTAEIAKIETSENNVQFWFKLQ--DSELMKYIVEKGSIAVDGISLTIGKVTETRFCVSL 161 (200)
T ss_pred CCCCccCCeeEeEEccEEEEEEEEEEcCCcEEEEEEEC--CHHHHhccccCCEEEEeeeEEEEEeEcCCEEEEEE
Confidence 666654 34555554 222 3344431 11112234444444333244555666678888765
No 254
>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=32.13 E-value=1.2e+02 Score=23.24 Aligned_cols=44 Identities=18% Similarity=0.117 Sum_probs=26.4
Q ss_pred EEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 381 G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
|++....+--.||...+.+-+-|||..+|. ...-||+|.|+++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~---------~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLN---------GAMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHT---------TS-TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHC---------CCCCCCEEEEEEec
Confidence 344433332257777654678889888874 35569999999997
No 255
>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=32.00 E-value=1.2e+02 Score=24.09 Aligned_cols=47 Identities=13% Similarity=0.144 Sum_probs=32.6
Q ss_pred EEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEE
Q 011538 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 301 ~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
+|+|+-.+. +|++..-+ |-+.|+|.|.+. ..... + ..|+.|.+.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~---l--~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRT---L--KAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCC---C--CCCCEEEEEEEE
Confidence 589999874 35554444 589999999993 22222 2 489999998654
No 256
>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=31.83 E-value=1.3e+02 Score=23.07 Aligned_cols=42 Identities=21% Similarity=0.230 Sum_probs=25.8
Q ss_pred EEEEEEECCeEEEEEC--CeEEEeeccccccccCChhhhhhhcCCEEEEEEEE
Q 011538 302 VKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 302 GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
|++....++=.||... +-+.|||..+|..- .-|++|.++++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEec
Confidence 4444444443555564 68899999988432 359999999988
No 257
>PRK14998 cold shock-like protein CspD; Provisional
Probab=31.81 E-value=1.4e+02 Score=24.34 Aligned_cols=48 Identities=15% Similarity=0.171 Sum_probs=33.2
Q ss_pred EEEEEEEEC---CeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEE
Q 011538 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRI 353 (483)
Q Consensus 301 ~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~I 353 (483)
+|+|+-.+. +|++..-+ |-+.|+|.+.+. ...+. + ..|+.|.+.+..-
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~---l--~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT---L--KAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCC---C--CCCCEEEEEEEEC
Confidence 589998875 35544443 579999999993 22222 2 4899999997653
No 258
>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=31.60 E-value=1.4e+02 Score=22.97 Aligned_cols=48 Identities=17% Similarity=0.217 Sum_probs=34.4
Q ss_pred EEEEEEEEC---CeEEEEEC-CeEEEeeccccccc-cCChhhhhhhcCCEEEEEEEEE
Q 011538 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRI 353 (483)
Q Consensus 301 ~GkV~~v~k---~G~fV~I~-Gi~gFVP~Sel~~r-v~~~~~l~~~VGq~V~vkVl~I 353 (483)
.|+|+.++. +|++..-+ |-+.|+|.+.+... .. .+ .+|+.|.+.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~---~~--~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFR---SL--EEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCC---cC--CCCCEEEEEEEEC
Confidence 588888875 46666555 78999999999432 22 22 5899999987553
No 259
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.43 E-value=2.1e+02 Score=27.68 Aligned_cols=27 Identities=26% Similarity=0.265 Sum_probs=20.9
Q ss_pred EEEEEEEEEeCCeEEEEeCC-ceeeEee
Q 011538 175 FVIGVVVSGNENKLDVNVGA-DLLGTML 201 (483)
Q Consensus 175 iV~G~Vv~V~~~gv~VdiG~-k~~G~lp 201 (483)
.+.|+|+.+.++.+.+++|. +.+-++|
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs 31 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAP 31 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeC
Confidence 57899999999999999953 4454443
No 260
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.89 E-value=1.4e+02 Score=28.95 Aligned_cols=48 Identities=17% Similarity=0.104 Sum_probs=37.9
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.|+.++.|+.-+++.+.+. .+..|+.|++.+..+
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~---------~l~~g~~v~l~t~~~ 51 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLA---------RLVEGQEAELHTRLV 51 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHHHH---------HcCCCCeEEEEEEEE
Confidence 478999999999999999887777777655442 246799999888766
No 261
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.80 E-value=1.5e+02 Score=28.75 Aligned_cols=49 Identities=12% Similarity=0.028 Sum_probs=38.8
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.++.++.|+.-+++.+.+. +..++|+.+++.+.-+
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~--------~l~~~g~~v~l~t~~~ 52 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLA--------AIGAIGDEVFLYTHLI 52 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHH--------HhccCCCeEEEEEEEE
Confidence 478999999999999999987888777765542 2236799999888765
No 262
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=30.40 E-value=63 Score=24.85 Aligned_cols=49 Identities=16% Similarity=0.272 Sum_probs=30.1
Q ss_pred cEEEEEEEEEeCceEEEEE----CCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEE
Q 011538 377 TLLEGTVKKIYPYGAQIRI----GDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (483)
Q Consensus 377 ~iv~G~V~~I~~~GaFV~I----~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi 432 (483)
-.+.|+|.++...|.++++ ++. -+.+.++.+.+. .-.+++|+.|.+.+.
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~-------~l~l~~G~~v~~~ik 60 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA-------ELGLKPGKEVYAVIK 60 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh-------hCCCCCCCEEEEEEE
Confidence 3578999999887765444 331 133344333221 234889999998775
No 263
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=30.10 E-value=4.3e+02 Score=26.61 Aligned_cols=76 Identities=12% Similarity=0.201 Sum_probs=44.4
Q ss_pred ccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE----EE-CC--eEEEeeccc
Q 011538 255 VETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT----RI-EG--LRAFLPKAE 327 (483)
Q Consensus 255 ~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV----~I-~G--i~gFVP~Se 327 (483)
+.+|+.+.+.|-. ..+.++...... ....-.+.|+|.++..+|..+ ++ +| +.+.++...
T Consensus 171 l~~G~~v~~~Ika----~~V~l~~~~~~~----------~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s 236 (263)
T PRK10676 171 LDEGKEVLVLIKA----PWVGITQDPAVA----------QAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNE 236 (263)
T ss_pred CCCCCeEEEEEEC----CEEEEEcCCCCC----------CChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHH
Confidence 5789999888753 335555322110 011237899999998776543 33 23 445555433
Q ss_pred cccccCChhhhhhhcCCEEEEEEE
Q 011538 328 LLSRVNNFTELKEKVGRRMYVQIT 351 (483)
Q Consensus 328 l~~rv~~~~~l~~~VGq~V~vkVl 351 (483)
+ +++.-.+|+.|.+.|.
T Consensus 237 ~-------~~L~L~~G~~V~a~iK 253 (263)
T PRK10676 237 A-------ARLSLQQGDAVTAYFN 253 (263)
T ss_pred H-------HhcCCCCCCEEEEEEE
Confidence 3 2222358999999864
No 264
>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=29.83 E-value=84 Score=25.44 Aligned_cols=57 Identities=11% Similarity=0.024 Sum_probs=36.4
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
...++|..+.+.=+.|.+.+++--..+|.+---.+-+..-++.+++||.+.|.++..
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~ 59 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDP 59 (69)
T ss_pred ccchhhhhhhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecC
Confidence 345667777777778888765545555554322222333357799999999988754
No 265
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=29.81 E-value=1.1e+02 Score=27.08 Aligned_cols=37 Identities=19% Similarity=0.311 Sum_probs=28.5
Q ss_pred ccccCCCCCcEE------EEEEEEEeCCeEEEEeCCceeeEee
Q 011538 165 VEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLGTML 201 (483)
Q Consensus 165 ~~~~~ik~GdiV------~G~Vv~V~~~gv~VdiG~k~~G~lp 201 (483)
.-..++++||.| .|+|++++++.+.|.++.+..-.+.
T Consensus 34 ~m~~~Lk~GD~VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~ 76 (109)
T PRK05886 34 DLHESLQPGDRVHTTSGLQATIVGITDDTVDLEIAPGVVTTWM 76 (109)
T ss_pred HHHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEE
Confidence 344678899987 6999999999999999766544433
No 266
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.50 E-value=1.8e+02 Score=28.03 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=37.7
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
.+.|+|..+.+..+.|+.++.|+.-.++.+.+. . +..|+.+++.+..
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 478999999999999999887777777765543 2 5789999988764
No 267
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=28.99 E-value=1.1e+02 Score=25.37 Aligned_cols=60 Identities=13% Similarity=0.227 Sum_probs=39.9
Q ss_pred CCeEEEEEEEEECCeEE-EEE-CCeE--EEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538 297 NEPIEVKFTEWNTGGLL-TRI-EGLR--AFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLIL 362 (483)
Q Consensus 297 GeiV~GkV~~v~k~G~f-V~I-~Gi~--gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiL 362 (483)
.-.+.|+|++...+|.| |.+ +|.. |-||-.--..++. + ..|+.|.+.....|..+++|.-
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~----I--~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIR----I--LPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEE----e--CCCCEEEEEecccccccccEEE
Confidence 45689999999998876 777 4543 4444221111111 1 5899999999998877777654
No 268
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.99 E-value=1.7e+02 Score=28.32 Aligned_cols=49 Identities=16% Similarity=0.106 Sum_probs=38.7
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.++.++.|+.-+++.+.+. ...+.|+.+++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~--------~l~~~g~~~~l~t~~~ 52 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPA--------LIGGLGQRVRVFTHLH 52 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHH--------hcccCCCeEEEEEEEE
Confidence 478999999999999999887888888766653 2235799999888765
No 269
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=28.35 E-value=1.1e+02 Score=31.29 Aligned_cols=49 Identities=29% Similarity=0.390 Sum_probs=38.6
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
...+|.+-+|.|.+..+.|.+|+||. ..++.. +..+.+|..|+++|++.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~---~~~~~l-----------~~~~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGK---DKLAKL-----------SSPAPPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecC---Ccceec-----------cCCCCCCceEEEEEEec
Confidence 46789999999999999999999986 222222 23388999999999875
No 270
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.97 E-value=1.9e+02 Score=28.17 Aligned_cols=48 Identities=15% Similarity=-0.013 Sum_probs=37.5
Q ss_pred EEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.|+.+|.|+.-.++.+.+. .+..|+.+++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~~---------~l~~g~~v~l~t~~~ 51 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCLA---------ELRLLEDVEILTYLH 51 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHHH---------hcCCCCcEEEEEEEE
Confidence 478999999999999999987787777765542 235799998887644
No 271
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.75 E-value=2.7e+02 Score=26.85 Aligned_cols=27 Identities=15% Similarity=0.154 Sum_probs=21.0
Q ss_pred EEEEEEEEEeCCeEEEEeC-CceeeEee
Q 011538 175 FVIGVVVSGNENKLDVNVG-ADLLGTML 201 (483)
Q Consensus 175 iV~G~Vv~V~~~gv~VdiG-~k~~G~lp 201 (483)
.+.|+|+.+.++.+.++++ -+.+-++|
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s 31 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMP 31 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeC
Confidence 5789999999999999995 34555444
No 272
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.80 E-value=1.7e+02 Score=28.04 Aligned_cols=48 Identities=13% Similarity=0.238 Sum_probs=37.4
Q ss_pred EEEEEEEEEeCceEEEE-ECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQIR-IGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (483)
Q Consensus 378 iv~G~V~~I~~~GaFV~-I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v 434 (483)
.+.|+|..+.+..+.|+ .+|.|+.-+++.+.+. .+..|+.|+..+.-+
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~~~~~~---------~l~~g~~v~l~t~~~ 52 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFISLFCSA---------KIQKGEKHELFITQI 52 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEecHHHHH---------HcCCCCeEEEEEEEE
Confidence 47899999999999998 5877787777765542 246899999888655
No 273
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=26.70 E-value=91 Score=30.23 Aligned_cols=46 Identities=17% Similarity=0.136 Sum_probs=36.8
Q ss_pred cccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccc
Q 011538 162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (483)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~ 207 (483)
.+...+..+-.|+++.|+|......|+-|.+|.--+-++|..-|.+
T Consensus 71 ~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~ 116 (202)
T KOG3297|consen 71 WFRVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPE 116 (202)
T ss_pred EEEEEEEecccceEEEEEeecCCccceEEEEEeeeceeechhhCCC
Confidence 4455556777899999999999999999999976677777666543
No 274
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=26.20 E-value=3.8e+02 Score=27.56 Aligned_cols=70 Identities=14% Similarity=0.203 Sum_probs=36.1
Q ss_pred CCCeEEEEEEEEE-CCeEEEEECC-eEEEeecccccc--ccC--ChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh
Q 011538 296 LNEPIEVKFTEWN-TGGLLTRIEG-LRAFLPKAELLS--RVN--NFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA 369 (483)
Q Consensus 296 ~GeiV~GkV~~v~-k~G~fV~I~G-i~gFVP~Sel~~--rv~--~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e 369 (483)
.--++.|+|..+. .-|-+|.-+. +--++|.+.++- .+. +...+ ++|+.+.+++ +.
T Consensus 211 I~AP~dG~V~~~~~~~G~~V~~g~~l~~I~~~~~l~v~~~v~e~~~~~v--~~Gq~v~i~~---~~-------------- 271 (346)
T PRK10476 211 VRAPFDGRVVGLKVSVGEFAAPMQPIFTLIDTDHWYAIANFRETDLKNI--RVGDCATVYS---MI-------------- 271 (346)
T ss_pred EECCCCcEEEeeecCCCCCcCCCCeEEEEecCCCEEEEEEEcHHHHhhC--CCCCEEEEEE---ec--------------
Confidence 3347888888864 3354443321 222333333321 110 11112 4798888764 21
Q ss_pred hcCCCCCcEEEEEEEEEeC
Q 011538 370 TLNLREGTLLEGTVKKIYP 388 (483)
Q Consensus 370 ~~~l~vG~iv~G~V~~I~~ 388 (483)
.+|..+.|+|..|.+
T Consensus 272 ----~~~~~~~G~V~~Is~ 286 (346)
T PRK10476 272 ----DRGRPFEGKVDSIGW 286 (346)
T ss_pred ----CCCceEEEEEEEECC
Confidence 135677888888866
No 275
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. 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
Probab=26.11 E-value=2.8e+02 Score=22.20 Aligned_cols=50 Identities=16% Similarity=0.118 Sum_probs=32.0
Q ss_pred EEEEEEEEEeCce--EEEEECC-Cc---eEEEEeccCcCcccccCcccccCCCCEEEEEE
Q 011538 378 LLEGTVKKIYPYG--AQIRIGD-SN---RSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431 (483)
Q Consensus 378 iv~G~V~~I~~~G--aFV~I~~-~g---i~GLlhiSels~~~i~~~~~~~kvGd~VkVkV 431 (483)
.+.|.|.++...| +|+.|.+ ++ +..++..+...+. . -..++.|+.|.+.=
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~---~-~~~l~~gs~V~v~G 58 (82)
T cd04318 3 TVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFK---E-ILKLSTGSSIRVEG 58 (82)
T ss_pred EEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHH---H-HhcCCCceEEEEEE
Confidence 4789999997754 7999933 22 6667765543211 1 23478888887643
No 276
>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=26.10 E-value=2.7e+02 Score=26.82 Aligned_cols=51 Identities=12% Similarity=0.133 Sum_probs=38.9
Q ss_pred eEEEEEEEEECCeEEEEECC--eEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCC
Q 011538 299 PIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTN 358 (483)
Q Consensus 299 iV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~ 358 (483)
.+.|+|..+.+..++++.+| ++.++|.+.+.. + ..|+.+++.+..+-+++.
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~~-------l--~~g~~v~l~t~~~vred~ 56 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYE-------L--NLEQKAQVFTHLVVREDA 56 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh-------c--CCCCeEEEEEEEEEecCC
Confidence 57999999999999999986 678888776631 2 248888888777655543
No 277
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=25.64 E-value=3.5e+02 Score=22.57 Aligned_cols=60 Identities=17% Similarity=0.091 Sum_probs=39.8
Q ss_pred cEEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538 377 TLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (483)
Q Consensus 377 ~iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~L 442 (483)
..+.|+|++....+.| |.+.+ |..-++|++--- .+ .-.++.||.|.|.....+ .+++|..
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK~----Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~ 66 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-GKERLARIPGKM----RK-KVWIRRGDIVLVDPWDFQDVKADIIY 66 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEchhh----cc-cEEEcCCCEEEEEecCCCCCEEEEEE
Confidence 3467999999998887 57666 677787776522 22 344889999988765443 3344433
No 278
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.47 E-value=3e+02 Score=26.66 Aligned_cols=26 Identities=23% Similarity=0.294 Sum_probs=20.1
Q ss_pred EEEEEEEEEeCCeEEEEeCC-ceeeEe
Q 011538 175 FVIGVVVSGNENKLDVNVGA-DLLGTM 200 (483)
Q Consensus 175 iV~G~Vv~V~~~gv~VdiG~-k~~G~l 200 (483)
.+.|+|+.+.++.+.|+++. +.+-++
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~v 30 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQC 30 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEc
Confidence 47899999999999999853 444443
No 279
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.43 E-value=5.6e+02 Score=25.54 Aligned_cols=108 Identities=9% Similarity=0.020 Sum_probs=0.0
Q ss_pred EEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHh---------hCCCeEEEEEEEEECCeEEEEEC-CeE------EEe
Q 011538 260 VLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIK---------QLNEPIEVKFTEWNTGGLLTRIE-GLR------AFL 323 (483)
Q Consensus 260 ~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~---------k~GeiV~GkV~~v~k~G~fV~I~-Gi~------gFV 323 (483)
.+++. ++.+.+.-..+++.-.+.+.+-+.+.+.+ +.|+++-|+.....+-|+-+.++ |+. +++
T Consensus 31 ~vk~e-isvt~~~w~~itleGed~e~sanli~eefgei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalv 109 (247)
T COG4044 31 DVKVE-ISVTKKQWAKITLEGEDEEVSANLIVEEFGEIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALV 109 (247)
T ss_pred eEEEE-EEeecccceEEEEECccHHHHHHHHHHHhCCCCccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccc
Q ss_pred ecccc-ccccCCh-----hhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538 324 PKAEL-LSRVNNF-----TELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (483)
Q Consensus 324 P~Sel-~~rv~~~-----~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~ 368 (483)
|.-++ ...-..+ +.+-.-..-.+++.|.++|+..+.|-+-....|
T Consensus 110 ply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~EIea~ltd~q 160 (247)
T COG4044 110 PLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQEIEARLTDKQ 160 (247)
T ss_pred cHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhhhhhhhhhHHH
No 280
>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=25.42 E-value=3.3e+02 Score=22.48 Aligned_cols=59 Identities=14% Similarity=0.148 Sum_probs=39.7
Q ss_pred EEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE-e-CCCeEEEE
Q 011538 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-M-FPDKISLS 443 (483)
Q Consensus 379 v~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v-d-ek~rI~LS 443 (483)
.-|+|++..+.+.| |.+.+ |..-++|++---.. .--++.||.|.|..... + .+++|..-
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~Rk-----~iwI~~GD~VlV~~~~~~~~~kg~Iv~r 63 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-GQRRLVSIPGKLRK-----NIWIKRGDFLIVDPIEEGEDVKADIIFV 63 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-CCEEEEEEchhhcc-----CEEEcCCCEEEEEecccCCCceEEEEEE
Confidence 35889999998887 67776 77888877653221 13488999999877665 2 34444433
No 281
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=24.29 E-value=5.9e+02 Score=26.97 Aligned_cols=72 Identities=14% Similarity=0.231 Sum_probs=40.2
Q ss_pred hCCCeEEEEEEEEE-CCeEEEEEC-CeEEEeeccccccccC----ChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538 295 QLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPKAELLSRVN----NFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (483)
Q Consensus 295 k~GeiV~GkV~~v~-k~G~fV~I~-Gi~gFVP~Sel~~rv~----~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~ 368 (483)
..--++.|+|..+. .-|-+|.-+ .+--++|.+.+|-... +...+ ++|+.+.+++-.
T Consensus 217 ~I~AP~dG~V~~~~v~~G~~V~~g~pl~~Iv~~~~l~V~a~v~E~~l~~v--~~Gq~V~I~~da---------------- 278 (390)
T PRK15136 217 KIVSPMTGYVSRRSVQVGAQISPTTPLMAVVPATNLWVDANFKETQLANM--RIGQPATITSDI---------------- 278 (390)
T ss_pred EEECCCCeEEEEEecCCCCEeCCCCeEEEEEeCCcEEEEEecCHHHHhcC--CCCCEEEEEEec----------------
Confidence 45557788888875 346555443 2444566666642211 11222 589988876422
Q ss_pred hhcCCCCCcEEEEEEEEEeC
Q 011538 369 ATLNLREGTLLEGTVKKIYP 388 (483)
Q Consensus 369 e~~~l~vG~iv~G~V~~I~~ 388 (483)
+..+..+.|+|..|.+
T Consensus 279 ----~p~~~~~~G~V~~I~~ 294 (390)
T PRK15136 279 ----YGDDVVYTGKVVGLDM 294 (390)
T ss_pred ----CCCCceEEEEEEEECC
Confidence 1123467888888843
No 282
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=24.15 E-value=1.4e+02 Score=25.88 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=27.4
Q ss_pred ccccCCCCCcEE------EEEEEEEeCCeEEEEeCCceeeE
Q 011538 165 VEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLGT 199 (483)
Q Consensus 165 ~~~~~ik~GdiV------~G~Vv~V~~~gv~VdiG~k~~G~ 199 (483)
..+.++++||.| .|+|+++.++.+-|.+|.+..-.
T Consensus 39 ~ml~sL~kGD~VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~ 79 (97)
T COG1862 39 ELLNSLKKGDEVVTIGGIVGTVTKVGDDTVEIELGDGTKIK 79 (97)
T ss_pred HHHHhccCCCEEEEcCCeEEEEEEEecCcEEEEECCCeEEE
Confidence 345678899986 78999999988888888655543
No 283
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=23.01 E-value=20 Score=39.17 Aligned_cols=66 Identities=24% Similarity=0.403 Sum_probs=44.4
Q ss_pred hCCCeEEEEEEEEECCeEEEEE--CCeEEEeeccccc-cc--cC-Ch--------hhhhhhcCCEEEEEEEEEECCCCce
Q 011538 295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL-SR--VN-NF--------TELKEKVGRRMYVQITRINEDTNDL 360 (483)
Q Consensus 295 k~GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel~-~r--v~-~~--------~~l~~~VGq~V~vkVl~ID~e~~rL 360 (483)
..+....+.|..+..+|+-|++ +|.-+|||..-+. .+ +. +. .+...++|+.|.+++.+|..+.+.|
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 4667889999999999999999 7999999988772 11 10 00 0112256677777666665444433
No 284
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=22.54 E-value=1.5e+02 Score=23.30 Aligned_cols=19 Identities=26% Similarity=0.324 Sum_probs=17.3
Q ss_pred EEEEEEEEeCCeEEEEeCC
Q 011538 176 VIGVVVSGNENKLDVNVGA 194 (483)
Q Consensus 176 V~G~Vv~V~~~gv~VdiG~ 194 (483)
++|+|.++.++.+.|++..
T Consensus 16 ~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cEEEEEEEecCcEEEEEEe
Confidence 6899999999999999964
No 285
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.00 E-value=3.9e+02 Score=26.03 Aligned_cols=27 Identities=7% Similarity=0.100 Sum_probs=20.7
Q ss_pred EEEEEEEEEeCCeEEEEeC-CceeeEee
Q 011538 175 FVIGVVVSGNENKLDVNVG-ADLLGTML 201 (483)
Q Consensus 175 iV~G~Vv~V~~~gv~VdiG-~k~~G~lp 201 (483)
.+.|+|+.+.++.+.|++| .+.+-.+|
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs 31 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVS 31 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEec
Confidence 5799999999999999985 34444433
No 286
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.66 E-value=3.7e+02 Score=25.82 Aligned_cols=46 Identities=13% Similarity=0.197 Sum_probs=35.7
Q ss_pred eEEEEEEEEECCeEEEEECC--eEEEeeccccccccCChhhhhhhcCCEEEEEEEEE
Q 011538 299 PIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRI 353 (483)
Q Consensus 299 iV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~I 353 (483)
.++|+|..+....++++.+| +..++|.+.+.. + ..|+.+++.+..+
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~~-------l--~~g~~v~l~t~~~ 51 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLST-------C--KIGDNIKLYIETY 51 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh-------h--CCCCeEEEEEEEE
Confidence 58999999999999999986 577888665532 1 3799998887544
No 287
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=21.46 E-value=34 Score=28.48 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=4.0
Q ss_pred ccccccccCCCCCcEE------EEEEEEEeCCeEEEEeCCce
Q 011538 161 DKVSVEYYEPKPGDFV------IGVVVSGNENKLDVNVGADL 196 (483)
Q Consensus 161 ~~~~~~~~~ik~GdiV------~G~Vv~V~~~gv~VdiG~k~ 196 (483)
+....-..++++||-| .|+|++++++.+.|+++.+.
T Consensus 28 k~~~~m~~~Lk~Gd~VvT~gGi~G~V~~i~~~~v~lei~~g~ 69 (82)
T PF02699_consen 28 KEHQEMLASLKPGDEVVTIGGIYGTVVEIDDDTVVLEIAPGV 69 (82)
T ss_dssp HHHTTGGG----------------------------------
T ss_pred HHHHHHHHcCCCCCEEEECCcEEEEEEEEeCCEEEEEECCCe
Confidence 3444456788899987 68999999999999987643
No 288
>PF05339 DUF739: Protein of unknown function (DUF739); InterPro: IPR008003 This entry is represented by Bacteriophage bIL285, Orf5. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several bacteriophage proteins. Three of the proteins in this family have been labelled putative cro repressor proteins.; PDB: 2PH7_A.
Probab=21.45 E-value=24 Score=32.43 Aligned_cols=16 Identities=38% Similarity=0.808 Sum_probs=12.1
Q ss_pred ChhhhhhhhhcccccC
Q 011538 117 DEEEALAPFLKFFKPR 132 (483)
Q Consensus 117 ~~~~~~~~~~~~~~~~ 132 (483)
.+++-++||++||+-.
T Consensus 75 pte~~~~pfm~ff~~~ 90 (138)
T PF05339_consen 75 PTEKNPAPFMNFFREH 90 (138)
T ss_dssp E--SSSHHHHHHHHHH
T ss_pred cccccccHHHHHHHHh
Confidence 4678899999999865
No 289
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.37 E-value=3.7e+02 Score=25.90 Aligned_cols=77 Identities=18% Similarity=0.128 Sum_probs=0.0
Q ss_pred cEEEEEEEEEeCCeEEEE-e-CCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCCC
Q 011538 174 DFVIGVVVSGNENKLDVN-V-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG 251 (483)
Q Consensus 174 diV~G~Vv~V~~~gv~Vd-i-G~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~~ 251 (483)
..+.|+|+.++++.+.|+ . |-+.+-++|.+-+
T Consensus 3 ~~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~---------------------------------------------- 36 (188)
T PRK14606 3 AGISGRVLKKSGNVLLVETKSGVVFEIVCDVQTS---------------------------------------------- 36 (188)
T ss_pred ceEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHH----------------------------------------------
Q ss_pred CCcccCCCEEEEEEEE-EcCCCcEEEEehHHHHHhhhHHHHHHhhCC
Q 011538 252 RPVVETGTVLFAEVLG-RTLSGRPLLSTRRLFRKMAWHRVRQIKQLN 297 (483)
Q Consensus 252 ~~~~kVGd~V~v~Vi~-~d~~G~iiLS~k~~~~~~~w~~L~~~~k~G 297 (483)
..+.+|+++...+.- ..+++..+.-......+..|..|...--.|
T Consensus 37 -~~l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIG 82 (188)
T PRK14606 37 -EEVEEGGECFLHTFLSVSQDGITLYGFSNERKKELFLSLTKVSRLG 82 (188)
T ss_pred -HHcCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhccCCcc
No 290
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=21.14 E-value=72 Score=31.82 Aligned_cols=58 Identities=14% Similarity=0.181 Sum_probs=43.5
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe
Q 011538 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd 435 (483)
..++|+++.|+|..+.+.-+=+-|.+ -..+-+|..+++.+|. .+..||+.+++|.+.|
T Consensus 104 ~Pk~Gd~LeG~Vn~vS~sHIglLIhg-~FNASIpk~nip~dw~-----fI~md~eee~~v~ntD 161 (253)
T KOG4134|consen 104 RPKAGDILEGVVNHVSRSHIGLLIHG-VFNASIPKTNIPADWE-----FIAMDQEEEIRVKNTD 161 (253)
T ss_pred CCCCCCeeeeeeeecchhhhceeehh-hhhccCCCCCCcccee-----eecCCchhhhceeecc
Confidence 35789999999999977543333334 3578889988876553 5788999999999875
No 291
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=21.12 E-value=3.2e+02 Score=25.73 Aligned_cols=63 Identities=21% Similarity=0.152 Sum_probs=42.2
Q ss_pred CCcEEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538 375 EGTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (483)
Q Consensus 375 vG~iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL 444 (483)
.|+ +-|+|+...+.|.| |.+.+ |..-++|++---.. .-.++.||.|.|..-..+ .+++|..-+
T Consensus 31 egq-~~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GKmRK-----~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 31 EGQ-EYAQVLRMLGNGRLEAYCFD-GVKRLCHIRGKMRK-----RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred CCc-EEEEEEEEcCCCEEEEEECC-CCEEEEEeecccee-----eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 455 45999999998877 67766 77888887653222 234888999988764443 445555443
No 292
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=21.00 E-value=4.4e+02 Score=21.08 Aligned_cols=56 Identities=23% Similarity=0.241 Sum_probs=37.4
Q ss_pred cEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538 377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442 (483)
Q Consensus 377 ~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L 442 (483)
..++|+|.+|.+...-|.+.+ | ..+--..+.. -+.+++|++|.+..-.. ..+|+.=
T Consensus 3 ~~veG~I~~id~~~~titLdD-G-ksy~lp~ef~-------~~~L~~G~kV~V~yd~~-~gk~vit 58 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDD-G-KSYKLPEEFD-------FDGLKPGMKVVVFYDEV-DGKRVIT 58 (61)
T ss_pred ccceEEEEEEcCCceEEEecC-C-CEEECCCccc-------ccccCCCCEEEEEEEcc-CCcEEee
Confidence 357899999999999999987 3 2333333332 25699999987755433 3445543
No 293
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.83 E-value=4.1e+02 Score=25.53 Aligned_cols=27 Identities=4% Similarity=0.007 Sum_probs=20.2
Q ss_pred EEEEEEEEEeCCeEEEE-eC-CceeeEee
Q 011538 175 FVIGVVVSGNENKLDVN-VG-ADLLGTML 201 (483)
Q Consensus 175 iV~G~Vv~V~~~gv~Vd-iG-~k~~G~lp 201 (483)
.+.|+|..+.++.+.|| +| -+.+-++|
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~ 32 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFIS 32 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEec
Confidence 57899999999999999 43 34454443
No 294
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=20.79 E-value=3e+02 Score=20.22 Aligned_cols=47 Identities=32% Similarity=0.452 Sum_probs=28.4
Q ss_pred EEEEEEeC-ceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538 381 GTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (483)
Q Consensus 381 G~V~~I~~-~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~ 433 (483)
|+|....+ +| |+...+..-+-++|.+.+.. . ...+..||.|.+++..
T Consensus 2 G~i~~~~~g~g-fv~~~~~~~~i~v~~~~~~~-~----~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 2 GVVKWFNKGFG-FIRPDDGGKDVFVHPSQIQG-G----LKSLREGDEVEFKVVS 49 (64)
T ss_pred eEEEEEcCCee-EEecCCCCccEEEEhHHhhc-C----CCcCCCCCEEEEEEEE
Confidence 55555543 34 55444312478888776421 1 2347789999999975
No 295
>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=20.65 E-value=1.7e+02 Score=23.10 Aligned_cols=49 Identities=18% Similarity=0.159 Sum_probs=31.5
Q ss_pred EEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEE
Q 011538 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (483)
Q Consensus 378 iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi 432 (483)
.+.|+|.+....+.| |.+.+ |..-+++++--... .-.++.||.|.|.+-
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~r~-----~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGKFRK-----RIWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HHHHT-----CC---TTEEEEEEES
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceee-----eEecCCCCEEEEEec
Confidence 467999999998876 77776 67777766543111 123889999987663
No 296
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=20.35 E-value=4.2e+02 Score=21.91 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=31.2
Q ss_pred CCCCCcEEEEEEEEEeCceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe
Q 011538 372 NLREGTLLEGTVKKIYPYGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (483)
Q Consensus 372 ~l~vG~iv~G~V~~I~~~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd 435 (483)
.++.|+++.-.|..+.+.|= .-++. |..-|+|- ..+||+|+++|.++.
T Consensus 12 PVeeGe~y~V~I~d~g~~GDGiarve--GfvVFVp~--------------a~~Gd~V~vkI~~v~ 60 (73)
T COG3269 12 PVEEGETYEVEIEDVGDQGDGIARVE--GFVVFVPG--------------AEVGDEVKVKITKVK 60 (73)
T ss_pred CcccCCEEEEEEEEeccCCCceEEEE--EEEEEeCC--------------CCCCCeeeEEEEEee
Confidence 56778888888888876552 22222 23444432 457999999998874
No 297
>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=20.23 E-value=3.3e+02 Score=20.62 Aligned_cols=51 Identities=14% Similarity=0.032 Sum_probs=30.0
Q ss_pred hcCCEEEEEEEEEECCCCceeechhhH----hhhcCCCCCcEEEEEEEEEeCceEE
Q 011538 341 KVGRRMYVQITRINEDTNDLILSEREA----WATLNLREGTLLEGTVKKIYPYGAQ 392 (483)
Q Consensus 341 ~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~~~l~vG~iv~G~V~~I~~~GaF 392 (483)
.+|+.+++.|.+.. ..+..+.-...- +.......|+.+..+|++..++-++
T Consensus 3 ~~G~~~~VlVe~~~-~~g~~~gr~~~~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~ 57 (61)
T PF01938_consen 3 YVGKTLEVLVEELG-DEGQGIGRTDNGKVVFVPGGLPLIGEFVKVRITKAKKNYLF 57 (61)
T ss_dssp -TTEEEEEEEEEE--TTSEEEEEET-TEEEEETT--T--TEEEEEEEEEE-SSEEE
T ss_pred cCCcEEEEEEEEec-CCCEEEEEeCCCeEEEECCCCCCCCCEEEEEEEEeeCCcEE
Confidence 58999999999987 444443332211 1111112699999999999987665
No 298
>COG1278 CspC Cold shock proteins [Transcription]
Probab=20.17 E-value=1.7e+02 Score=23.76 Aligned_cols=47 Identities=15% Similarity=0.298 Sum_probs=31.6
Q ss_pred EEEEEEEEC---CeEEEEECC-eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEE
Q 011538 301 EVKFTEWNT---GGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITR 352 (483)
Q Consensus 301 ~GkV~~v~k---~G~fV~I~G-i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ 352 (483)
.|+|.-.+. +|++--=+| -+.|+|+|.+ ...++. | ..||+|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~---L--~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRT---L--REGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcc---c--CCCCEEEEEEec
Confidence 467776664 355443344 7999999999 444433 3 489999998754
No 299
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=20.03 E-value=2.4e+02 Score=20.93 Aligned_cols=17 Identities=24% Similarity=0.468 Sum_probs=12.1
Q ss_pred EEEEECCeEEEeecccc
Q 011538 312 LLTRIEGLRAFLPKAEL 328 (483)
Q Consensus 312 ~fV~I~Gi~gFVP~Sel 328 (483)
..+..+|..|++|.+.+
T Consensus 36 w~~~~~g~~G~~P~~~v 52 (55)
T PF07653_consen 36 WLGENNGRRGWFPSSYV 52 (55)
T ss_dssp EEEEETTEEEEEEGGGE
T ss_pred EEEEECCcEEEEcHHHE
Confidence 33444688899998865
Done!