Query 010232
Match_columns 514
No_of_seqs 354 out of 2400
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 22:35:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07400 30S ribosomal protein 100.0 1E-46 2.2E-51 387.6 32.5 281 156-480 15-300 (318)
2 COG0539 RpsA Ribosomal protein 100.0 1.2E-47 2.6E-52 411.8 26.5 281 158-504 4-300 (541)
3 PRK07899 rpsA 30S ribosomal pr 100.0 5.6E-44 1.2E-48 384.4 28.6 286 156-505 19-317 (486)
4 COG0539 RpsA Ribosomal protein 100.0 2.8E-42 6.1E-47 370.4 25.8 284 157-503 90-385 (541)
5 PRK06299 rpsA 30S ribosomal pr 100.0 8.9E-41 1.9E-45 367.6 31.2 283 156-504 12-309 (565)
6 PRK06676 rpsA 30S ribosomal pr 100.0 4.7E-40 1E-44 346.6 29.6 284 157-504 3-300 (390)
7 PRK13806 rpsA 30S ribosomal pr 100.0 3E-40 6.5E-45 357.9 28.9 282 157-505 15-316 (491)
8 TIGR00717 rpsA ribosomal prote 100.0 1.9E-38 4E-43 345.4 28.7 279 158-504 2-295 (516)
9 PRK12269 bifunctional cytidyla 100.0 3.2E-38 7E-43 358.1 30.5 312 112-505 266-602 (863)
10 PRK12269 bifunctional cytidyla 100.0 1.1E-38 2.5E-43 361.8 26.2 283 159-503 385-687 (863)
11 PRK13806 rpsA 30S ribosomal pr 100.0 4.6E-38 9.9E-43 340.8 26.9 279 163-504 106-402 (491)
12 PRK00087 4-hydroxy-3-methylbut 100.0 4.1E-37 8.9E-42 343.3 28.6 285 157-504 287-585 (647)
13 PRK06299 rpsA 30S ribosomal pr 100.0 1.2E-35 2.6E-40 326.9 26.9 281 162-504 191-483 (565)
14 TIGR00717 rpsA ribosomal prote 100.0 7.4E-35 1.6E-39 317.2 26.8 278 162-502 90-380 (516)
15 PRK07899 rpsA 30S ribosomal pr 100.0 2.2E-34 4.9E-39 310.1 30.0 248 160-451 110-369 (486)
16 PRK06676 rpsA 30S ribosomal pr 100.0 3.8E-34 8.2E-39 301.8 29.6 255 161-458 94-360 (390)
17 PRK00087 4-hydroxy-3-methylbut 100.0 9.7E-31 2.1E-35 292.2 30.3 251 161-454 378-641 (647)
18 COG2996 Predicted RNA-bindinin 100.0 4.9E-28 1.1E-32 238.3 23.2 250 169-513 2-261 (287)
19 PRK07400 30S ribosomal protein 99.9 1.1E-23 2.4E-28 217.2 18.9 190 283-502 18-217 (318)
20 COG1098 VacB Predicted RNA bin 99.7 2.6E-18 5.6E-23 151.7 5.6 81 372-453 2-82 (129)
21 PTZ00248 eukaryotic translatio 99.7 3.8E-17 8.1E-22 167.4 7.3 116 372-507 13-133 (319)
22 KOG1070 rRNA processing protei 99.7 8.9E-16 1.9E-20 175.8 16.7 244 166-448 1061-1326(1710)
23 KOG1070 rRNA processing protei 99.7 3.3E-16 7.1E-21 179.3 12.9 195 253-449 466-673 (1710)
24 PRK08582 hypothetical protein; 99.6 1.9E-14 4.1E-19 132.1 13.3 82 372-454 2-83 (139)
25 PTZ00248 eukaryotic translatio 99.6 1.3E-15 2.9E-20 156.1 2.8 136 296-433 17-172 (319)
26 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 3.8E-14 8.3E-19 116.4 8.6 70 373-443 1-74 (74)
27 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 1E-13 2.2E-18 113.0 8.5 71 373-445 1-72 (72)
28 PF00575 S1: S1 RNA binding do 99.5 2.7E-13 5.9E-18 110.0 9.8 73 372-445 1-74 (74)
29 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 3.6E-13 7.7E-18 109.9 9.7 71 374-444 2-72 (73)
30 PRK08059 general stress protei 99.4 2.5E-13 5.3E-18 122.1 8.8 105 372-499 4-109 (123)
31 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 9.2E-13 2E-17 108.3 10.3 71 372-449 1-73 (74)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 5.3E-13 1.2E-17 107.2 8.7 69 376-445 1-70 (70)
33 PLN00207 polyribonucleotide nu 99.4 3.4E-13 7.3E-18 153.5 10.2 89 372-461 750-839 (891)
34 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 6.4E-13 1.4E-17 108.8 9.0 69 376-445 1-72 (73)
35 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 5.4E-13 1.2E-17 111.2 8.6 73 371-444 10-83 (83)
36 PRK07252 hypothetical protein; 99.4 9.5E-13 2.1E-17 118.0 10.6 77 374-451 2-79 (120)
37 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 1.6E-12 3.4E-17 105.5 10.1 72 373-445 1-73 (73)
38 cd05684 S1_DHX8_helicase S1_DH 99.4 1.5E-12 3.3E-17 107.4 10.1 75 376-451 1-78 (79)
39 PRK05807 hypothetical protein; 99.4 1.5E-12 3.3E-17 119.1 10.7 75 372-448 2-76 (136)
40 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 1.6E-12 3.5E-17 104.5 8.7 68 376-444 1-69 (69)
41 cd04452 S1_IF2_alpha S1_IF2_al 99.4 2.4E-12 5.3E-17 104.8 9.8 74 373-446 1-76 (76)
42 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 2E-12 4.4E-17 105.1 8.7 68 376-444 1-71 (71)
43 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 3.6E-12 7.8E-17 103.6 9.9 74 374-447 1-75 (77)
44 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 3.4E-12 7.3E-17 102.9 9.6 72 376-448 1-73 (73)
45 cd05707 S1_Rrp5_repeat_sc11 S1 99.3 2.9E-12 6.3E-17 102.7 8.0 67 376-443 1-68 (68)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 3.1E-12 6.7E-17 102.2 8.1 67 376-443 1-69 (69)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 6.7E-12 1.4E-16 99.2 9.0 69 376-445 1-69 (69)
48 COG1093 SUI2 Translation initi 99.3 2.5E-12 5.4E-17 127.1 6.2 96 373-468 9-106 (269)
49 PHA02945 interferon resistance 99.3 1.7E-11 3.7E-16 102.8 9.3 75 373-450 9-87 (88)
50 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 1.8E-11 3.9E-16 98.4 9.1 69 376-445 1-70 (70)
51 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 2.7E-11 5.7E-16 98.0 9.2 70 373-443 1-72 (72)
52 PF00575 S1: S1 RNA binding do 99.2 4.9E-11 1.1E-15 96.7 9.7 71 294-365 2-74 (74)
53 PRK03987 translation initiatio 99.2 4.9E-11 1.1E-15 120.2 11.0 79 373-451 6-86 (262)
54 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 2.4E-11 5.1E-16 105.6 7.4 74 373-447 1-97 (100)
55 cd05685 S1_Tex S1_Tex: The C-t 99.2 3.6E-11 7.8E-16 94.8 7.8 67 376-443 1-68 (68)
56 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 4.5E-11 9.7E-16 100.1 8.5 74 373-447 4-81 (86)
57 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 1.1E-10 2.4E-15 93.3 9.8 66 297-365 1-67 (67)
58 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 7.5E-11 1.6E-15 94.6 8.4 65 376-443 1-66 (66)
59 COG2996 Predicted RNA-bindinin 99.2 4.2E-10 9.1E-15 112.1 15.2 144 168-366 69-217 (287)
60 cd04472 S1_PNPase S1_PNPase: P 99.2 1E-10 2.2E-15 92.7 8.6 68 376-444 1-68 (68)
61 smart00316 S1 Ribosomal protei 99.2 1.8E-10 3.9E-15 90.7 9.2 71 374-445 1-72 (72)
62 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 1.5E-10 3.4E-15 92.4 8.9 66 376-445 1-67 (67)
63 COG1098 VacB Predicted RNA bin 99.2 7.6E-11 1.7E-15 104.7 7.2 74 294-369 3-78 (129)
64 cd05688 S1_RPS1_repeat_ec3 S1_ 99.1 1.6E-10 3.5E-15 91.4 8.4 67 375-443 1-68 (68)
65 cd05705 S1_Rrp5_repeat_hs14 S1 99.1 1.9E-10 4.1E-15 94.5 8.5 69 294-363 1-74 (74)
66 TIGR02696 pppGpp_PNP guanosine 99.1 8.6E-11 1.9E-15 131.6 7.2 71 372-443 644-718 (719)
67 cd04453 S1_RNase_E S1_RNase_E: 99.1 3E-10 6.5E-15 96.5 8.9 72 372-444 4-81 (88)
68 PRK11824 polynucleotide phosph 99.1 5.3E-10 1.2E-14 126.6 12.2 75 372-447 618-692 (693)
69 cd04471 S1_RNase_R S1_RNase_R: 99.1 8.1E-10 1.7E-14 91.1 10.0 70 375-444 1-82 (83)
70 cd05698 S1_Rrp5_repeat_hs6_sc5 99.1 5.1E-10 1.1E-14 89.8 8.5 68 297-365 1-70 (70)
71 cd05703 S1_Rrp5_repeat_hs12_sc 99.1 6.7E-10 1.4E-14 90.9 9.2 68 297-365 1-72 (73)
72 COG2183 Tex Transcriptional ac 99.1 2.7E-10 5.8E-15 127.2 7.8 80 371-451 654-734 (780)
73 PRK09202 nusA transcription el 99.0 7.2E-10 1.6E-14 120.0 10.4 108 253-367 85-201 (470)
74 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 1.1E-09 2.5E-14 90.9 8.9 73 373-446 4-76 (82)
75 cd05694 S1_Rrp5_repeat_hs2_sc2 99.0 1.1E-09 2.4E-14 90.0 8.6 67 294-366 2-70 (74)
76 cd04473 S1_RecJ_like S1_RecJ_l 99.0 1.9E-09 4.1E-14 88.9 9.7 65 371-444 12-76 (77)
77 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.0 1.8E-09 3.9E-14 86.7 9.0 67 297-364 1-69 (69)
78 cd04461 S1_Rrp5_repeat_hs8_sc7 99.0 1.6E-09 3.5E-14 90.3 8.9 70 294-364 12-83 (83)
79 COG1185 Pnp Polyribonucleotide 99.0 1.3E-09 2.9E-14 120.0 9.2 77 371-448 615-691 (692)
80 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 1.9E-09 4.1E-14 87.1 7.7 63 376-439 1-65 (70)
81 PRK09521 exosome complex RNA-b 98.9 3.4E-09 7.4E-14 102.0 10.0 89 353-446 43-142 (189)
82 cd05687 S1_RPS1_repeat_ec1_hs1 98.9 4.8E-09 1E-13 84.2 9.0 68 297-365 1-70 (70)
83 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 3.3E-09 7.1E-14 86.3 8.1 67 297-364 1-71 (71)
84 cd05707 S1_Rrp5_repeat_sc11 S1 98.9 4E-09 8.6E-14 84.4 8.2 66 297-363 1-68 (68)
85 cd00164 S1_like S1_like: Ribos 98.9 3E-09 6.5E-14 82.2 7.1 64 379-443 1-65 (65)
86 cd05686 S1_pNO40 S1_pNO40: pNO 98.9 5.7E-09 1.2E-13 85.1 9.0 68 295-364 2-72 (73)
87 cd05706 S1_Rrp5_repeat_sc10 S1 98.9 6.1E-09 1.3E-13 84.3 9.1 70 295-365 2-73 (73)
88 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.9 4.6E-09 1E-13 84.2 8.1 64 297-363 1-66 (66)
89 cd04452 S1_IF2_alpha S1_IF2_al 98.9 9.1E-09 2E-13 83.6 9.4 71 295-366 2-76 (76)
90 cd05704 S1_Rrp5_repeat_hs13 S1 98.9 8.8E-09 1.9E-13 84.0 8.4 68 295-365 2-72 (72)
91 cd05708 S1_Rrp5_repeat_sc12 S1 98.9 1.1E-08 2.3E-13 83.1 8.9 71 296-367 2-75 (77)
92 cd04460 S1_RpoE S1_RpoE: RpoE, 98.9 1.1E-08 2.4E-13 88.3 9.2 79 377-457 1-96 (99)
93 cd05691 S1_RPS1_repeat_ec6 S1_ 98.8 1.6E-08 3.5E-13 81.3 8.9 69 297-366 1-71 (73)
94 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2.4E-08 5.2E-13 78.9 8.6 67 296-363 1-68 (68)
95 TIGR03591 polynuc_phos polyrib 98.8 1.2E-08 2.7E-13 115.4 9.6 70 372-442 615-684 (684)
96 PRK07252 hypothetical protein; 98.8 2.1E-08 4.5E-13 90.0 9.0 72 295-367 2-75 (120)
97 cd05692 S1_RPS1_repeat_hs4 S1_ 98.8 2.8E-08 6.1E-13 78.3 8.8 67 297-365 1-69 (69)
98 cd05690 S1_RPS1_repeat_ec5 S1_ 98.8 2E-08 4.4E-13 80.0 7.9 66 297-363 1-69 (69)
99 smart00316 S1 Ribosomal protei 98.8 3.3E-08 7E-13 77.7 9.0 69 296-365 2-72 (72)
100 PRK04163 exosome complex RNA-b 98.8 3.4E-08 7.4E-13 98.3 10.9 75 372-447 60-138 (235)
101 PRK08582 hypothetical protein; 98.8 2E-08 4.3E-13 92.4 8.6 72 294-367 3-76 (139)
102 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 5.1E-08 1.1E-12 81.0 9.9 75 168-280 2-76 (82)
103 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.8 5E-08 1.1E-12 81.6 9.5 80 168-281 2-81 (86)
104 TIGR01953 NusA transcription t 98.7 4.7E-08 1E-12 102.2 10.8 108 253-367 82-199 (341)
105 PRK05807 hypothetical protein; 98.7 3.6E-08 7.9E-13 90.3 8.8 72 294-367 3-75 (136)
106 KOG1067 Predicted RNA-binding 98.7 1.6E-08 3.5E-13 108.7 7.0 83 372-455 665-747 (760)
107 cd05685 S1_Tex S1_Tex: The C-t 98.7 8.1E-08 1.8E-12 75.5 8.4 66 297-363 1-68 (68)
108 cd05693 S1_Rrp5_repeat_hs1_sc1 98.7 5.5E-08 1.2E-12 84.6 7.8 72 295-367 2-97 (100)
109 cd05684 S1_DHX8_helicase S1_DH 98.7 8E-08 1.7E-12 79.2 8.3 67 297-366 1-73 (79)
110 PRK09202 nusA transcription el 98.7 6.8E-08 1.5E-12 104.8 9.2 112 320-446 72-200 (470)
111 cd05689 S1_RPS1_repeat_ec4 S1_ 98.7 1E-07 2.2E-12 77.0 8.0 68 295-363 2-72 (72)
112 cd04455 S1_NusA S1_NusA: N-uti 98.6 1.5E-07 3.2E-12 75.6 8.5 62 374-443 2-66 (67)
113 TIGR02696 pppGpp_PNP guanosine 98.6 2.1E-07 4.5E-12 104.9 12.5 95 267-363 612-718 (719)
114 PRK08059 general stress protei 98.6 1.5E-07 3.1E-12 84.8 8.8 73 294-367 5-79 (123)
115 cd04455 S1_NusA S1_NusA: N-uti 98.6 1.5E-07 3.4E-12 75.5 8.0 64 295-364 2-67 (67)
116 COG1093 SUI2 Translation initi 98.6 7.4E-08 1.6E-12 95.8 7.4 71 295-366 10-84 (269)
117 cd04472 S1_PNPase S1_PNPase: P 98.6 2.1E-07 4.5E-12 73.6 8.5 66 297-364 1-68 (68)
118 PLN00207 polyribonucleotide nu 98.6 1.8E-07 4E-12 107.3 10.9 99 270-370 723-832 (891)
119 PHA02945 interferon resistance 98.6 1.7E-07 3.8E-12 78.9 7.3 69 295-367 10-84 (88)
120 PRK12327 nusA transcription el 98.5 3.9E-07 8.4E-12 96.0 9.9 109 253-367 85-201 (362)
121 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.5 4.2E-07 9.1E-12 77.9 7.9 74 373-447 4-87 (92)
122 TIGR00448 rpoE DNA-directed RN 98.5 8.6E-07 1.9E-11 84.7 10.4 81 373-455 79-176 (179)
123 TIGR02063 RNase_R ribonuclease 98.5 5.2E-07 1.1E-11 102.9 10.3 73 372-444 624-708 (709)
124 PRK03987 translation initiatio 98.5 6E-07 1.3E-11 90.8 9.2 70 295-365 7-80 (262)
125 cd00164 S1_like S1_like: Ribos 98.5 5.4E-07 1.2E-11 69.4 6.8 63 300-363 1-65 (65)
126 cd04453 S1_RNase_E S1_RNase_E: 98.4 1E-06 2.3E-11 74.8 8.4 71 294-365 5-82 (88)
127 PRK11824 polynucleotide phosph 98.4 1.5E-06 3.3E-11 98.9 11.2 98 268-367 589-692 (693)
128 PF13509 S1_2: S1 domain; PDB: 98.4 1.4E-06 3E-11 69.1 7.7 61 172-279 1-61 (61)
129 cd04471 S1_RNase_R S1_RNase_R: 98.3 2.1E-06 4.6E-11 70.6 8.0 68 296-364 1-82 (83)
130 PRK11642 exoribonuclease R; Pr 98.3 2.2E-06 4.8E-11 98.9 10.9 77 373-449 641-729 (813)
131 COG1095 RPB7 DNA-directed RNA 98.3 1.6E-06 3.5E-11 82.5 7.7 75 373-449 79-170 (183)
132 TIGR00358 3_prime_RNase VacB a 98.3 2.5E-06 5.5E-11 96.6 10.4 73 372-444 569-653 (654)
133 cd05702 S1_Rrp5_repeat_hs11_sc 98.3 3.8E-06 8.2E-11 67.8 8.3 61 297-358 1-65 (70)
134 PRK09521 exosome complex RNA-b 98.3 3.9E-06 8.4E-11 80.9 9.7 103 252-366 24-142 (189)
135 cd04473 S1_RecJ_like S1_RecJ_l 98.3 6.3E-06 1.4E-10 67.9 9.3 62 294-364 14-76 (77)
136 COG2183 Tex Transcriptional ac 98.2 1.8E-06 3.9E-11 97.1 7.3 74 293-367 655-730 (780)
137 PRK08563 DNA-directed RNA poly 98.2 6.2E-06 1.3E-10 79.2 9.8 77 373-451 79-172 (187)
138 TIGR03591 polynuc_phos polyrib 98.2 8.2E-06 1.8E-10 92.8 11.4 93 268-362 586-684 (684)
139 PHA02858 EIF2a-like PKR inhibi 98.2 4.5E-06 9.8E-11 69.7 6.5 71 372-444 13-85 (86)
140 TIGR01953 NusA transcription t 98.2 6.3E-06 1.4E-10 86.4 8.8 96 341-446 85-198 (341)
141 PRK04163 exosome complex RNA-b 98.1 2.4E-05 5.1E-10 78.1 12.0 159 252-445 26-191 (235)
142 PRK12327 nusA transcription el 98.1 5.4E-06 1.2E-10 87.4 7.3 95 341-444 88-198 (362)
143 cd04460 S1_RpoE S1_RpoE: RpoE, 98.0 1.4E-05 3E-10 68.9 7.0 69 298-367 1-86 (99)
144 COG1185 Pnp Polyribonucleotide 98.0 2.3E-05 5E-10 87.2 9.9 98 268-367 587-690 (692)
145 COG1095 RPB7 DNA-directed RNA 97.9 1E-05 2.2E-10 77.2 4.5 107 261-367 44-168 (183)
146 PRK12328 nusA transcription el 97.9 4.3E-05 9.4E-10 80.5 9.6 108 253-367 89-207 (374)
147 KOG2916 Translation initiation 97.8 8.3E-06 1.8E-10 81.2 2.0 88 372-459 13-102 (304)
148 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.8 0.00013 2.9E-09 62.4 8.8 77 168-280 2-86 (92)
149 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.7 0.00021 4.5E-09 60.8 9.3 59 375-435 1-70 (88)
150 PF13509 S1_2: S1 domain; PDB: 97.7 0.00014 3E-09 57.7 7.6 61 375-445 1-61 (61)
151 TIGR00448 rpoE DNA-directed RN 97.7 8.1E-05 1.8E-09 71.2 7.4 73 295-367 80-168 (179)
152 COG1096 Predicted RNA-binding 97.7 0.00024 5.2E-09 68.0 9.9 88 357-446 45-142 (188)
153 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.7 0.00034 7.3E-09 59.4 9.2 73 168-279 2-74 (86)
154 PRK05054 exoribonuclease II; P 97.7 0.00017 3.6E-09 81.8 9.6 71 374-444 558-643 (644)
155 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.6 0.00026 5.7E-09 58.0 6.9 67 376-445 1-72 (72)
156 TIGR00757 RNaseEG ribonuclease 97.5 0.00023 4.9E-09 76.6 8.1 62 372-434 22-97 (414)
157 COG1097 RRP4 RNA-binding prote 97.5 0.00042 9.1E-09 68.8 8.4 76 372-448 61-140 (239)
158 PTZ00162 DNA-directed RNA poly 97.4 0.00066 1.4E-08 65.0 9.1 73 373-447 79-166 (176)
159 TIGR02063 RNase_R ribonuclease 97.4 0.00052 1.1E-08 78.6 9.8 69 295-364 626-708 (709)
160 COG1097 RRP4 RNA-binding prote 97.4 0.00074 1.6E-08 67.1 9.3 80 167-280 59-138 (239)
161 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.4 0.00094 2E-08 56.7 8.6 72 373-446 4-75 (86)
162 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00068 1.5E-08 55.6 7.3 65 297-365 1-72 (72)
163 PRK08563 DNA-directed RNA poly 97.4 0.00038 8.2E-09 66.9 6.6 72 295-366 80-167 (187)
164 PRK12329 nusA transcription el 97.3 0.00085 1.8E-08 72.1 9.6 109 253-367 101-226 (449)
165 PF10447 EXOSC1: Exosome compo 97.3 0.00076 1.6E-08 56.8 6.6 61 374-434 3-82 (82)
166 PRK12328 nusA transcription el 97.2 0.001 2.2E-08 70.4 7.5 94 341-444 92-204 (374)
167 TIGR02062 RNase_B exoribonucle 97.1 0.0014 2.9E-08 74.5 8.7 68 376-443 558-638 (639)
168 TIGR00358 3_prime_RNase VacB a 97.1 0.0021 4.6E-08 73.1 10.2 69 295-364 571-653 (654)
169 COG0557 VacB Exoribonuclease R 97.1 0.0015 3.2E-08 75.0 8.6 74 372-445 619-704 (706)
170 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.1 0.0025 5.5E-08 54.2 7.8 33 296-328 1-33 (88)
171 PRK11642 exoribonuclease R; Pr 97.0 0.002 4.4E-08 74.8 9.2 71 295-365 642-725 (813)
172 PHA02858 EIF2a-like PKR inhibi 97.0 0.0022 4.8E-08 53.9 6.8 67 295-364 15-85 (86)
173 KOG1067 Predicted RNA-binding 97.0 0.004 8.7E-08 68.1 9.9 72 295-368 667-740 (760)
174 PRK12329 nusA transcription el 96.9 0.0051 1.1E-07 66.3 9.6 72 168-283 148-228 (449)
175 COG1107 Archaea-specific RecJ- 96.8 0.001 2.2E-08 73.0 4.3 72 370-448 117-189 (715)
176 KOG1856 Transcription elongati 96.8 0.0014 3E-08 76.5 5.0 76 372-448 982-1061(1299)
177 PTZ00162 DNA-directed RNA poly 96.7 0.0049 1.1E-07 59.1 7.6 35 295-329 80-114 (176)
178 PRK10811 rne ribonuclease E; R 95.8 0.02 4.4E-07 66.6 7.5 60 374-434 37-107 (1068)
179 KOG2916 Translation initiation 95.8 0.011 2.4E-07 59.4 4.6 71 295-366 15-89 (304)
180 PRK11712 ribonuclease G; Provi 95.6 0.03 6.5E-07 61.7 7.4 62 372-434 35-110 (489)
181 TIGR00757 RNaseEG ribonuclease 95.6 0.035 7.6E-07 60.0 7.7 57 295-352 24-96 (414)
182 PF10447 EXOSC1: Exosome compo 95.4 0.062 1.3E-06 45.3 6.9 23 170-192 2-24 (82)
183 PRK05054 exoribonuclease II; P 95.2 0.071 1.5E-06 60.8 9.0 67 297-363 562-642 (644)
184 COG1096 Predicted RNA-binding 95.1 0.15 3.2E-06 49.2 9.3 105 251-365 23-141 (188)
185 TIGR02062 RNase_B exoribonucle 94.7 0.13 2.9E-06 58.6 9.3 67 297-363 558-638 (639)
186 COG1107 Archaea-specific RecJ- 94.6 0.18 3.9E-06 56.0 9.6 149 166-363 116-281 (715)
187 KOG1856 Transcription elongati 94.5 0.062 1.3E-06 63.3 6.2 72 294-366 983-1059(1299)
188 KOG3298 DNA-directed RNA polym 93.8 0.29 6.4E-06 46.1 8.0 61 373-435 79-150 (170)
189 KOG3013 Exosomal 3'-5' exoribo 93.6 0.099 2.1E-06 52.6 4.9 97 157-282 66-167 (301)
190 PF10246 MRP-S35: Mitochondria 93.6 0.32 6.9E-06 42.6 7.3 46 157-203 5-54 (104)
191 KOG3409 Exosomal 3'-5' exoribo 93.2 0.5 1.1E-05 45.1 8.6 73 372-445 65-147 (193)
192 PF08292 RNA_pol_Rbc25: RNA po 92.9 0.3 6.6E-06 44.2 6.5 36 172-207 3-38 (122)
193 COG0557 VacB Exoribonuclease R 91.2 0.77 1.7E-05 53.0 8.9 71 294-364 620-703 (706)
194 KOG3409 Exosomal 3'-5' exoribo 90.9 0.95 2.1E-05 43.2 7.6 75 170-280 66-148 (193)
195 COG1530 CafA Ribonucleases G a 90.8 0.36 7.9E-06 53.3 5.5 62 372-435 34-102 (487)
196 PRK12442 translation initiatio 90.3 1.6 3.4E-05 37.3 7.6 64 378-446 8-73 (87)
197 PF08292 RNA_pol_Rbc25: RNA po 89.7 1.7 3.6E-05 39.4 7.9 60 375-435 3-75 (122)
198 KOG3298 DNA-directed RNA polym 89.7 1.4 3.1E-05 41.7 7.5 30 296-325 81-110 (170)
199 PRK10811 rne ribonuclease E; R 88.8 0.82 1.8E-05 53.8 6.4 62 296-358 38-112 (1068)
200 TIGR00008 infA translation ini 88.4 2.5 5.5E-05 34.5 7.3 59 378-441 6-66 (68)
201 PRK11712 ribonuclease G; Provi 88.3 1.3 2.9E-05 49.0 7.4 57 295-352 37-109 (489)
202 KOG1004 Exosomal 3'-5' exoribo 88.0 2.7 5.9E-05 41.5 8.5 63 168-269 61-123 (230)
203 PF10246 MRP-S35: Mitochondria 86.3 2.8 6.1E-05 36.8 6.8 54 373-434 21-74 (104)
204 PF00313 CSD: 'Cold-shock' DNA 83.1 13 0.00028 29.3 8.9 59 379-443 1-62 (66)
205 cd05700 S1_Rrp5_repeat_hs9 S1_ 80.4 5.7 0.00012 31.7 5.7 64 376-444 1-65 (65)
206 COG0361 InfA Translation initi 77.3 16 0.00034 30.5 7.7 65 376-445 6-72 (75)
207 PF09883 DUF2110: Uncharacteri 76.9 6.3 0.00014 39.1 6.2 97 159-289 59-157 (225)
208 KOG4078 Putative mitochondrial 76.7 4.5 9.7E-05 37.5 4.8 47 155-201 62-111 (173)
209 PRK09937 stationary phase/star 73.5 27 0.00059 28.8 8.3 63 380-447 3-67 (74)
210 PF01330 RuvA_N: RuvA N termin 69.0 33 0.00071 26.9 7.5 48 378-434 4-51 (61)
211 cd04458 CSP_CDS Cold-Shock Pro 68.3 34 0.00074 26.7 7.6 58 380-443 2-62 (65)
212 PRK15464 cold shock-like prote 66.8 37 0.00081 27.7 7.6 58 379-441 5-64 (70)
213 COG4148 ModC ABC-type molybdat 66.3 69 0.0015 33.6 11.0 113 295-434 230-348 (352)
214 PRK10943 cold shock-like prote 65.8 47 0.001 26.8 8.0 51 378-433 3-56 (69)
215 PRK09890 cold shock protein Cs 65.4 58 0.0013 26.4 8.5 58 379-442 5-65 (70)
216 PRK09507 cspE cold shock prote 64.6 51 0.0011 26.6 8.0 51 378-433 3-56 (69)
217 COG1530 CafA Ribonucleases G a 63.3 8.5 0.00018 42.7 4.3 69 295-363 36-111 (487)
218 PRK14998 cold shock-like prote 63.0 53 0.0012 27.0 7.9 63 380-447 3-67 (73)
219 PRK10354 RNA chaperone/anti-te 62.3 67 0.0015 26.0 8.4 54 379-438 5-61 (70)
220 KOG3013 Exosomal 3'-5' exoribo 61.2 8.8 0.00019 39.0 3.6 75 372-447 82-166 (301)
221 TIGR00008 infA translation ini 61.1 31 0.00067 28.2 6.1 57 299-361 6-66 (68)
222 PRK12442 translation initiatio 60.7 30 0.00064 29.7 6.1 62 298-365 7-72 (87)
223 PF03459 TOBE: TOBE domain; I 58.1 36 0.00078 26.2 6.0 49 377-432 5-58 (64)
224 PF00313 CSD: 'Cold-shock' DNA 58.0 77 0.0017 24.7 7.9 49 300-352 1-53 (66)
225 TIGR02381 cspD cold shock doma 57.1 58 0.0013 26.2 7.1 60 380-444 3-64 (68)
226 PRK10943 cold shock-like prote 56.9 43 0.00093 27.1 6.3 49 299-352 3-56 (69)
227 PRK04012 translation initiatio 56.4 59 0.0013 28.5 7.5 64 375-444 19-84 (100)
228 PRK15463 cold shock-like prote 55.6 43 0.00092 27.3 6.1 51 379-433 5-57 (70)
229 cd05793 S1_IF1A S1_IF1A: Trans 55.1 43 0.00094 27.8 6.2 58 379-442 2-61 (77)
230 PRK15463 cold shock-like prote 54.4 42 0.00092 27.3 5.9 48 300-352 5-57 (70)
231 PRK15464 cold shock-like prote 53.5 44 0.00095 27.3 5.8 48 300-352 5-57 (70)
232 COG1545 Predicted nucleic-acid 52.8 88 0.0019 28.9 8.5 55 375-437 63-126 (140)
233 PRK09507 cspE cold shock prote 52.2 59 0.0013 26.3 6.4 49 299-352 3-56 (69)
234 PRK09937 stationary phase/star 49.7 55 0.0012 27.0 5.9 47 301-352 3-54 (74)
235 KOG4078 Putative mitochondrial 49.5 41 0.00088 31.4 5.5 56 372-435 79-134 (173)
236 PRK14604 ruvA Holliday junctio 48.2 53 0.0012 32.1 6.6 52 378-437 4-56 (195)
237 PF01330 RuvA_N: RuvA N termin 47.7 1.1E+02 0.0024 23.8 7.2 46 299-353 4-51 (61)
238 PRK14605 ruvA Holliday junctio 46.4 63 0.0014 31.5 6.8 52 378-437 4-56 (194)
239 PRK14600 ruvA Holliday junctio 45.8 64 0.0014 31.3 6.7 47 378-433 4-50 (186)
240 PRK09890 cold shock protein Cs 45.6 90 0.0019 25.3 6.5 48 300-352 5-57 (70)
241 PRK10354 RNA chaperone/anti-te 45.3 81 0.0017 25.5 6.2 48 300-352 5-57 (70)
242 TIGR00084 ruvA Holliday juncti 44.8 66 0.0014 31.3 6.6 51 378-437 4-55 (191)
243 PF09883 DUF2110: Uncharacteri 44.6 1E+02 0.0022 30.8 7.8 82 284-366 60-148 (225)
244 PRK14603 ruvA Holliday junctio 43.9 67 0.0014 31.4 6.6 51 378-437 4-55 (197)
245 PRK14604 ruvA Holliday junctio 41.7 1.1E+02 0.0025 29.8 7.8 29 174-202 3-32 (195)
246 COG3269 Predicted RNA-binding 40.9 1.3E+02 0.0028 25.0 6.7 47 295-355 14-61 (73)
247 PRK14998 cold shock-like prote 39.6 1.1E+02 0.0024 25.0 6.3 47 301-352 3-54 (73)
248 PRK13901 ruvA Holliday junctio 39.5 90 0.002 30.6 6.7 51 378-437 4-55 (196)
249 TIGR02381 cspD cold shock doma 39.4 79 0.0017 25.4 5.3 47 301-352 3-54 (68)
250 cd04322 LysRS_N LysRS_N: N-ter 38.6 1.5E+02 0.0033 25.5 7.4 67 378-444 3-74 (108)
251 PRK14601 ruvA Holliday junctio 37.9 88 0.0019 30.3 6.3 51 378-437 4-56 (183)
252 PRK14605 ruvA Holliday junctio 36.2 1.6E+02 0.0035 28.6 7.9 29 174-202 3-32 (194)
253 cd04458 CSP_CDS Cold-Shock Pro 36.0 1.4E+02 0.003 23.2 6.1 47 301-352 2-53 (65)
254 PF08206 OB_RNB: Ribonuclease 35.6 99 0.0021 23.9 5.1 42 302-352 1-44 (58)
255 KOG3297 DNA-directed RNA polym 34.7 61 0.0013 31.6 4.5 33 296-328 81-114 (202)
256 KOG3297 DNA-directed RNA polym 34.7 74 0.0016 31.0 5.1 84 164-268 73-156 (202)
257 smart00652 eIF1a eukaryotic tr 34.5 1.8E+02 0.0039 24.5 6.8 60 377-442 5-66 (83)
258 PRK10676 DNA-binding transcrip 34.2 3.4E+02 0.0074 27.5 10.2 112 299-433 129-254 (263)
259 COG1278 CspC Cold shock protei 34.1 76 0.0016 25.9 4.3 47 301-352 3-54 (67)
260 TIGR00084 ruvA Holliday juncti 33.8 2E+02 0.0043 27.9 8.1 28 175-202 4-32 (191)
261 COG1278 CspC Cold shock protei 33.7 1.6E+02 0.0034 24.1 6.1 59 380-444 3-64 (67)
262 PRK14603 ruvA Holliday junctio 33.5 2E+02 0.0044 28.1 8.0 27 175-201 4-31 (197)
263 cd05701 S1_Rrp5_repeat_hs10 S1 33.3 67 0.0015 26.1 3.8 56 378-434 3-59 (69)
264 PF01938 TRAM: TRAM domain; I 32.9 1.9E+02 0.0041 22.2 6.4 53 341-394 3-59 (61)
265 PF13742 tRNA_anti_2: OB-fold 32.9 3E+02 0.0064 23.6 8.2 70 375-449 22-99 (99)
266 COG4148 ModC ABC-type molybdat 32.5 4.7E+02 0.01 27.7 10.7 203 34-316 79-312 (352)
267 PRK14646 hypothetical protein; 31.8 2.2E+02 0.0047 26.8 7.7 66 329-415 86-151 (155)
268 cd04456 S1_IF1A_like S1_IF1A_l 31.6 2.3E+02 0.005 23.6 7.0 60 379-444 2-64 (78)
269 PRK14600 ruvA Holliday junctio 31.5 2.3E+02 0.0049 27.5 8.0 27 175-201 4-31 (186)
270 COG4044 Uncharacterized protei 31.1 58 0.0013 32.4 3.8 48 157-208 62-111 (247)
271 PF03459 TOBE: TOBE domain; I 31.0 1.8E+02 0.0039 22.2 6.0 45 299-350 6-57 (64)
272 TIGR00523 eIF-1A eukaryotic/ar 30.8 3.1E+02 0.0067 24.0 7.9 52 376-433 18-70 (99)
273 PF01176 eIF-1a: Translation i 30.5 96 0.0021 24.7 4.4 49 378-432 4-53 (65)
274 PF07653 SH3_2: Variant SH3 do 30.5 88 0.0019 23.5 4.0 35 168-205 16-52 (55)
275 PTZ00329 eukaryotic translatio 30.1 1.9E+02 0.0042 27.4 6.9 64 374-444 30-95 (155)
276 PRK14602 ruvA Holliday junctio 30.0 1.3E+02 0.0028 29.6 6.1 52 378-437 4-57 (203)
277 PRK10676 DNA-binding transcrip 29.6 2.8E+02 0.0061 28.2 8.7 76 255-351 171-253 (263)
278 PRK13901 ruvA Holliday junctio 29.2 2.6E+02 0.0056 27.5 8.0 28 174-201 3-31 (196)
279 COG4044 Uncharacterized protei 29.2 3.5E+02 0.0076 27.1 8.7 98 268-365 38-159 (247)
280 PRK14606 ruvA Holliday junctio 28.6 2.4E+02 0.0051 27.4 7.6 28 174-201 3-32 (188)
281 PRK14601 ruvA Holliday junctio 28.5 2.6E+02 0.0055 27.1 7.7 27 175-201 4-32 (183)
282 PF14604 SH3_9: Variant SH3 do 27.8 1.1E+02 0.0024 22.8 4.0 34 169-205 14-48 (49)
283 PRK10476 multidrug resistance 26.6 3.8E+02 0.0082 27.9 9.3 14 375-388 273-286 (346)
284 COG4776 Rnb Exoribonuclease II 25.9 17 0.00037 39.9 -0.9 67 295-361 560-640 (645)
285 CHL00010 infA translation init 25.8 3.8E+02 0.0083 22.1 8.2 65 379-448 9-75 (78)
286 PLN00208 translation initiatio 25.8 2.6E+02 0.0055 26.3 6.8 62 374-442 30-93 (145)
287 TIGR00638 Mop molybdenum-pteri 25.6 1.2E+02 0.0027 23.4 4.3 49 377-432 7-60 (69)
288 TIGR00638 Mop molybdenum-pteri 25.3 2.3E+02 0.005 21.8 5.8 46 299-351 8-60 (69)
289 KOG1004 Exosomal 3'-5' exoribo 25.1 2.1E+02 0.0046 28.6 6.4 58 295-355 64-124 (230)
290 COG2106 Uncharacterized conser 25.0 1.4E+02 0.003 30.8 5.4 49 372-434 102-150 (272)
291 PRK14606 ruvA Holliday junctio 25.0 1.8E+02 0.0039 28.2 6.0 51 378-437 4-56 (188)
292 PF08206 OB_RNB: Ribonuclease 24.9 2.2E+02 0.0047 22.0 5.4 34 391-433 11-44 (58)
293 PRK14640 hypothetical protein; 24.4 4E+02 0.0086 24.9 8.0 61 329-410 83-143 (152)
294 PRK00116 ruvA Holliday junctio 24.2 2E+02 0.0043 27.8 6.2 49 378-434 4-52 (192)
295 COG3269 Predicted RNA-binding 22.8 3.7E+02 0.008 22.4 6.5 48 372-435 12-60 (73)
296 COG0361 InfA Translation initi 22.8 2.9E+02 0.0062 23.1 5.9 61 297-363 6-70 (75)
297 PRK05585 yajC preprotein trans 22.4 1.9E+02 0.004 25.6 5.1 37 165-201 48-90 (106)
298 PRK14602 ruvA Holliday junctio 22.0 3.3E+02 0.0071 26.7 7.3 28 174-201 3-32 (203)
299 PRK00276 infA translation init 21.5 4.4E+02 0.0095 21.3 7.8 60 378-442 8-69 (72)
300 KOG4134 DNA-dependent RNA poly 21.4 65 0.0014 32.3 2.2 58 372-435 104-161 (253)
301 PRK00286 xseA exodeoxyribonucl 21.2 5.1E+02 0.011 28.1 9.3 91 375-480 24-121 (438)
302 PRK00116 ruvA Holliday junctio 21.2 2.6E+02 0.0056 27.0 6.3 28 174-201 3-31 (192)
303 TIGR00739 yajC preprotein tran 20.8 2.3E+02 0.0051 23.8 5.2 33 166-198 34-72 (84)
304 PRK15136 multidrug efflux syst 20.2 7.2E+02 0.016 26.6 10.1 72 295-388 217-294 (390)
305 PF11213 DUF3006: Protein of u 20.1 4.7E+02 0.01 21.1 8.0 28 178-205 2-30 (71)
No 1
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1e-46 Score=387.62 Aligned_cols=281 Identities=34% Similarity=0.480 Sum_probs=252.8
Q ss_pred chhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232 156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (514)
Q Consensus 156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v 235 (514)
..+|+++|+.+.+.+++|++|.|+|++++++|+|||+|++..||||.+|++..+ ..++
T Consensus 15 ~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~-----------~~~~----------- 72 (318)
T PRK07400 15 HEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINR-----------VEGP----------- 72 (318)
T ss_pred HHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc-----------ccCH-----------
Confidence 367999998766779999999999999999999999999999999999985321 0111
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (514)
Q Consensus 236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV 314 (514)
...+++|+.|.|.|++.+ .+++++||+|+......|+.+.++++.|+++.|+|++++++|++|
T Consensus 73 ----------------~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V 136 (318)
T PRK07400 73 ----------------EEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV 136 (318)
T ss_pred ----------------HHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 234789999999999965 578999999999878899999999999999999999999999999
Q ss_pred EECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh---hccCCCCceEEEEEEEEecceE
Q 010232 315 RIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---TLNLREGTLLEGTVKKIYPYGA 391 (514)
Q Consensus 315 di~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~---~~~l~~G~iV~G~V~~I~~~Ga 391 (514)
+++|++||||.++++.+. ..+. .+|+.+.|+|+++|+++++|+||+|.++. ...+++|+++.|+|++|++||+
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 999999999999994331 2222 59999999999999999999999997653 2479999999999999999999
Q ss_pred EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHH
Q 010232 392 QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAK 470 (514)
Q Consensus 392 FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~ 470 (514)
||+++ |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++.++||+++.+++.++.+|++||.
T Consensus 213 fV~i~--gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~~~~~~ 290 (318)
T PRK07400 213 FIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAA 290 (318)
T ss_pred EEEEC--CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHHHHHHH
Confidence 99996 6999999999999999999999999999999999998 78999999999999999999999999999999999
Q ss_pred HHHhhCccCC
Q 010232 471 KYRQKLPAVS 480 (514)
Q Consensus 471 ~~~~kl~~~~ 480 (514)
++++++.+..
T Consensus 291 ~~~~~~~~~~ 300 (318)
T PRK07400 291 KYRQMLLAQA 300 (318)
T ss_pred HHHHHhhhhh
Confidence 9999998774
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-47 Score=411.82 Aligned_cols=281 Identities=30% Similarity=0.397 Sum_probs=253.8
Q ss_pred hhhhchh---ccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccce
Q 010232 158 VGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG 234 (514)
Q Consensus 158 ~~~~~~~---~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~ 234 (514)
.|++.+. .+.+.+++|++|.|+|+++++++++||+|++.+|++|.+|+....
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 3445554 456789999999999999999999999999999999999985320
Q ss_pred eeeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEE
Q 010232 235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313 (514)
Q Consensus 235 v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~-d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~f 313 (514)
....+++||.+.+.|... +.+|+++||++++....+|..|.++++.|+++.|+|+..+++|++
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 022588999999999984 567899999999999999999999999999999999999999999
Q ss_pred EEECCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEE
Q 010232 314 TRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGT 382 (514)
Q Consensus 314 Vdi~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~ 382 (514)
|+++|++||+|.|++. +++++... ++|.++.++|+++|.+++++++|+|..++ ...+++|++|+|+
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 58999999999999999999999998765 2489999999999
Q ss_pred EEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhh
Q 010232 383 VKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERV 461 (514)
Q Consensus 383 V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v 461 (514)
|++|++|||||+|+ |++||+|+++|||.|+.+|++++++||+|+|+|+++| +++||+||||++.++||+.+.+++++
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 89999999999999999999988864
Q ss_pred hhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 462 FSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 462 ~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
|++++|+|+++.|||+|++.+.-
T Consensus 278 --------------------g~~v~G~Vt~i~~~GafVei~~G 300 (541)
T COG0539 278 --------------------GDKVEGKVTNLTDYGAFVEIEEG 300 (541)
T ss_pred --------------------CCEEEEEEEEeecCcEEEEecCC
Confidence 88999999999999999987653
No 3
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=5.6e-44 Score=384.36 Aligned_cols=286 Identities=24% Similarity=0.378 Sum_probs=252.6
Q ss_pred chhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232 156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (514)
Q Consensus 156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v 235 (514)
.++|.++++..+..++.|++|+|+|++++++|++||||++.+|+||.+|++... ..++
T Consensus 19 ~e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~-----------~~~~----------- 76 (486)
T PRK07899 19 AEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKH-----------DVDP----------- 76 (486)
T ss_pred HHHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccc-----------cCCh-----------
Confidence 367999998888889999999999999999999999999999999999985320 0111
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (514)
Q Consensus 236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV 314 (514)
...+++|+.|+|.|++.+ .+|+++||++++.....|..+.++++.|++++|+|+++.++|++|
T Consensus 77 ----------------~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~V 140 (486)
T PRK07899 77 ----------------NEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLIL 140 (486)
T ss_pred ----------------hhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEE
Confidence 234799999999999865 678999999999888999999999999999999999999999999
Q ss_pred EECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh--------h--ccCCCCceEEEEE
Q 010232 315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA--------T--LNLREGTLLEGTV 383 (514)
Q Consensus 315 di~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~--------~--~~l~~G~iV~G~V 383 (514)
++ |++||||.+++ +.++.++.. ++|+.|.|+|+++|+++++++||+|..++ . ..+++|+++.|+|
T Consensus 141 dl-Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V 216 (486)
T PRK07899 141 DI-GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVV 216 (486)
T ss_pred EE-CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEE
Confidence 99 89999999999 555555544 59999999999999999999999995322 1 3799999999999
Q ss_pred EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF 462 (514)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~ 462 (514)
++++++|+||+|+ |+.||||+|+|+|.++.+|.+.|++||.|+|+|+++| +++||.||+|++.++||..+.++
T Consensus 217 ~~i~~~G~FVdlg--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~---- 290 (486)
T PRK07899 217 SSIVNFGAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART---- 290 (486)
T ss_pred EEEECCeEEEEEC--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh----
Confidence 9999999999996 6999999999999999999999999999999999998 78999999999999999654433
Q ss_pred hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhcc
Q 010232 463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANW 505 (514)
Q Consensus 463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~~ 505 (514)
..+|.++.|+|+++.|||.|+.++..+
T Consensus 291 ----------------~~vG~vv~G~V~~I~~fGvFVeL~~gi 317 (486)
T PRK07899 291 ----------------HAIGQIVPGKVTKLVPFGAFVRVEEGI 317 (486)
T ss_pred ----------------cCCCCEEEEEEEEEeccEEEEEeCCCc
Confidence 246899999999999999999987543
No 4
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-42 Score=370.45 Aligned_cols=284 Identities=21% Similarity=0.262 Sum_probs=253.4
Q ss_pred hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (514)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~ 236 (514)
-+..+.|......+..|.+|.|+|+...++|+.|+++. ..||||.+++....
T Consensus 90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~--------------------------- 141 (541)
T COG0539 90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRP--------------------------- 141 (541)
T ss_pred HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhcccc---------------------------
Confidence 46777787777888899999999999999999999964 89999999984220
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (514)
Q Consensus 237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~ 312 (514)
+. .....+|..+.+.|+..| .++++++|+|..... .....+.+.++.|++++|+|++++++|+
T Consensus 142 -------v~------d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga 208 (541)
T COG0539 142 -------VR------DLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA 208 (541)
T ss_pred -------cc------cccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence 00 112358999999999987 578999999988653 2334455667999999999999999999
Q ss_pred EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEE
Q 010232 313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKK 385 (514)
Q Consensus 313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~ 385 (514)
||+++|++||+|.++| |.++.+|.++. ++||+|+|+|+++|++++||.||+|+ ||+. ..+.+|+.+.|+|++
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 99999999999999999999999996 6765 479999999999999
Q ss_pred EecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhH
Q 010232 386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSE 464 (514)
Q Consensus 386 I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ 464 (514)
+++|||||++.+ |++||+|+|||||.+...|++++++||+|.|+|+.+| +++||+||||++..|||+.+.++++
T Consensus 288 i~~~GafVei~~-GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~---- 362 (541)
T COG0539 288 LTDYGAFVEIEE-GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHP---- 362 (541)
T ss_pred eecCcEEEEecC-CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcC----
Confidence 999999999999 9999999999999999999999999999999999999 8899999999999999999887765
Q ss_pred HHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhh
Q 010232 465 AEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCA 503 (514)
Q Consensus 465 ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~ 503 (514)
+|++++|.+++..+||+|+.++.
T Consensus 363 ----------------~g~~v~g~v~~~t~~g~fv~le~ 385 (541)
T COG0539 363 ----------------VGDVVEGKVKSITDFGAFVELEG 385 (541)
T ss_pred ----------------CCCeEEEEEeeecccceEEccCC
Confidence 58899999999999999999987
No 5
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=8.9e-41 Score=367.59 Aligned_cols=283 Identities=25% Similarity=0.378 Sum_probs=252.5
Q ss_pred chhhhhchhccc--cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccc
Q 010232 156 DKVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKM 233 (514)
Q Consensus 156 ~~~~~~~~~~~~--~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~ 233 (514)
.++|+++++.+. +++++|++|+|+|++++++|++||+|.+.+||||.+|+.+..
T Consensus 12 ~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~------------------------ 67 (565)
T PRK06299 12 EESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ------------------------ 67 (565)
T ss_pred hHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc------------------------
Confidence 368999998876 779999999999999999999999999999999999984210
Q ss_pred eeeeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232 234 GIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (514)
Q Consensus 234 ~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~ 312 (514)
....+++|++++|.|++.+ .+|+++||++++.....|+.+.++++.|++++|+|++++++|+
T Consensus 68 -----------------~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~ 130 (565)
T PRK06299 68 -----------------GELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGF 130 (565)
T ss_pred -----------------ccccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEE
Confidence 0234789999999999965 5789999999999999999999999999999999999999999
Q ss_pred EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEE
Q 010232 313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG 381 (514)
Q Consensus 313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G 381 (514)
+|+++|++||||.+++ +.+..++. .++|+++.|+|+++|++++++++|+|.+++ ...+++|+++.|
T Consensus 131 ~V~~~g~~gfip~s~~~~~~~~~~~---~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g 207 (565)
T PRK06299 131 TVDLNGVEAFLPGSQVDVRPVRDTD---PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEG 207 (565)
T ss_pred EEEECCEEEEEEHHHccCcCCCChH---HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEE
Confidence 9999999999999999 44555543 359999999999999999999999997642 137999999999
Q ss_pred EEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhh
Q 010232 382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKER 460 (514)
Q Consensus 382 ~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~ 460 (514)
+|++++++|+||+++ |+.||+|+++++|.++.+|.+.|++||+|+|+|+++| +++||.||+|.+.++||+.+.+.
T Consensus 208 ~V~~v~~~G~~V~i~--g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~-- 283 (565)
T PRK06299 208 VVKNITDYGAFVDLG--GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK-- 283 (565)
T ss_pred EEEEEeCCeEEEEEC--CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh--
Confidence 999999999999997 6999999999999999999999999999999999998 78999999999999999875432
Q ss_pred hhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 461 VFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 461 v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
..+|..+.|+|.++.+||.|+++...
T Consensus 284 ------------------~~~G~~v~g~V~~i~~~G~fV~l~~~ 309 (565)
T PRK06299 284 ------------------YPVGSKVKGKVTNITDYGAFVELEEG 309 (565)
T ss_pred ------------------CCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence 34799999999999999999988654
No 6
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.7e-40 Score=346.62 Aligned_cols=284 Identities=30% Similarity=0.420 Sum_probs=249.9
Q ss_pred hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEe-CCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (514)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdI-G~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v 235 (514)
.+|++.+. ...++++|++|+|+|++++++|++|++ |.+.+|+||.+|+.... .++
T Consensus 3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~-----------~~~------------ 58 (390)
T PRK06676 3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDH-----------IED------------ 58 (390)
T ss_pred HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhcccc-----------ccC------------
Confidence 57888887 788999999999999999999999999 88999999999985310 011
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (514)
Q Consensus 236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV 314 (514)
....+++|+.|+|+|+..+ .+++++||++++.....|+.+.++++.|++++|+|+++.++|++|
T Consensus 59 ---------------~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V 123 (390)
T PRK06676 59 ---------------INDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV 123 (390)
T ss_pred ---------------cccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 1235799999999999976 567899999999888899999999999999999999999999999
Q ss_pred EECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEEE
Q 010232 315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV 383 (514)
Q Consensus 315 di~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~V 383 (514)
+++|++||||++++ +.+..++.+ ++|+.+.|+|+++|++++++.||+|.+.. ...+++|+++.|+|
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 555566654 48999999999999999999999996422 13689999999999
Q ss_pred EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF 462 (514)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~ 462 (514)
++++++|+||+++ ++.||||.++++|.++.++.+.|++||.|+|+|+.++ +++||.||+|++.++||..+.+
T Consensus 201 ~~v~~~G~fV~l~--~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~----- 273 (390)
T PRK06676 201 ARLTDFGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE----- 273 (390)
T ss_pred EEEecceEEEEeC--CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchh-----
Confidence 9999999999996 6999999999999999999999999999999999998 7899999999999999975432
Q ss_pred hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
...+|.++.|+|.++.|||.|++++..
T Consensus 274 ---------------~~~~G~~v~g~V~~i~~~G~fV~l~~g 300 (390)
T PRK06676 274 ---------------KLPEGDVIEGTVKRLTDFGAFVEVLPG 300 (390)
T ss_pred ---------------hhcCCcEEEEEEEEEeCceEEEEECCC
Confidence 345689999999999999999988743
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=3e-40 Score=357.86 Aligned_cols=282 Identities=24% Similarity=0.336 Sum_probs=246.2
Q ss_pred hhhhhchhccccC----CCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcc
Q 010232 157 KVGEDKVSVEYYE----PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK 232 (514)
Q Consensus 157 ~~~~~~~~~~~~~----ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~ 232 (514)
.+|+++|+.+.++ +++|++|+|+|++++++|++||+|++.+|+||.+|+... .
T Consensus 15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~---------------~-------- 71 (491)
T PRK13806 15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDA---------------D-------- 71 (491)
T ss_pred HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCc---------------c--------
Confidence 5799999876543 999999999999999999999999999999999997421 0
Q ss_pred ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232 233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (514)
Q Consensus 233 ~~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~ 312 (514)
....+++|+.|++.|++.+ ++.++||++.. ....|+.+.++++.|++++|+|++++++|+
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 0123789999999999765 35789997644 467999999999999999999999999999
Q ss_pred EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEE
Q 010232 313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG 381 (514)
Q Consensus 313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G 381 (514)
+|+++|++||||.+++ +.+..++.. .+|+++.|+|+++|+++++++||+|+.++ ...+++|++++|
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 555666655 49999999999999999999999996532 136999999999
Q ss_pred EEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC----CeEEEEEecCcCCCCcccc
Q 010232 382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP----DKISLSIADLESEPGLFVS 456 (514)
Q Consensus 382 ~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~----~rI~LSlK~l~~~P~~~~~ 456 (514)
+|++++++|+||+|++ |+.||||+|+++|.++.++.+.|++||.|+|+|++++ ++ +||.||+|++.++||+.+.
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 44 4899999999999997765
Q ss_pred chhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhcc
Q 010232 457 DKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANW 505 (514)
Q Consensus 457 ~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~~ 505 (514)
++ ..+|+.++|+|+++.|||+|+++....
T Consensus 288 ~~--------------------~~~G~~v~G~V~~v~~~G~fV~l~~gv 316 (491)
T PRK13806 288 DR--------------------LKAGDKVTGKVVRLAPFGAFVEILPGI 316 (491)
T ss_pred cc--------------------CCCCCEEEEEEEEEeCceEEEEeCCCc
Confidence 44 356999999999999999999997543
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=1.9e-38 Score=345.40 Aligned_cols=279 Identities=25% Similarity=0.391 Sum_probs=245.8
Q ss_pred hhhhchhccc--cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232 158 VGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (514)
Q Consensus 158 ~~~~~~~~~~--~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v 235 (514)
+|+++++.++ ..+++|++|.|+|+++++++++||+|++.+|+||.+|+...
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 5888887663 46999999999999999999999999999999999888421
Q ss_pred eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (514)
Q Consensus 236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV 314 (514)
+..+++||.|.+.|++.+ ..|+++||.++......|..+..+++.|++++|+|++++++|++|
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 134789999999999854 579999999999888899999999999999999999999999999
Q ss_pred EECCEEEEEeccccccc-cCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEEE
Q 010232 315 RIEGLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV 383 (514)
Q Consensus 315 di~Gi~gFVP~sel~~~-i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~V 383 (514)
+++|++||||.+++..+ .++.. .++|+++.|+|+++|+.++++++|+|+++. ...+++|++++|+|
T Consensus 119 ~i~g~~~flP~s~~~~~~~~~~~---~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V 195 (516)
T TIGR00717 119 DLNGVEAFLPGSQVDVKPIKDLD---SLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVV 195 (516)
T ss_pred EECCEEEEEeHHHhcCcccCchh---hhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEE
Confidence 99999999999999533 23322 259999999999999999999999997642 13799999999999
Q ss_pred EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF 462 (514)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~ 462 (514)
+++.++|+||+++ |++||+|.++++|.++.++.+.|++||+|.|+|+.+| +++++.||+|.+.++||+.+.
T Consensus 196 ~~i~~~G~~V~l~--g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~------ 267 (516)
T TIGR00717 196 KNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE------ 267 (516)
T ss_pred EEEECCeEEEEEC--CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHH------
Confidence 9999999999996 6999999999999999999999999999999999998 788999999999988886532
Q ss_pred hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
....+|+.++|+|+++.+||+|+++...
T Consensus 268 --------------~~~~~G~i~~g~V~~v~~~G~fV~l~~~ 295 (516)
T TIGR00717 268 --------------KKFPVGDKITGRVTNLTDYGVFVEIEEG 295 (516)
T ss_pred --------------hhccCCCEEEEEEEEeeCCcEEEEeCCC
Confidence 2235799999999999999999988644
No 9
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=3.2e-38 Score=358.12 Aligned_cols=312 Identities=21% Similarity=0.297 Sum_probs=259.8
Q ss_pred CCCCCChhhhhhhhhccccCCC--ChHHHhhhccccccccccccc--cchhhhhchhcc-ccCCCCCCEEEEEEEEEeCC
Q 010232 112 KSEKPDEEEALAPFLKFFKPRD--SAEEVEEEGSEVGVSRESIDV--DDKVGEDKVSVE-YYEPKPGDFVIGVVVSGNEN 186 (514)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~ik~GdiV~G~Vv~v~~~ 186 (514)
.+..++-+|.+.=.++..+.+. .+| ..+ ++.++ ..---..+++.+ +..+++|++|+|+|++++++
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 3567889999998898888765 111 111 11111 111223455555 57899999999999999999
Q ss_pred eEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCCCCCCCCcccCCCEEEEEEE
Q 010232 187 KLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVL 266 (514)
Q Consensus 187 Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl 266 (514)
++|||+|++.+|++|.+|+. ..+++||+|+|.|+
T Consensus 336 ~v~VdiG~K~eGiI~~~E~~----------------------------------------------~~~kvGd~i~~~V~ 369 (863)
T PRK12269 336 TVFVDIGGKSEGRVPVEEFE----------------------------------------------APPKAGDGVRVYVE 369 (863)
T ss_pred EEEEEeCCCceEEeEHHHhc----------------------------------------------cCCCCCCEEEEEEE
Confidence 99999999999999988872 11479999999999
Q ss_pred EEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEE--CCeEEEEEC-CEEEEEeccccc-cccCChhhHhhhc
Q 010232 267 GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN--TGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKV 342 (514)
Q Consensus 267 ~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~--~~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~V 342 (514)
+.+.+| ++||.+++.....|+.+.++++.|++|+|+|++++ ++|++|+++ |++||||.+|+. ....++.. .+
T Consensus 370 ~~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~---~v 445 (863)
T PRK12269 370 RVTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPES---LI 445 (863)
T ss_pred EEcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHH---hC
Confidence 876666 89999999989999999999999999999999984 589999996 799999999994 33344433 58
Q ss_pred CCEEEEEEEEEeC-----CCCceEeehhhhhhh----------ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEee
Q 010232 343 GRRMYVQITRINE-----DTNDLILSEREAWAT----------LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS 407 (514)
Q Consensus 343 Gq~V~vkVl~vD~-----e~~rIiLS~K~~~~~----------~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S 407 (514)
|++++|+|+++|+ +++++++|+|++++. .++++|++|.|+|++++++|+||+++ |++||||+|
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 346899999975321 36889999999999999999999996 699999999
Q ss_pred ccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCccc
Q 010232 408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSE 486 (514)
Q Consensus 408 els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e 486 (514)
+++|.++.+|.+.+++||+|+|+|+++| +++||.||+|++.++||..+.++ ..+|++++
T Consensus 524 eiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~--------------------~~vG~iV~ 583 (863)
T PRK12269 524 DMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK--------------------FGVNDVVK 583 (863)
T ss_pred hccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc--------------------CCCCCEEE
Confidence 9999999999999999999999999998 78999999999999999776554 35799999
Q ss_pred CCCCCCCCCCCccchhhcc
Q 010232 487 SLPTDTPPFDSEASMCANW 505 (514)
Q Consensus 487 ~~v~~~~pfg~~~~~~~~~ 505 (514)
|+|.++.|||+|+++..+.
T Consensus 584 G~V~~I~~fG~fVeL~~gv 602 (863)
T PRK12269 584 GRVTKIADFGAFIELAEGI 602 (863)
T ss_pred EEEEEEeCCeEEEEecCCc
Confidence 9999999999999997554
No 10
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=1.1e-38 Score=361.85 Aligned_cols=283 Identities=16% Similarity=0.236 Sum_probs=244.8
Q ss_pred hhhchhccccCCCCCCEEEEEEEEEe--CCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232 159 GEDKVSVEYYEPKPGDFVIGVVVSGN--ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (514)
Q Consensus 159 ~~~~~~~~~~~ik~GdiV~G~Vv~v~--~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~ 236 (514)
..+.|+.-...++.|++|+|+|++++ ++|++||+|++.+||||.+|+.... .++
T Consensus 385 ~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~-----------~~~------------- 440 (863)
T PRK12269 385 RLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQK-----------VDA------------- 440 (863)
T ss_pred hhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhcccc-----------ccc-------------
Confidence 34556655667889999999999985 4799999998999999999983210 000
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEc------CCCcEEEEehHHHHHhhhhHHHhhh---cCCCEEEEEEEEE
Q 010232 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT------LSGRPLLSTRRLFRKMAWHRVRQIK---QLNEPIEVKFTEW 307 (514)
Q Consensus 237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d------~~grliLS~kk~~~~~~w~~l~~~~---k~GeiV~GkV~~v 307 (514)
....+|+.+++.|+..+ .++++++|+|++..+..|+.+.+++ +.|+++.|+|.++
T Consensus 441 ----------------~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i 504 (863)
T PRK12269 441 ----------------PESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSF 504 (863)
T ss_pred ----------------hHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEE
Confidence 11247999999999854 3468999999998888888877665 4799999999999
Q ss_pred ECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEE
Q 010232 308 NTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLE 380 (514)
Q Consensus 308 ~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~ 380 (514)
.++|+||+++|++||||.+++ +.++.++.+.. ++||+++|+|+++|++++++.||+|+ +|.. ..+++|++++
T Consensus 505 ~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~ 583 (863)
T PRK12269 505 TSFGAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVK 583 (863)
T ss_pred eCCcEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEE
Confidence 999999999999999999999 77888888765 89999999999999999999999995 4543 3699999999
Q ss_pred EEEEEEecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccch
Q 010232 381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK 458 (514)
Q Consensus 381 G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k 458 (514)
|+|+++++||+||++++ |++||+|+|+++| .++.+|.+.|++||+|+|+|+.+| +++||.||+|++.+|||+.+.++
T Consensus 584 G~V~~I~~fG~fVeL~~-gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~ 662 (863)
T PRK12269 584 GRVTKIADFGAFIELAE-GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR 662 (863)
T ss_pred EEEEEEeCCeEEEEecC-CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh
Confidence 99999999999999998 8999999999999 689999999999999999999998 78999999999999999887543
Q ss_pred hhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhh
Q 010232 459 ERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCA 503 (514)
Q Consensus 459 ~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~ 503 (514)
..+|+.++|+|+++.+||.|++++.
T Consensus 663 --------------------~~vG~~v~G~V~~i~~~G~fV~l~~ 687 (863)
T PRK12269 663 --------------------YPVGARFTRRIVKVTNAGAFIEMEE 687 (863)
T ss_pred --------------------CCCCCEEEEEEEEEecceEEEEeCC
Confidence 3579999999999999999999864
No 11
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=4.6e-38 Score=340.84 Aligned_cols=279 Identities=22% Similarity=0.265 Sum_probs=240.1
Q ss_pred hhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccc
Q 010232 163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI 242 (514)
Q Consensus 163 ~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~ 242 (514)
|......++.|++|+|+|.++.++|++|+++ +..||||.+++.... .+++
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 3333445678999999999999999999997 589999999984210 0111
Q ss_pred cccCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-
Q 010232 243 AMSGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE- 317 (514)
Q Consensus 243 ~l~~~~~~~~~~~~vGd~V~v~Vl~~d~-~grliLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~- 317 (514)
.. .+|+.+.|.|+..|. +++++||++.... ...|+.+...++.|++++|+|+++.++|+||+++
T Consensus 156 ----------~~-~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~ 224 (491)
T PRK13806 156 ----------ES-YVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAP 224 (491)
T ss_pred ----------HH-cCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCC
Confidence 11 289999999999874 6789999988753 4678888788999999999999999999999995
Q ss_pred CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCC----CceEeehhhh----hhh--ccCCCCceEEEEEEEE
Q 010232 318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT----NDLILSEREA----WAT--LNLREGTLLEGTVKKI 386 (514)
Q Consensus 318 Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~----~rIiLS~K~~----~~~--~~l~~G~iV~G~V~~I 386 (514)
|++||||.+++ +.++.++.+++ ++|+.++|+|+++|.++ +||.||+|++ |.. ..+++|+++.|+|+++
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 79999999999 77777887764 89999999999999876 4799999964 543 3799999999999999
Q ss_pred ecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhH
Q 010232 387 YPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSE 464 (514)
Q Consensus 387 ~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ 464 (514)
++||+||++++ |++||+|+|+|+| .++.++.+.|++||.|+|+|+.+| +++||.||+|++..+||+.+.+.+
T Consensus 304 ~~~G~fV~l~~-gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~----- 377 (491)
T PRK13806 304 APFGAFVEILP-GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERF----- 377 (491)
T ss_pred eCceEEEEeCC-CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhC-----
Confidence 99999999988 8999999999999 578899999999999999999998 789999999999999998876543
Q ss_pred HHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 465 AEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 465 ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
.+|+.++|+|+++.|||+|++++..
T Consensus 378 ---------------~vG~~v~G~V~~i~~~G~FV~l~~g 402 (491)
T PRK13806 378 ---------------APGTTVTGTVEKRAQFGLFVNLAPG 402 (491)
T ss_pred ---------------CCCCEEEEEEEEEecCceEEEcCCC
Confidence 4699999999999999999998743
No 12
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=4.1e-37 Score=343.30 Aligned_cols=285 Identities=29% Similarity=0.398 Sum_probs=249.2
Q ss_pred hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (514)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~ 236 (514)
.++.+.|+.....+++|++|+|+|.+++++|+||++|.+.+|+||.+|+... ...++
T Consensus 287 ~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~-----------~~~~~------------ 343 (647)
T PRK00087 287 NEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLD-----------EISSL------------ 343 (647)
T ss_pred HHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc-----------ccCCh------------
Confidence 4555666778889999999999999999999999999999999999998521 00111
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (514)
Q Consensus 237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd 315 (514)
...+++|+.|+|+|++.+ .+|+++||++++.....|+.+.++++.|+++.|+|+++.++|++|+
T Consensus 344 ---------------~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~ 408 (647)
T PRK00087 344 ---------------KESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD 408 (647)
T ss_pred ---------------hhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence 235899999999999965 6899999999998888999999999999999999999999999999
Q ss_pred ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCc-eEeehhhhhh----------hccCCCCceEEEEE
Q 010232 316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTND-LILSEREAWA----------TLNLREGTLLEGTV 383 (514)
Q Consensus 316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~r-IiLS~K~~~~----------~~~l~~G~iV~G~V 383 (514)
++|++||||.+++ +.+..++.. ++|+.+.|+|+++|+++++ +.+|+|.++. ..++++|+++.|+|
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 455556544 4999999999999999998 9999997642 13689999999999
Q ss_pred EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF 462 (514)
Q Consensus 384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~ 462 (514)
++++++|+||++ + ++.||+|+|+++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||..+.+
T Consensus 486 ~~v~~~G~fV~l-~-gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~----- 558 (647)
T PRK00087 486 KRLTDFGAFVDI-G-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEE----- 558 (647)
T ss_pred EEEeCCcEEEEE-C-CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhh-----
Confidence 999999999999 5 7999999999999999999999999999999999998 7899999999999999965422
Q ss_pred hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
...+|..+.|+|.++.+||.|+.++.+
T Consensus 559 ---------------~~~~G~~v~g~V~~i~~~G~fV~l~~~ 585 (647)
T PRK00087 559 ---------------KYPVGSIVLGKVVRIAPFGAFVELEPG 585 (647)
T ss_pred ---------------hccCCeEEEEEEEEEECCeEEEEECCC
Confidence 235689999999999999999988643
No 13
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.2e-35 Score=326.94 Aligned_cols=281 Identities=20% Similarity=0.290 Sum_probs=242.5
Q ss_pred chhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232 162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (514)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~ 241 (514)
.+...+.++++|+++.|+|+++++.|+||++| +.+|+||.+|+... ...++
T Consensus 191 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~-----------~~~~~----------------- 241 (565)
T PRK06299 191 EREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWK-----------RVNHP----------------- 241 (565)
T ss_pred HHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccc-----------ccCCH-----------------
Confidence 44555678999999999999999999999998 89999999998521 01111
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CE
Q 010232 242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GL 319 (514)
Q Consensus 242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi 319 (514)
...+++||.|.|+|+..| .++++.||++.... ..|..+...++.|+++.|+|+++.++|+||+++ |+
T Consensus 242 ----------~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v 310 (565)
T PRK06299 242 ----------SEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGI 310 (565)
T ss_pred ----------hhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCC
Confidence 234899999999999987 47899999998764 689999888999999999999999999999995 79
Q ss_pred EEEEecccc-cc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh----hhh--ccCCCCceEEEEEEEEecceE
Q 010232 320 RAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYGA 391 (514)
Q Consensus 320 ~gFVP~sel-~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~----~~~--~~l~~G~iV~G~V~~I~~~Ga 391 (514)
.||+|.+++ +. +..++.+.. .+|+.|.|+|+++|+++++|.||+|+. |.. ..+++|++|.|+|++++++|+
T Consensus 311 ~Glv~~sel~~~~~~~~~~~~~-~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~ 389 (565)
T PRK06299 311 EGLVHVSEMSWTKKNKHPSKVV-SVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGA 389 (565)
T ss_pred EEEEEHHHcCccccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceE
Confidence 999999999 43 345665543 799999999999999999999999853 442 368899999999999999999
Q ss_pred EEEECCCceEEEEEeeccccccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHH
Q 010232 392 QIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMA 469 (514)
Q Consensus 392 FV~I~~~gi~GLvh~Sels~~~v-~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a 469 (514)
||++++ ++.||+|+++++|.+. .++.+.|++||.|+|+|+.+| +++||.||+|++..+||..+.+
T Consensus 390 fV~l~~-~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~------------ 456 (565)
T PRK06299 390 FVGLEG-GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAK------------ 456 (565)
T ss_pred EEECCC-CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHh------------
Confidence 999998 7999999999999887 889999999999999999998 7899999999999999964322
Q ss_pred HHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232 470 KKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN 504 (514)
Q Consensus 470 ~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~ 504 (514)
....|+++.|+|.++.++|.|+.++.+
T Consensus 457 --------~~~~G~vV~G~V~~v~~~G~fV~l~~g 483 (565)
T PRK06299 457 --------KHKKGSIVTGTVTEVKDKGAFVELEDG 483 (565)
T ss_pred --------hcCCCCEEEEEEEEEecCceEEecCCC
Confidence 246799999999999999999998743
No 14
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=7.4e-35 Score=317.19 Aligned_cols=278 Identities=17% Similarity=0.239 Sum_probs=237.3
Q ss_pred chhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232 162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (514)
Q Consensus 162 ~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~ 241 (514)
.|....+.++.|++|+|+|++++++|++|++| +.+||||.+++.... .+
T Consensus 90 ~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~-g~~~flP~s~~~~~~-----------~~------------------- 138 (516)
T TIGR00717 90 LWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLN-GVEAFLPGSQVDVKP-----------IK------------------- 138 (516)
T ss_pred HHHHHHHHhhCCCeEEEEEEEEECCEEEEEEC-CEEEEEeHHHhcCcc-----------cC-------------------
Confidence 44444456678999999999999999999998 789999999974210 00
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC
Q 010232 242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE 317 (514)
Q Consensus 242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~ 317 (514)
.....+|+.++++|+..+ ..+++++|+|.+... ..|..+...++.|++++|+|+++.++|+||+++
T Consensus 139 ----------~~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~ 208 (516)
T TIGR00717 139 ----------DLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG 208 (516)
T ss_pred ----------chhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC
Confidence 112468999999999976 467899999987533 457777778899999999999999999999999
Q ss_pred CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEecce
Q 010232 318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYPYG 390 (514)
Q Consensus 318 Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~~G 390 (514)
|++||||.+++ +.+..++.++. ++|+.+.|+|+++|++++++.+|+|. +|+. ..+++|+++.|+|++++++|
T Consensus 209 g~~g~lp~~e~s~~~~~~~~~~~-~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G 287 (516)
T TIGR00717 209 GVDGLLHITDMSWKRVKHPSEYV-KVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYG 287 (516)
T ss_pred CEEEEEEHHHcCCCCCCCHHHhc-cCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCc
Confidence 99999999999 67777777654 79999999999999999999999985 4554 36899999999999999999
Q ss_pred EEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHH
Q 010232 391 AQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEM 468 (514)
Q Consensus 391 aFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~ 468 (514)
+||++++ ++.||+|+++++|. ...++.+.+++||.|+|+|+.+| +++++.||+|++..+||..+.+
T Consensus 288 ~fV~l~~-~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~----------- 355 (516)
T TIGR00717 288 VFVEIEE-GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEE----------- 355 (516)
T ss_pred EEEEeCC-CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHH-----------
Confidence 9999988 89999999999986 46778888999999999999998 7899999999999999865321
Q ss_pred HHHHHhhCccCCCCCcccCCCCCCCCCCCccchh
Q 010232 469 AKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMC 502 (514)
Q Consensus 469 a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~ 502 (514)
...+|+.+.|+|+++.+||.|+++.
T Consensus 356 ---------~~~~G~~v~g~V~~v~~~G~fV~l~ 380 (516)
T TIGR00717 356 ---------KHPVGDRVTGKIKKITDFGAFVELE 380 (516)
T ss_pred ---------hCCCCCEEEEEEEEEecceEEEECC
Confidence 2357999999999999999999886
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.2e-34 Score=310.09 Aligned_cols=248 Identities=20% Similarity=0.271 Sum_probs=212.4
Q ss_pred hhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232 160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (514)
Q Consensus 160 ~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~ 239 (514)
.+.|+......+.|++|+|+|+++.++|++|++| ..||||.+++.... ..+
T Consensus 110 ~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~-----------~~~---------------- 160 (486)
T PRK07899 110 ERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRR-----------VRD---------------- 160 (486)
T ss_pred cchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccc-----------cCC----------------
Confidence 3455543334468999999999999999999995 68999999874210 000
Q ss_pred ccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (514)
Q Consensus 240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd 315 (514)
..-.+|+.|.|+|+..| .+++++||+|.... ...|+.+...++.|+++.|+|+++.++|+||+
T Consensus 161 -------------~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVd 227 (486)
T PRK07899 161 -------------LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVD 227 (486)
T ss_pred -------------hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence 01148999999999987 46789999987543 35788888889999999999999999999999
Q ss_pred ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEec
Q 010232 316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYP 388 (514)
Q Consensus 316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~ 388 (514)
++|++||||.+++ +.++.++.++. .+||.|+|+|+++|+++++|.||+|. +|.. ..+.+|+++.|+|+++++
T Consensus 228 lggv~Glv~~Sels~~~v~~~~~~~-kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~ 306 (486)
T PRK07899 228 LGGVDGLVHVSELSWKHIDHPSEVV-EVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVP 306 (486)
T ss_pred ECCEEEEEEHHHCCCcccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEec
Confidence 9999999999999 77888887764 89999999999999999999999995 4643 257899999999999999
Q ss_pred ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCC
Q 010232 389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP 451 (514)
Q Consensus 389 ~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P 451 (514)
+|+||++.+ |+.||+|++++++.++.++.+.|++||+|+|+|+++| +++||.||+|++.++-
T Consensus 307 fGvFVeL~~-gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 307 FGAFVRVEE-GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred cEEEEEeCC-CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence 999999988 8999999999999999999999999999999999998 8999999999887643
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.8e-34 Score=301.78 Aligned_cols=255 Identities=25% Similarity=0.329 Sum_probs=219.9
Q ss_pred hchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccc
Q 010232 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD 240 (514)
Q Consensus 161 ~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d 240 (514)
+.|......++.|+++.|+|+++.++|++|+++ +..||||.+|+.... ..++
T Consensus 94 ~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~-----------~~~~---------------- 145 (390)
T PRK06676 94 KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRF-----------VEDF---------------- 145 (390)
T ss_pred hhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCcc-----------CCCh----------------
Confidence 345545556789999999999999999999995 459999999985320 0001
Q ss_pred cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE
Q 010232 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI 316 (514)
Q Consensus 241 ~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi 316 (514)
.. .+|+.+.|+|+..| ..+++.||++.+... ..|..+...++.|++++|+|+++.++|+||++
T Consensus 146 ------------~~-~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l 212 (390)
T PRK06676 146 ------------SD-FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI 212 (390)
T ss_pred ------------HH-cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe
Confidence 11 28999999999977 467899999987443 57888878889999999999999999999999
Q ss_pred CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEecc
Q 010232 317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYPY 389 (514)
Q Consensus 317 ~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~~ 389 (514)
+|++||||.+++ +.++.++.+.. .+|+.|+|+|+.+|+++++|.+|+|. +|.. ..+++|+++.|+|++++++
T Consensus 213 ~~v~g~v~~sels~~~~~~~~~~~-~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~ 291 (390)
T PRK06676 213 GGVDGLVHISELSHERVEKPSEVV-SVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDF 291 (390)
T ss_pred CCeEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCc
Confidence 999999999999 66677777664 79999999999999999999999985 3543 3689999999999999999
Q ss_pred eEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccch
Q 010232 390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK 458 (514)
Q Consensus 390 GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k 458 (514)
|+||++.+ |+.||+|+|++++.++.++.+.|++||.|+|+|+++| +++||.||+|++..+||..+.++
T Consensus 292 G~fV~l~~-gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~ 360 (390)
T PRK06676 292 GAFVEVLP-GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR 360 (390)
T ss_pred eEEEEECC-CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence 99999998 8999999999999999999999999999999999998 88999999999999999987655
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.98 E-value=9.7e-31 Score=292.18 Aligned_cols=251 Identities=24% Similarity=0.339 Sum_probs=214.0
Q ss_pred hchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccc
Q 010232 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD 240 (514)
Q Consensus 161 ~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d 240 (514)
..|......+++|+++.|+|+++.++|++|++|. .+||||.+|+...+ .+++
T Consensus 378 ~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~-----------~~d~---------------- 429 (647)
T PRK00087 378 KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGY-----------VEDL---------------- 429 (647)
T ss_pred hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccc-----------cCCH----------------
Confidence 3444444557899999999999999999999986 89999999985321 0011
Q ss_pred cccccCCCCCCCCcccCCCEEEEEEEEEcC-CCc-EEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGR-PLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (514)
Q Consensus 241 ~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~-~gr-liLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd 315 (514)
.. .+|+.+.|+|+..|. +++ +.+|++.... ...|....+.++.|+++.|+|+++.++|+||+
T Consensus 430 ------------~~-~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~ 496 (647)
T PRK00087 430 ------------SE-YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVD 496 (647)
T ss_pred ------------HH-hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEE
Confidence 11 289999999999774 667 9999988753 23455565667899999999999999999999
Q ss_pred ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEec
Q 010232 316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYP 388 (514)
Q Consensus 316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~ 388 (514)
++|++||||.+++ +.++.++.+.. .+|+.+.++|+++|++++++.+|+|+ +|.. ..+++|+++.|+|+++++
T Consensus 497 l~gv~Gll~~sels~~~~~~~~~~~-~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~ 575 (647)
T PRK00087 497 IGGVDGLLHVSEISWGRVEKPSDVL-KVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAP 575 (647)
T ss_pred ECCEEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEEC
Confidence 9999999999999 66777776654 89999999999999999999999996 4543 368999999999999999
Q ss_pred ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCcc
Q 010232 389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLF 454 (514)
Q Consensus 389 ~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~ 454 (514)
+|+||++.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +++||.||+|++.++|++.
T Consensus 576 ~G~fV~l~~-~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~~~~ 641 (647)
T PRK00087 576 FGAFVELEP-GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDI 641 (647)
T ss_pred CeEEEEECC-CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence 999999988 8999999999999999999999999999999999998 7899999999999999443
No 18
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.96 E-value=4.9e-28 Score=238.31 Aligned_cols=250 Identities=18% Similarity=0.119 Sum_probs=209.3
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCce-eEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232 169 EPKPGDFVIGVVVSGNENKLDVNVGADL-LGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (514)
Q Consensus 169 ~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~-~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~ 247 (514)
.+++|+++++.|++.++.|+|++-|... .-++|.++.-
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~----------------------------------------- 40 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE----------------------------------------- 40 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCc-----------------------------------------
Confidence 4679999999999999999999987653 4444544331
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEE-CCeEEEEEC-CEEEEEec
Q 010232 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPK 325 (514)
Q Consensus 248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~-~~G~fVdi~-Gi~gFVP~ 325 (514)
....++||.|.+++| .|.++|+++|++.+... .|+.-.++|++++ +-|+||++| .-+.|||.
T Consensus 41 ----~~e~evGdev~vFiY-~D~~~rl~aTt~~p~~t-----------vg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~ 104 (287)
T COG2996 41 ----EDELEVGDEVTVFIY-VDSEDRLIATTREPKAT-----------VGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPL 104 (287)
T ss_pred ----CCccccCcEEEEEEE-ECCCCceeheeecceEe-----------ecceeEEEEEEEcCCcceEEecCCCcceeeeh
Confidence 123689999999999 89999999999988754 8999999999999 779999993 24899999
Q ss_pred cccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh--hhhh--ccC---CCCceEEEEEEEEecceEEEEECCC
Q 010232 326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--AWAT--LNL---REGTLLEGTVKKIYPYGAQIRIGDS 398 (514)
Q Consensus 326 sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~--~~~~--~~l---~~G~iV~G~V~~I~~~GaFV~I~~~ 398 (514)
+++.. .++++.++|+++.|+++ +|+.+ ||....+. .++. ... -.++.+.|+|+++...|.||.+++
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----LKSLWPQKGDKLLVYLY-VDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN- 177 (287)
T ss_pred hhccc----ccccCCCCCCEEEEEEE-EccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-
Confidence 99842 12344579999999998 77654 88877763 2221 122 359999999999999999999988
Q ss_pred ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCcc
Q 010232 399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPA 478 (514)
Q Consensus 399 gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~ 478 (514)
++.||||.||.. ..++.|++++++|+.++++++|.||++ ....+.+++.|+.+...|..
T Consensus 178 ~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~-------------p~~~E~l~~daq~Il~yL~~ 236 (287)
T COG2996 178 GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLR-------------PRAHEMLDEDAQMILTYLES 236 (287)
T ss_pred CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccc-------------cccHHhhhhhHHHHHHHHHH
Confidence 899999999987 568999999999999999999999994 45567788999999999999
Q ss_pred CCCCCcccCCCCCCCCCCCccchhhccceeeeecC
Q 010232 479 VSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQD 513 (514)
Q Consensus 479 ~~~g~~~e~~v~~~~pfg~~~~~~~~~~~~~~~~~ 513 (514)
.+ |++||+|+|+|++|.+.|+|||-
T Consensus 237 ~g----------G~mpf~DKSsPEdIk~~FgiSKg 261 (287)
T COG2996 237 NG----------GFMPFNDKSSPEDIKATFGISKG 261 (287)
T ss_pred cC----------CccccCCCCCHHHHHHHhCcCHH
Confidence 99 99999999999999999999984
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.91 E-value=1.1e-23 Score=217.15 Aligned_cols=190 Identities=18% Similarity=0.204 Sum_probs=159.8
Q ss_pred HHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECC-EEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232 283 RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDL 360 (514)
Q Consensus 283 ~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~G-i~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rI 360 (514)
....|+.....++.|++++|+|+++.++|++|++++ .+||||.+++ +.+..++.++. .+|+.+.|+|+++|.+++++
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 344555554557999999999999999999999975 8999999999 66777777764 79999999999999999999
Q ss_pred Eeehhh-----hhhhc--cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 361 ILSERE-----AWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 361 iLS~K~-----~~~~~--~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
+||+|+ +|+.. ....|++|.|+|+++.++|+||+++ |+.||||+|+++|.+.. +.+ +|+.|.++|++
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---EEL-VGEELPLKFLE 170 (318)
T ss_pred EEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCccCCc---ccc-CCCEEEEEEEE
Confidence 999985 35542 4567999999999999999999996 79999999999986533 334 99999999999
Q ss_pred Ee-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchh
Q 010232 434 SM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMC 502 (514)
Q Consensus 434 vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~ 502 (514)
+| +++||.||+|....++ .+....+|++++|+|+++.+||.|++..
T Consensus 171 id~~~~~i~lS~K~~~~~~-----------------------~~~~~k~G~vv~G~V~~I~~~G~fV~i~ 217 (318)
T PRK07400 171 VDEERNRLVLSHRRALVER-----------------------KMNRLEVGEVVVGTVRGIKPYGAFIDIG 217 (318)
T ss_pred EEcccCEEEEEhhHhhhhh-----------------------hhccCCCCCEEEEEEEEEECCeEEEEEC
Confidence 98 7899999998654311 2455778999999999999999999864
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=2.6e-18 Score=151.71 Aligned_cols=81 Identities=38% Similarity=0.594 Sum_probs=77.6
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P 451 (514)
.+++|++++|+|++|++|||||.|++ |-.||||+|++++.|++++.+++++||.|+|+|+.+|++++|+||||.++..|
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 47899999999999999999999999 89999999999999999999999999999999999999999999999999877
Q ss_pred Cc
Q 010232 452 GL 453 (514)
Q Consensus 452 ~~ 453 (514)
-.
T Consensus 81 e~ 82 (129)
T COG1098 81 EK 82 (129)
T ss_pred cc
Confidence 54
No 21
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.68 E-value=3.8e-17 Score=167.41 Aligned_cols=116 Identities=21% Similarity=0.273 Sum_probs=101.8
Q ss_pred cCC-CCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 372 NLR-EGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 372 ~l~-~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
.+. +|++|.|+|++|++||+||.|.++ |++||||+|+|||.++.++++++++||.|.|+|+++| ++++|.||+|++.
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 344 899999999999999999999632 7999999999999999999999999999999999998 8899999999999
Q ss_pred CCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCC-CCCccc-hhhccce
Q 010232 449 SEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPP-FDSEAS-MCANWKW 507 (514)
Q Consensus 449 ~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~p-fg~~~~-~~~~~~~ 507 (514)
++||..+.++++. |..+++++..+.. ||.+.+ +|..+-|
T Consensus 93 ~~pw~~~~e~~~~--------------------g~~v~~~V~~ia~~~g~~~eely~~i~~ 133 (319)
T PTZ00248 93 PEDIEACEEKFSK--------------------SKKVHSIMRHIAQKHGMSVEELYTKIIW 133 (319)
T ss_pred cchHHHHHHhCcC--------------------CCEEEEEEEEchhhcCCCHHHHHHHHHH
Confidence 9999988777654 7788888888865 888876 5555544
No 22
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.67 E-value=8.9e-16 Score=175.77 Aligned_cols=244 Identities=22% Similarity=0.285 Sum_probs=192.2
Q ss_pred cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecc-cccccccchhhhhhhhhchhhhHHhhhccceeeeccccccc
Q 010232 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTK-EVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM 244 (514)
Q Consensus 166 ~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~s-El~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l 244 (514)
......+|++..|+|..++++++.|+.+.+..|-...- ++...+ ..+|
T Consensus 1061 ~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~-----------~~~P-------------------- 1109 (1710)
T KOG1070|consen 1061 SDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY-----------SMTP-------------------- 1109 (1710)
T ss_pred CCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc-----------cCCh--------------------
Confidence 34455589999999999999998999988877733222 322110 0011
Q ss_pred cCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEeh-------HHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE
Q 010232 245 SGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTR-------RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI 316 (514)
Q Consensus 245 ~~~~~~~~~~~~vGd~V~v~Vl~~d~-~grliLS~k-------k~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi 316 (514)
...+..++.+.+.++.++. ++.+-||.+ .+.....--...+.++.|+++.|.|..+.+.|+|+.+
T Consensus 1110 -------~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~l 1182 (1710)
T KOG1070|consen 1110 -------VEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIAL 1182 (1710)
T ss_pred -------HHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEE
Confidence 1235677889999998774 444888888 3332222222356779999999999999999999999
Q ss_pred C-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh---------hhhccCCCCceEEEEEEE
Q 010232 317 E-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA---------WATLNLREGTLLEGTVKK 385 (514)
Q Consensus 317 ~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~---------~~~~~l~~G~iV~G~V~~ 385 (514)
. ++.||+|++++ ......++... .+|+.+.++|+.+|+..+|+-+|.|.. .....++.|+...|+|..
T Consensus 1183 s~~v~a~v~is~~~ds~~k~w~k~~-~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~ 1261 (1710)
T KOG1070|consen 1183 SRKVEAFVPISGLSDSFEKEWEKHL-PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEV 1261 (1710)
T ss_pred ccceEEEEEccccccchhhhhhccC-CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEE
Confidence 6 69999999999 44444455443 799999999999999999999999842 223479999999999999
Q ss_pred EecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 386 IYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 386 I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
+.++|.||+++.+ +..|++|++++.+.+..+....+..|+.|+|.+++++ +.+||.|.+|..-
T Consensus 1262 ~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~ 1326 (1710)
T KOG1070|consen 1262 VDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSY 1326 (1710)
T ss_pred ecCCceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhc
Confidence 9999999999885 3699999999999999999999999999999999998 8899999998764
No 23
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.66 E-value=3.3e-16 Score=179.26 Aligned_cols=195 Identities=20% Similarity=0.249 Sum_probs=166.8
Q ss_pred CcccCCCEEEEEEEEEcC-CCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE--CCEEEEEeccccc
Q 010232 253 PVVETGTVLFAEVLGRTL-SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL 329 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~d~-~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel~ 329 (514)
+.+++|.++.++|..+-. +..+++|.++......+.++.+ ++.|+.|.|+|..+.+.|+.|.+ +.+.|++|..++.
T Consensus 466 ~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hls 544 (1710)
T KOG1070|consen 466 PIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLS 544 (1710)
T ss_pred CceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccceeeeEEEEecCCcEEEEEecCceeeecChHhhh
Confidence 568899999999998654 4455788887766555555544 79999999999999999999998 3499999999995
Q ss_pred cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh---------hccCCCCceEEEEEEEEecceEEEEECCCce
Q 010232 330 SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---------TLNLREGTLLEGTVKKIYPYGAQIRIGDSNR 400 (514)
Q Consensus 330 ~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~---------~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi 400 (514)
+....+....+.+|..++++|+.++...+++.|++|..+- ..+..+|.++.|+|..+.++|+||.+.+ |+
T Consensus 545 d~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g-~l 623 (1710)
T KOG1070|consen 545 DHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTG-GL 623 (1710)
T ss_pred hcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecC-cc
Confidence 4433344444579999999999999999999999997542 2468899999999999999999999999 89
Q ss_pred EEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232 401 SGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (514)
Q Consensus 401 ~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~ 449 (514)
+||.|.++++++++.++++.|.+||+|.|+|.++| +++||.+++|+..+
T Consensus 624 sGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~ 673 (1710)
T KOG1070|consen 624 SGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC 673 (1710)
T ss_pred ccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence 99999999999999999999999999999999998 88999999987654
No 24
>PRK08582 hypothetical protein; Provisional
Probab=99.58 E-value=1.9e-14 Score=132.08 Aligned_cols=82 Identities=30% Similarity=0.497 Sum_probs=77.7
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P 451 (514)
.+++|++|.|+|++|+++|+||+|++ ++.||||+|++++.++.++.+.|++||.|+|+|++++.+++|.||+|++.++|
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 89999999999999999999999999999999999986699999999999999
Q ss_pred Ccc
Q 010232 452 GLF 454 (514)
Q Consensus 452 ~~~ 454 (514)
|..
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=99.55 E-value=1.3e-15 Score=156.05 Aligned_cols=136 Identities=16% Similarity=0.256 Sum_probs=119.5
Q ss_pred CCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----h
Q 010232 296 LNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----A 367 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~ 367 (514)
.|++|.|+|+++.++|+||++ +|++||||.|++ +.++.+++++. ++|+++.|+|+++|+++++|.||.|+ +
T Consensus 17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v-kvGd~v~vkVl~VD~ekg~IdLS~K~v~~~p 95 (319)
T PTZ00248 17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI-RVGRHEVVVVLRVDKEKGYIDLSKKRVSPED 95 (319)
T ss_pred CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEeeecccch
Confidence 799999999999999999999 489999999999 88899999886 89999999999999999999999995 5
Q ss_pred hhh--ccCCCCceEEEEEEEEec-ceEEEE------ECCCceEEEEEeeccccccccCcccccC---CCCEEEEEEEE
Q 010232 368 WAT--LNLREGTLLEGTVKKIYP-YGAQIR------IGDSNRSGLLHISNMSRTRVTSVSDLLN---EGERVKVLVVK 433 (514)
Q Consensus 368 ~~~--~~l~~G~iV~G~V~~I~~-~GaFV~------I~~~gi~GLvh~Sels~~~v~~~~~~~k---vGd~VkvkVi~ 433 (514)
|.. ..++.|+++.|+|..+.. +|++++ ..+ .+.++.|..+++...+.++.+.|. +++.++..++.
T Consensus 96 w~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~p-l~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~ 172 (319)
T PTZ00248 96 IEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWP-LYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQ 172 (319)
T ss_pred HHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHH-HHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHH
Confidence 654 479999999999999955 999998 455 689999999999888888887777 67666555543
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=3.8e-14 Score=116.36 Aligned_cols=70 Identities=24% Similarity=0.367 Sum_probs=65.0
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc---ccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV---SDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~---~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
+++|++|.|+|++++++|+||++++ ++.|+||+++++|.++.++ .+.|++||.|+|+|+++| +++||.||
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 5799999999999999999999998 8999999999999997775 588999999999999998 78899886
No 27
>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=99.49 E-value=1e-13 Score=113.05 Aligned_cols=71 Identities=24% Similarity=0.386 Sum_probs=66.8
Q ss_pred CCCCceEEEEEEEEec-ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232 373 LREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~-~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK 445 (514)
+++|++|.|+|+++.+ +|+||++.+ +..|++|+|+++++++.++.+.|++||.|+|+|++++. +|+.||+|
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 5799999999999986 899999998 89999999999999999999999999999999999865 99999986
No 28
>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=99.47 E-value=2.7e-13 Score=109.96 Aligned_cols=73 Identities=30% Similarity=0.562 Sum_probs=69.2
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
.+++|+++.|+|+++.++|+||++++ ++.||||.+++++.+..++...+++||+|+|+|++++ +++++.||+|
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 37899999999999999999999997 8999999999999999999999999999999999998 8889999986
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=3.6e-13 Score=109.90 Aligned_cols=71 Identities=34% Similarity=0.534 Sum_probs=65.1
Q ss_pred CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl 444 (514)
+.|+++.|+|++|++||+||++.+.+.+||+|+|+++|.++.++.+.|++||+|+|+|++++..+|+.||+
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 58999999999999999999996433699999999999999999999999999999999998545999987
No 30
>PRK08059 general stress protein 13; Validated
Probab=99.45 E-value=2.5e-13 Score=122.14 Aligned_cols=105 Identities=30% Similarity=0.446 Sum_probs=90.3
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~ 450 (514)
++++|+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++ +++++.||+|.+..+
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 789999999999888
Q ss_pred CCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCcc
Q 010232 451 PGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEA 499 (514)
Q Consensus 451 P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~ 499 (514)
|. ..+.+..+.+.+...+ |++||++.-
T Consensus 83 ~~------------~~~~~~~~l~~~~~~~----------g~~~l~~~~ 109 (123)
T PRK08059 83 PE------------AKRKKGKILIPNPSEQ----------GFNTLRDKL 109 (123)
T ss_pred cc------------cccccccccccccccC----------CchhHHHHH
Confidence 73 1122445556666666 888887764
No 31
>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=99.43 E-value=9.2e-13 Score=108.27 Aligned_cols=71 Identities=25% Similarity=0.302 Sum_probs=65.2
Q ss_pred cCCCCceEEEEEEEEecceEEEEEC-CCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIG-DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~-~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~ 449 (514)
+++.|+++.|+|++|+++|+||+++ + |+.||+|.++++|. +.+++||.+.|+|++++ +++++.||+|++.+
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 DLVEGMVLSGCVSSVEDHGYILDIGIP-GTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCC-CcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 4789999999999999999999997 5 79999999999976 77999999999999998 88999999998764
No 32
>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=99.43 E-value=5.3e-13 Score=107.20 Aligned_cols=69 Identities=26% Similarity=0.352 Sum_probs=65.8
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
|+++.|+|++++++|+||++++ ++.||+|++++++.++.++.+.+++||.|+|+|++++ +++++.||+|
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 7899999999999999999998 7999999999999999999999999999999999998 6889999986
No 33
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.43 E-value=3.4e-13 Score=153.48 Aligned_cols=89 Identities=27% Similarity=0.384 Sum_probs=82.8
Q ss_pred cCCCCceEE-EEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCC
Q 010232 372 NLREGTLLE-GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE 450 (514)
Q Consensus 372 ~l~~G~iV~-G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~ 450 (514)
..++|+++. |+|++|++||+||+|.+ |++||||+|+|+|.++.++.+.|++||.|+|+|+++|.++||.||+|++.++
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 69999999999999998 8999999999999999999999999999999999998889999999999999
Q ss_pred CCccccchhhh
Q 010232 451 PGLFVSDKERV 461 (514)
Q Consensus 451 P~~~~~~k~~v 461 (514)
||+.+.++++-
T Consensus 829 Pw~~~~~~~~~ 839 (891)
T PLN00207 829 ANSEKSSQKQQ 839 (891)
T ss_pred chhhhhhhhhh
Confidence 99988665544
No 34
>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=6.4e-13 Score=108.75 Aligned_cols=69 Identities=17% Similarity=0.162 Sum_probs=65.4
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeecccccc--ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~--v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
|++|.|+|++++++|+||.+++ +++|+||.++++|.+ ..++.+.|++||.|+|+|+.+| +++||.||+|
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 GQEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999998 899999999999864 8899999999999999999998 7899999996
No 35
>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=5.4e-13 Score=111.24 Aligned_cols=73 Identities=27% Similarity=0.346 Sum_probs=69.4
Q ss_pred ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
.++++|+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++ ++++|.|||
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 368999999999999999999999998 7999999999999999999999999999999999998 789999986
No 36
>PRK07252 hypothetical protein; Provisional
Probab=99.42 E-value=9.5e-13 Score=117.98 Aligned_cols=77 Identities=38% Similarity=0.592 Sum_probs=72.7
Q ss_pred CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCC
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP 451 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P 451 (514)
++|+++.|+|++|+++|+||+|.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +.+++.||+|++++++
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 689999999999999999999998 7999999999999999999999999999999999998 6899999999998743
No 37
>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=1.6e-12 Score=105.46 Aligned_cols=72 Identities=21% Similarity=0.309 Sum_probs=67.8
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
+++|+++.|+|++++++|+||++++ +++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|
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 5789999999999999999999998 7999999999999988888999999999999999998 6789999985
No 38
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.41 E-value=1.5e-12 Score=107.38 Aligned_cols=75 Identities=32% Similarity=0.573 Sum_probs=69.4
Q ss_pred CceEEEEEEEEecceEEEEECCC--ceEEEEEeeccccccc-cCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~--gi~GLvh~Sels~~~v-~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P 451 (514)
|+++.|+|+++++||+||+|++. ++.||+|.+++++.++ .++.+.|++||+|+|+|++++ ++++.||+|++.++.
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 6899999999999986 999999999999999999998 899999999998764
No 39
>PRK05807 hypothetical protein; Provisional
Probab=99.40 E-value=1.5e-12 Score=119.11 Aligned_cols=75 Identities=39% Similarity=0.582 Sum_probs=70.9
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCc
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE 448 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~ 448 (514)
.+++|++|.|+|++|+++|+||.|. +..||||++++++.++.++.+.|++||.|+|+|++++++++|.||+|.+.
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 3689999999999999999999994 68999999999999999999999999999999999987799999999987
No 40
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.39 E-value=1.6e-12 Score=104.46 Aligned_cols=68 Identities=22% Similarity=0.449 Sum_probs=64.8
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
|+++.|+|++|.++|+||++++ +++||+|.+++++.+..++.+.|++||.++|+|+++| +++++.||+
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 7899999999999999999988 7999999999999999999999999999999999998 789999985
No 41
>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=99.38 E-value=2.4e-12 Score=104.76 Aligned_cols=74 Identities=31% Similarity=0.395 Sum_probs=68.2
Q ss_pred CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD 446 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~ 446 (514)
++.|+++.|+|.++.++|+||++.+. ++.||+|++++++.++.++.+.|++||.|+|+|++++ +.+++.||+|+
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 36899999999999999999999742 5899999999999999999999999999999999998 67899999974
No 42
>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=99.37 E-value=2e-12 Score=105.08 Aligned_cols=68 Identities=25% Similarity=0.403 Sum_probs=64.2
Q ss_pred CceEE-EEEEEE-ecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 376 GTLLE-GTVKKI-YPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 376 G~iV~-G~V~~I-~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
|++++ |+|+++ .++|+||++.+ |++||+|+|++++.++.++.+.|++||.++|+|+.+| .+++|.||+
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 78899 999999 69999999998 8999999999999999999999999999999999998 788999986
No 43
>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=3.6e-12 Score=103.61 Aligned_cols=74 Identities=35% Similarity=0.542 Sum_probs=68.5
Q ss_pred CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL 447 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l 447 (514)
++|+++.|+|++++++|+||++.+.++.|++|.+++++.+..++.+.|++||.|+|+|++++ +.+++.||+|..
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 46999999999999999999998436999999999999999999999999999999999998 689999999864
No 44
>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=99.37 E-value=3.4e-12 Score=102.87 Aligned_cols=72 Identities=31% Similarity=0.527 Sum_probs=67.7
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
|+++.|+|+++.++|+||++++ +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||+|.++
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 6689999998753
No 45
>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=102.66 Aligned_cols=67 Identities=21% Similarity=0.311 Sum_probs=63.7
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
|+++.|+|+++.++|+||++.+ ++.||+|++++++.+..++.+.|++||.|+|+|+++| ++++|.||
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 68899876
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=99.34 E-value=3.1e-12 Score=102.21 Aligned_cols=67 Identities=31% Similarity=0.560 Sum_probs=62.4
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
|+++.|+|++++++|+||++.+ +++||+|.++++| .++.++.+.|++||+|+|+|+++| +++||.||
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 7899999999999999999998 8999999999997 578889999999999999999998 78899875
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=99.33 E-value=6.7e-12 Score=99.16 Aligned_cols=69 Identities=45% Similarity=0.755 Sum_probs=65.3
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK 445 (514)
|+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++.++++.||+|
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 7899999999999999999998 79999999999999999999999999999999999877789999986
No 48
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.30 E-value=2.5e-12 Score=127.15 Aligned_cols=96 Identities=24% Similarity=0.410 Sum_probs=81.6
Q ss_pred CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~ 450 (514)
.++|++|-|+|.+|.+||+||.|..+ |++||+|+||++.+|+.++++++++||++-|+|+++| .++-|+||||.+.++
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 58999999999999999999999765 7999999999999999999999999999999999999 789999999999876
Q ss_pred CCccccchhhhhhHHHHH
Q 010232 451 PGLFVSDKERVFSEAEEM 468 (514)
Q Consensus 451 P~~~~~~k~~v~~~ae~~ 468 (514)
--..-...++..++|...
T Consensus 89 q~~~k~~~wk~~qka~kl 106 (269)
T COG1093 89 QRRKKIQEWKKEQKADKL 106 (269)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 544433334444444333
No 49
>PHA02945 interferon resistance protein; Provisional
Probab=99.28 E-value=1.7e-11 Score=102.79 Aligned_cols=75 Identities=23% Similarity=0.227 Sum_probs=69.3
Q ss_pred CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeecc--ccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNM--SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sel--s~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
.++|+++.|+|+. .+||+||.+.++ |.+||||+|++ +..++++ ++++ .||+|.|+|+++| .++-|+||||+..
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 4899999999999 999999999876 89999999955 9999999 9999 9999999999998 7899999999886
Q ss_pred CC
Q 010232 449 SE 450 (514)
Q Consensus 449 ~~ 450 (514)
++
T Consensus 86 ~~ 87 (88)
T PHA02945 86 RH 87 (88)
T ss_pred cC
Confidence 53
No 50
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.28 E-value=1.8e-11 Score=98.42 Aligned_cols=69 Identities=25% Similarity=0.379 Sum_probs=65.5
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
|++|.|+|.++.++|+||+++. +.+|++|.+++++.++.++.+.|++||.++|+|++++ +.++|.||+|
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 6789999985
No 51
>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=99.26 E-value=2.7e-11 Score=97.95 Aligned_cols=70 Identities=31% Similarity=0.488 Sum_probs=63.0
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
+.+|+++.|+|++|+++|+||++.+ +++||+|.++++|. +..++.+.|++||.|+|+|++++ +++++.|+
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 4689999999999999999999998 79999999999975 55577888999999999999998 77888764
No 52
>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=99.24 E-value=4.9e-11 Score=96.69 Aligned_cols=71 Identities=23% Similarity=0.450 Sum_probs=62.9
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
++.|+++.|+|++++++|+||+++ |++||||.+++ +.+..++.... .+||++.|+|+++|++++++.+|+|
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 468999999999999999999998 89999999999 44444555543 7999999999999999999999986
No 53
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.22 E-value=4.9e-11 Score=120.25 Aligned_cols=79 Identities=28% Similarity=0.507 Sum_probs=73.3
Q ss_pred CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE 450 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~ 450 (514)
.++|++|.|+|++|.++|+||++.++ |+.||||+|+++++++.++.+.+++||.|.|+|+++| ++++|.||+|.+.++
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 57999999999999999999999754 7999999999999999999999999999999999998 778999999988865
Q ss_pred C
Q 010232 451 P 451 (514)
Q Consensus 451 P 451 (514)
.
T Consensus 86 e 86 (262)
T PRK03987 86 Q 86 (262)
T ss_pred h
Confidence 4
No 54
>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=99.22 E-value=2.4e-11 Score=105.61 Aligned_cols=74 Identities=30% Similarity=0.407 Sum_probs=66.4
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-------------------cCcccccCCCCEEEEEEEE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-------------------~~~~~~~kvGd~VkvkVi~ 433 (514)
|++|++|.|+|++|.++|+||.+.+ |+.|++|+++++|.+. .++.+.|++||.|+|+|++
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 5799999999999999999999998 8999999999998763 3477889999999999999
Q ss_pred Ee-C---CCeEEEEEecC
Q 010232 434 SM-F---PDKISLSIADL 447 (514)
Q Consensus 434 vd-e---~~rI~LSlK~l 447 (514)
++ + ++||.||+|..
T Consensus 80 ~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 80 LDKSKSGKKRIELSLEPE 97 (100)
T ss_pred ccCCcCCCcEEEEEecHH
Confidence 98 4 68999999753
No 55
>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=99.22 E-value=3.6e-11 Score=94.85 Aligned_cols=67 Identities=39% Similarity=0.583 Sum_probs=63.0
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
|+++.|+|++++++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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 7899999999999999999998 7999999999999999999999999999999999998 67898876
No 56
>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=99.21 E-value=4.5e-11 Score=100.13 Aligned_cols=74 Identities=18% Similarity=0.199 Sum_probs=67.3
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccc----ccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR----TRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~----~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
+++|++|.|+|++++++|++|++++ +++|++|.+++++ .+..++.+.+++||.|+|+|+++++++++.||+|..
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 5899999999999999999999998 7999999999996 456778888999999999999998669999999864
No 57
>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=1.1e-10 Score=93.31 Aligned_cols=66 Identities=41% Similarity=0.700 Sum_probs=58.9
Q ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
|++++|+|+++.++|++|+++|++||||.+++ +.+..++.+ .+|+.+.|+|+++|++++++.+|+|
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 78999999999999999999889999999999 455555544 4899999999999999999999986
No 58
>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=99.19 E-value=7.5e-11 Score=94.62 Aligned_cols=65 Identities=18% Similarity=0.328 Sum_probs=58.7
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
|++|+|+|+++.++|+||++.+ +++|++|.++++..+.. .+.|++||+|+|+|+.+| +++||.||
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 678999999999999998 67888876
No 59
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.19 E-value=4.2e-10 Score=112.05 Aligned_cols=144 Identities=18% Similarity=0.164 Sum_probs=116.1
Q ss_pred cCCCCCCEEEEEEEEEe-CCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232 168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~-~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~ 246 (514)
..+..|++-.++|+.++ +.|+|||.|-..+.++|.+++... +++
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 46788999999999999 899999999999999999998532 111
Q ss_pred CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHh-hhc--CCCEEEEEEEEEECCeEEEEEC-CEEEE
Q 010232 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQ-IKQ--LNEPIEVKFTEWNTGGLLTRIE-GLRAF 322 (514)
Q Consensus 247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~-~~k--~GeiV~GkV~~v~~~G~fVdi~-Gi~gF 322 (514)
=+++||.+-|.++ .|+.+|+..+++....- +.+.. +.. .|+.++|+|.+....|.||-++ +..||
T Consensus 114 -------wpq~Gd~l~v~l~-~Dkk~Ri~g~~a~~~~l---~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~Gf 182 (287)
T COG2996 114 -------WPQKGDKLLVYLY-VDKKGRIWGTLAIEKIL---ENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGF 182 (287)
T ss_pred -------CCCCCCEEEEEEE-EccCCcEEEEecchhHH---HhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEE
Confidence 1579999999988 89999999887654322 11111 221 5999999999999999999995 69999
Q ss_pred EeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 323 LPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 323 VP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
||.||..... .+|++++++|+.+.+ .++|-||.+.
T Consensus 183 Ih~sEr~~~p--------rlG~~l~~rVi~~re-Dg~lnLSl~p 217 (287)
T COG2996 183 IHKSERFAEP--------RLGERLTARVIGVRE-DGKLNLSLRP 217 (287)
T ss_pred Ecchhhcccc--------cCCceEEEEEEEEcc-CCeeeccccc
Confidence 9999984332 489999999999976 8999999985
No 60
>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=99.18 E-value=1e-10 Score=92.69 Aligned_cols=68 Identities=43% Similarity=0.605 Sum_probs=63.6
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl 444 (514)
|+++.|+|.++.++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++..+++.||+
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 6899999999999999999998 7999999999999999999999999999999999997777999885
No 61
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.16 E-value=1.8e-10 Score=90.74 Aligned_cols=71 Identities=37% Similarity=0.597 Sum_probs=66.0
Q ss_pred CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
++|+++.|+|.+++++|+||++++ ++.|++|.+++++.+..++...|++||.|+|+|++++ +++++.||++
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 479999999999999999999998 7999999999999888888889999999999999998 6699999985
No 62
>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=99.16 E-value=1.5e-10 Score=92.45 Aligned_cols=66 Identities=21% Similarity=0.309 Sum_probs=60.4
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
|+++.|+|+++.++|++|++ + |+.||||.+++++.+..++... +||.++|+|+++| ++++|.||.|
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-GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 5 7999999999999888877663 8999999999998 6889999985
No 63
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.15 E-value=7.6e-11 Score=104.66 Aligned_cols=74 Identities=22% Similarity=0.301 Sum_probs=68.1
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA 369 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~ 369 (514)
++.|.+++|+|+.+.++||||.++ |-.||||+|++ ...++++.++. .+||.|.|+|+.+|+ +++|.||.|.+.+
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L-~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL-KVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh-cCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence 579999999999999999999996 58999999999 67888888886 899999999999998 9999999998755
No 64
>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=99.15 E-value=1.6e-10 Score=91.37 Aligned_cols=67 Identities=46% Similarity=0.671 Sum_probs=62.5
Q ss_pred CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
+|+++.|+|.++.++|+||+++ +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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 5899999999999999999997 5899999999999999999999999999999999998 67899876
No 65
>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=99.14 E-value=1.9e-10 Score=94.51 Aligned_cols=69 Identities=12% Similarity=0.124 Sum_probs=60.3
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChh---hHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFT---ELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~---el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
++.|+++.|+|+++.++|+||+++ |++||||.+++ +.++.+++ +. +++|+.+.|+|+++|+++++|.||
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 368999999999999999999996 79999999999 55655553 33 389999999999999999999886
No 66
>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=8.6e-11 Score=131.61 Aligned_cols=71 Identities=32% Similarity=0.456 Sum_probs=66.4
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccc----cccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels----~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LS 443 (514)
.+++|++|.|+|++|++||+||+|.+ |++||||+|+|+ +.++.++.+++++||+|+|+|+++|+++||.|+
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 47899999999999999999999988 899999999996 468999999999999999999999988899886
No 67
>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=99.11 E-value=3e-10 Score=96.48 Aligned_cols=72 Identities=32% Similarity=0.450 Sum_probs=62.9
Q ss_pred cCCCCceEEEEEEEEecc--eEEEEECCCceEEEEEeecccc---ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSR---TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~--GaFV~I~~~gi~GLvh~Sels~---~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
.+++|+++.|+|++|.++ ||||++++ |.+||||+|+++| .++.++.+.+++||.|.|+|++.. ..+-..||.
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence 468999999999999997 99999998 8999999999999 678899999999999999999875 444444444
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.08 E-value=5.3e-10 Score=126.61 Aligned_cols=75 Identities=36% Similarity=0.546 Sum_probs=71.6
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
.+++|+++.|+|++|.+||+||+|.+ +.+||+|+|++++.++.++.+.|++||.|+|+|+++|..+||.||+|.+
T Consensus 618 ~~~vG~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~ 692 (693)
T PRK11824 618 EPEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692 (693)
T ss_pred cCcCCeEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 68999999999999999999999998 8999999999999999999999999999999999998559999999976
No 69
>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=99.08 E-value=8.1e-10 Score=91.14 Aligned_cols=70 Identities=21% Similarity=0.422 Sum_probs=61.4
Q ss_pred CCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
+|+++.|+|++|+++|+||++++.+++|++|.+++++.++. .....|++||.|+|+|+.++ ++++|.+
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 48999999999999999999997569999999999876432 44578999999999999998 6899999
Q ss_pred EE
Q 010232 443 SI 444 (514)
Q Consensus 443 Sl 444 (514)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 86
No 70
>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=99.08 E-value=5.1e-10 Score=89.83 Aligned_cols=68 Identities=21% Similarity=0.328 Sum_probs=60.6
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
|+++.|+|+++.++|+||++. ++.||+|.+++ ..+..++.+.. ++||.++|+|+++|++++++.||+|
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 69999999999 45566666643 7999999999999999999999975
No 71
>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=99.08 E-value=6.7e-10 Score=90.91 Aligned_cols=68 Identities=12% Similarity=0.179 Sum_probs=60.5
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-c--ccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-S--RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~--~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
|+++.|+|+++.++|+||.++ +++||||.+++. . +..++.+.+ ++|+.++|+|+++|+++++|.||.|
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 799999999994 3 256666654 8999999999999999999999986
No 72
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.05 E-value=2.7e-10 Score=127.19 Aligned_cols=80 Identities=35% Similarity=0.545 Sum_probs=75.3
Q ss_pred ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (514)
Q Consensus 371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~ 449 (514)
.+|++|+++.|+|+++++||+||+|+- +.+||||+|++++.++.+|.+++++||.|+|+|+++| .++||.|||+....
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 7999999999999999999999999999999999999 88999999997665
Q ss_pred CC
Q 010232 450 EP 451 (514)
Q Consensus 450 ~P 451 (514)
.+
T Consensus 733 ~~ 734 (780)
T COG2183 733 EG 734 (780)
T ss_pred cc
Confidence 43
No 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=99.04 E-value=7.2e-10 Score=120.01 Aligned_cols=108 Identities=20% Similarity=0.270 Sum_probs=86.6
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhh-----HHHhhhc--CCCEEEEEEEEEECCeEEEEECCEEEEEec
Q 010232 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH-----RVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK 325 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~-----~l~~~~k--~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~ 325 (514)
+.+++||.+.+.|...+ -||..++..+......|. .+.+.++ .|++|+|+|.++.++|++|+++|++||||.
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 34789999999987555 566655554444334444 7777776 999999999999999999999999999999
Q ss_pred cccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeehhhh
Q 010232 326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA 367 (514)
Q Consensus 326 sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~K~~ 367 (514)
+++.. .+. +++|++++|+|++||++++ +|+|||+.+
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 99942 222 2699999999999999877 999999864
No 74
>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=1.1e-09 Score=90.94 Aligned_cols=73 Identities=16% Similarity=0.145 Sum_probs=68.2
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD 446 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~ 446 (514)
.++|++|.|+|+++.+.|++|+++. +.+|++|.++++..+..++.+.+++||.|.|+|+++++.+++.||++.
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 4799999999999999999999988 799999999999888889999999999999999999755899999976
No 75
>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=99.03 E-value=1.1e-09 Score=90.03 Aligned_cols=67 Identities=21% Similarity=0.289 Sum_probs=59.1
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
++.|+++.|+|+++.++|+||+++ |+.||+|.+++... ..+ ++||.+.|+|+++|++++++.||.|+
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----~~~--~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----SKL--KVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----ccc--CCCCEEEEEEEEEECCCCEEEEEEee
Confidence 468999999999999999999996 79999999999432 112 69999999999999999999999875
No 76
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=99.02 E-value=1.9e-09 Score=88.95 Aligned_cols=65 Identities=29% Similarity=0.394 Sum_probs=59.9
Q ss_pred ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (514)
Q Consensus 371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl 444 (514)
.+++.|+.+.|+|++++++|+||++.+ ++.||+|.+++. +.+++||+++++|+++.+++|+.||+
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 468999999999999999999999998 799999999975 56999999999999987789999986
No 77
>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=99.01 E-value=1.8e-09 Score=86.67 Aligned_cols=67 Identities=12% Similarity=0.309 Sum_probs=58.9
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
|+++.|+|+++.++|+||+++ |++||+|.+++ +.+..++.+. +++|+.+.|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~-~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKK-FKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHc-CCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999995 79999999999 5555555554 3799999999999999999999884
No 78
>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=99.01 E-value=1.6e-09 Score=90.26 Aligned_cols=70 Identities=17% Similarity=0.200 Sum_probs=63.1
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
++.|+++.|+|+++.++|+||+++ |++||+|.+++ +.++.++.+.. .+||.++|+|+++|.+++++.+|+
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 579999999999999999999995 79999999999 56666777654 899999999999999999999985
No 79
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.97 E-value=1.3e-09 Score=120.01 Aligned_cols=77 Identities=36% Similarity=0.578 Sum_probs=73.8
Q ss_pred ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCc
Q 010232 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE 448 (514)
Q Consensus 371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~ 448 (514)
.++++|+++.|+|+++.+||+||.+.+ |-.||+|+|++++.|+.+..+++++||.|.|+|+.+|+.+|+.||+|...
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 479999999999999999999999999 89999999999999999999999999999999999999999999998754
No 80
>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=98.97 E-value=1.9e-09 Score=87.06 Aligned_cols=63 Identities=21% Similarity=0.345 Sum_probs=57.8
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeecccccc--ccCcccccCCCCEEEEEEEEEeCCCe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSMFPDK 439 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~--v~~~~~~~kvGd~VkvkVi~vde~~r 439 (514)
|++|.|+|+++.++|++|.+++ +++|++|++++++.+ ..++.+.|++||.|+|+|++++..++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 7899999999999999999998 899999999999885 88899999999999999999974443
No 81
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.95 E-value=3.4e-09 Score=102.01 Aligned_cols=89 Identities=24% Similarity=0.368 Sum_probs=75.6
Q ss_pred EeCCCCceEeehhhhhhh--ccCCCCceEEEEEEEEecceEEEEECC---------CceEEEEEeeccccccccCccccc
Q 010232 353 INEDTNDLILSEREAWAT--LNLREGTLLEGTVKKIYPYGAQIRIGD---------SNRSGLLHISNMSRTRVTSVSDLL 421 (514)
Q Consensus 353 vD~e~~rIiLS~K~~~~~--~~l~~G~iV~G~V~~I~~~GaFV~I~~---------~gi~GLvh~Sels~~~v~~~~~~~ 421 (514)
+|.++++|.+. +|.. ..+++|++|.|+|++|.++|+||+|.. .++.|++|.+++++.+..++.+.|
T Consensus 43 id~~~~~Isv~---P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~ 119 (189)
T PRK09521 43 IDDINRKISVI---PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAF 119 (189)
T ss_pred EcCCCCEEEEe---cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhcc
Confidence 46666666664 4433 367899999999999999999999952 157899999999999999999999
Q ss_pred CCCCEEEEEEEEEeCCCeEEEEEec
Q 010232 422 NEGERVKVLVVKSMFPDKISLSIAD 446 (514)
Q Consensus 422 kvGd~VkvkVi~vde~~rI~LSlK~ 446 (514)
++||.|.|+|++++ +++.||+|+
T Consensus 120 ~~GD~V~akV~~i~--~~i~LS~k~ 142 (189)
T PRK09521 120 KIGDIVRAKVISYT--DPLQLSTKG 142 (189)
T ss_pred CCCCEEEEEEEecC--CcEEEEEec
Confidence 99999999999886 899999985
No 82
>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=98.94 E-value=4.8e-09 Score=84.25 Aligned_cols=68 Identities=19% Similarity=0.339 Sum_probs=60.9
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
|+++.|+|.++.++|++|+++ +.+|++|.+++ +.+..++.+.. ++|+.++|+|+++|++++++.||+|
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 56666776654 7999999999999988899999985
No 83
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.94 E-value=3.3e-09 Score=86.26 Aligned_cols=67 Identities=24% Similarity=0.197 Sum_probs=57.7
Q ss_pred CCEEE-EEEEEE-ECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 297 NEPIE-VKFTEW-NTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 297 GeiV~-GkV~~v-~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
|+++. |+|+++ .++|+||++. |++||+|.+++ +.+..++.+.. ++|+.+.++|+.+|+.++++.||.
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 67888 999999 6999999994 79999999999 55555554433 799999999999999999999984
No 84
>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=98.93 E-value=4e-09 Score=84.43 Aligned_cols=66 Identities=18% Similarity=0.282 Sum_probs=58.5
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
|+++.|+|+++.++|+||++. ++.||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.||
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 69999999999 55566666644 79999999999999999999886
No 85
>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=98.93 E-value=3e-09 Score=82.17 Aligned_cols=64 Identities=33% Similarity=0.497 Sum_probs=58.9
Q ss_pred EEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232 379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS 443 (514)
Q Consensus 379 V~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS 443 (514)
+.|+|.++.++|+||++++ ++.|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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 4799999999999999998 7999999999999888888899999999999999998 67888775
No 86
>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=98.92 E-value=5.7e-09 Score=85.10 Aligned_cols=68 Identities=19% Similarity=0.324 Sum_probs=60.3
Q ss_pred cCCCEEEEEEEEEECCeEEEEECC--EEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~G--i~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
+.|+++.|+|+++.++|+||++.| .+||+|.+++ +.++.++.+.. ++||++.|+|+++|.++ ++.||+
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 66777777654 79999999999999876 888886
No 87
>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=98.92 E-value=6.1e-09 Score=84.34 Aligned_cols=70 Identities=10% Similarity=0.037 Sum_probs=60.8
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
+.|+++.|+|+++.++|++|+++ +++||+|.+++ +.+..++.+.. ++||.++++|+++|..++++.||.|
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 44444444443 7999999999999999999999974
No 88
>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=98.92 E-value=4.6e-09 Score=84.24 Aligned_cols=64 Identities=14% Similarity=0.188 Sum_probs=54.9
Q ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEecccccc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
|++++|+|+++.++|++|++ ++++||+|.+|+.. +.. .+.+ ++|++++|+|+.+|+++++|.||
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-KSTY--KEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc-ccCc--CCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999 57999999999942 322 3333 79999999999999999999887
No 89
>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=98.90 E-value=9.1e-09 Score=83.63 Aligned_cols=71 Identities=21% Similarity=0.353 Sum_probs=62.9
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
+.|+++.|+|+++.++|+||++. |+.||+|.+++ +.++.++.+.. .+||.++++|+++|..++++.+|+|+
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 58999999999 66677776654 79999999999999999999999873
No 90
>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=98.87 E-value=8.8e-09 Score=83.96 Aligned_cols=68 Identities=21% Similarity=0.095 Sum_probs=60.3
Q ss_pred cCCCEEEEEEEEEEC-CeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 295 QLNEPIEVKFTEWNT-GGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 295 k~GeiV~GkV~~v~~-~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
+.|+++.|+|+++.+ +|+||++. |.+|++|.+++ +.+..++.+.. .+||.++|+|+++|+ +++.||+|
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 89999995 79999999999 67777777754 799999999999985 89999975
No 91
>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=98.87 E-value=1.1e-08 Score=83.10 Aligned_cols=71 Identities=17% Similarity=0.354 Sum_probs=62.1
Q ss_pred CCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
.|+++.|+|+++.++|+||++. ++.|++|.+++ +.+..++.+.. .+||.++|+|+++|.+++++.+|+|.+
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 6899999999999999999997 58999999999 55555555543 799999999999999999999998753
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=98.86 E-value=1.1e-08 Score=88.25 Aligned_cols=79 Identities=27% Similarity=0.433 Sum_probs=68.5
Q ss_pred ceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccC-----------cccccCCCCEEEEEEEEEe-CC-----Ce
Q 010232 377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-----------VSDLLNEGERVKVLVVKSM-FP-----DK 439 (514)
Q Consensus 377 ~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~-----------~~~~~kvGd~VkvkVi~vd-e~-----~r 439 (514)
+++.|+|++|.++|+||++. ++.|++|.++++++++.. ....|++||.|+|+|.+++ +. .+
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 47899999999999999998 489999999999876653 3578999999999999998 32 58
Q ss_pred EEEEEecCcCCCCccccc
Q 010232 440 ISLSIADLESEPGLFVSD 457 (514)
Q Consensus 440 I~LSlK~l~~~P~~~~~~ 457 (514)
+.||+|+....||+.+.+
T Consensus 79 i~ls~k~~~~g~~~~~~~ 96 (99)
T cd04460 79 IGLTMRQPGLGKLEWIEE 96 (99)
T ss_pred EEEEEecCCCCcHHHhhh
Confidence 999999999999987653
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=98.84 E-value=1.6e-08 Score=81.31 Aligned_cols=69 Identities=30% Similarity=0.422 Sum_probs=61.2
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
|+++.|+|+++.++|++|+++ +++||+|.+++ ..++.++.+.. .+|+.++|+|+++|.+++++.||+|.
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 789999999999999999994 79999999999 55566666654 89999999999999999999999874
No 94
>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=98.81 E-value=2.4e-08 Score=78.87 Aligned_cols=67 Identities=18% Similarity=0.345 Sum_probs=59.0
Q ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
.|+++.|+|+++.++|++|+++++.||+|.+++ +.+..++.+. +.+||.++|+|+++|.+++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHE-ECCCCEEEEEEEEEECCCCEEecC
Confidence 488999999999999999999889999999999 5555556554 379999999999999999998876
No 95
>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=98.80 E-value=1.2e-08 Score=115.43 Aligned_cols=70 Identities=37% Similarity=0.593 Sum_probs=65.8
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~L 442 (514)
.+++|+++.|+|++|.+||+||++.+ +++||+|+|+++|.++.++.+.|++||.|+|+|++++.++||.|
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 57999999999999999999999998 89999999999999999999999999999999999987677764
No 96
>PRK07252 hypothetical protein; Provisional
Probab=98.80 E-value=2.1e-08 Score=90.05 Aligned_cols=72 Identities=24% Similarity=0.364 Sum_probs=63.6
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
+.|+++.|+|+++.++|+||+++ ++.||+|.+++ +.++.++.+.. .+||.|.|+|+++|.+++++.+|+|..
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~-~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLL-KVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhcc-CCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 47999999999999999999995 69999999999 56666665543 799999999999999999999999864
No 97
>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=98.80 E-value=2.8e-08 Score=78.28 Aligned_cols=67 Identities=18% Similarity=0.337 Sum_probs=59.0
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+|+.+.++|+++|. ++++.+|.|
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 55666665543 799999999999998 899999875
No 98
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.80 E-value=2e-08 Score=80.04 Aligned_cols=66 Identities=15% Similarity=0.318 Sum_probs=57.2
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-c-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
|+++.|+|+++.++|+||+++ +++||+|.+++ + .+..++.+.. ++||.++|+|+++|.+++++.+|
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 69999999999 3 3455565543 79999999999999999998875
No 99
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.79 E-value=3.3e-08 Score=77.74 Aligned_cols=69 Identities=28% Similarity=0.463 Sum_probs=59.5
Q ss_pred CCCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
.|+++.|+|+++++.|++|+++ ++.||+|.+++. .+..++.+. +.+|+.+.|+|+++|..++++.+|++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 6999999999999999999997 799999999994 334444443 37999999999999999899999874
No 100
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.79 E-value=3.4e-08 Score=98.32 Aligned_cols=75 Identities=19% Similarity=0.225 Sum_probs=69.2
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
..++|++|.|+|++++++|+||+|+. .+.|+||.+++++.++ .++++.|++||.|.|+|++++..+++.||+|+.
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 46999999999999999999999997 6899999999999987 889999999999999999998767899999864
No 101
>PRK08582 hypothetical protein; Provisional
Probab=98.79 E-value=2e-08 Score=92.39 Aligned_cols=72 Identities=18% Similarity=0.280 Sum_probs=62.9
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
++.|+++.|+|+.++++|+||+++ ++.||||++++ +.++.++.+.. .+||.|+|+|+++|. .++|.||+|++
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 568999999999999999999996 69999999999 56666665543 799999999999997 48999999865
No 102
>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=98.77 E-value=5.1e-08 Score=81.01 Aligned_cols=75 Identities=25% Similarity=0.325 Sum_probs=62.1
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~ 247 (514)
|-+++|++|.|+|+++++++++|+++.+.+|++|.+++.... .++.
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~-----------~~~~----------------------- 47 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKD-----------KKEI----------------------- 47 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcc-----------hHHH-----------------------
Confidence 567899999999999999999999999999999999985321 0011
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (514)
Q Consensus 248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk 280 (514)
...+++||.|.|+|++.+.++++.||.+.
T Consensus 48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 48 ----RKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred ----HhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 23479999999999998766899999875
No 103
>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=98.76 E-value=5e-08 Score=81.63 Aligned_cols=80 Identities=28% Similarity=0.349 Sum_probs=63.0
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~ 247 (514)
|.+++|++|.|+|+++.+.|++|+++.+.+|+||.+++.... .. +...+.
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~~----~~~~~~----------------------- 51 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---TD----EDELNM----------------------- 51 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---Cc----cchHHH-----------------------
Confidence 567899999999999999999999999999999999985200 00 000000
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (514)
Q Consensus 248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~ 281 (514)
...+++||.+.|+|++.+.++++.||+++.
T Consensus 52 ----~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 52 ----RSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred ----HhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 234799999999999988779999999875
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=98.74 E-value=4.7e-08 Score=102.19 Aligned_cols=108 Identities=23% Similarity=0.286 Sum_probs=84.1
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHH-----HHHhhhhHHHhhh--cCCCEEEEEEEEEECCe-EEEEECCEEEEEe
Q 010232 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLP 324 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~-----~~~~~w~~l~~~~--k~GeiV~GkV~~v~~~G-~fVdi~Gi~gFVP 324 (514)
+.+++||.|.+.+. ...-||..++..+. ..+..++.+.+.+ +.|++++|+|.++.++| ++|+++|++||||
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 PDVQIGDEVKKEIP-PENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILP 160 (341)
T ss_pred cccccCCEEEEEec-ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEec
Confidence 45789999998875 33456665555444 3356777777777 49999999999999988 6999999999999
Q ss_pred ccccccccCChhhHhhhcCCEEEEEEEEEeCCC--CceEeehhhh
Q 010232 325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSEREA 367 (514)
Q Consensus 325 ~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rIiLS~K~~ 367 (514)
.+++... +. +.+|++++|+|++++... ..|+||++.+
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 9999522 11 269999999999999654 5799999864
No 105
>PRK05807 hypothetical protein; Provisional
Probab=98.74 E-value=3.6e-08 Score=90.32 Aligned_cols=72 Identities=18% Similarity=0.253 Sum_probs=63.7
Q ss_pred hcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
++.|++++|+|+.+.++|+||++++..||||.+++ +.++.++.+.. .+||.|.|+|+++|. +++|.||+|.+
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~-kvGd~V~VkV~~id~-~gkI~LSlk~~ 75 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHL-KEQDKVKVKVISIDD-NGKISLSIKQA 75 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccC-CCCCEEEEEEEEECC-CCcEEEEEEec
Confidence 46899999999999999999999889999999999 56666665543 799999999999998 79999999865
No 106
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.73 E-value=1.6e-08 Score=108.67 Aligned_cols=83 Identities=25% Similarity=0.357 Sum_probs=78.8
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP 451 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P 451 (514)
++..|-+++|+|+++.++|+||++.+ +..||+|+|+++..++.+|++.+.+||+|.|+.+..|+.+.+.+|-|.+.++|
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 78999999999999999999999999 99999999999999999999999999999999999999999999999999988
Q ss_pred Cccc
Q 010232 452 GLFV 455 (514)
Q Consensus 452 ~~~~ 455 (514)
-...
T Consensus 744 ~~~~ 747 (760)
T KOG1067|consen 744 ATKE 747 (760)
T ss_pred ccCC
Confidence 6553
No 107
>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=98.70 E-value=8.1e-08 Score=75.55 Aligned_cols=66 Identities=18% Similarity=0.206 Sum_probs=57.2
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. ++||.+.|+|+++|.+++++.+|
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 58999999999 45555665543 79999999999999999998876
No 108
>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=98.69 E-value=5.5e-08 Score=84.59 Aligned_cols=72 Identities=14% Similarity=0.248 Sum_probs=61.4
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccc-------------------cCChhhHhhhcCCEEEEEEEEE
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-------------------VNNFTELKEKVGRRMYVQITRI 353 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~-------------------i~~~~el~~~VGq~V~vkVl~v 353 (514)
+.|++|.|+|+++.+.|++|.+. |+.||+|++++ +.+ ..++.+.+ ++||.++|+|+++
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 79999999999 432 12345554 8999999999999
Q ss_pred eCC---CCceEeehhhh
Q 010232 354 NED---TNDLILSEREA 367 (514)
Q Consensus 354 D~e---~~rIiLS~K~~ 367 (514)
|++ +++|.||.|..
T Consensus 81 d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 81 DKSKSGKKRIELSLEPE 97 (100)
T ss_pred cCCcCCCcEEEEEecHH
Confidence 987 78999999864
No 109
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.68 E-value=8e-08 Score=79.21 Aligned_cols=67 Identities=18% Similarity=0.259 Sum_probs=58.8
Q ss_pred CCEEEEEEEEEECCeEEEEEC----CEEEEEecccc-cccc-CChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-LSRV-NNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~----Gi~gFVP~sel-~~~i-~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
|+++.|+|+++.++|+||+++ ++.||+|.+++ +.+. .++.+.. ++||.++|+|+++| ++++.+|+|.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~-~~Gd~v~v~v~~vd--~~~i~~s~k~ 73 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVV-KRGQKVKVKVISIQ--NGKISLSMKD 73 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhee-CCCCEEEEEEEEEe--CCEEEEEEEe
Confidence 678999999999999999997 68999999999 5554 6666553 89999999999999 7899999875
No 110
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.66 E-value=6.8e-08 Score=104.81 Aligned_cols=112 Identities=15% Similarity=0.207 Sum_probs=85.2
Q ss_pred EEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh-hhh----hh-------hccCC--CCceEEEEEEE
Q 010232 320 RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE-REA----WA-------TLNLR--EGTLLEGTVKK 385 (514)
Q Consensus 320 ~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~-K~~----~~-------~~~l~--~G~iV~G~V~~ 385 (514)
.++||.++.... ++. ..+|+.+.+.|...+ .+|+.++. |+. |. ...++ .|++|.|+|.+
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 259999999998766 44444443 332 22 12454 99999999999
Q ss_pred EecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEec
Q 010232 386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIAD 446 (514)
Q Consensus 386 I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LSlK~ 446 (514)
+.++|+||+++ |++||||.++++ |.+.|++||+|+|+|++++ +++ +|.||.+.
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 99999999997 689999999996 6789999999999999997 444 89999853
No 111
>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=98.66 E-value=1e-07 Score=76.96 Aligned_cols=68 Identities=16% Similarity=0.265 Sum_probs=56.6
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-cc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
..|+++.|+|+++.++|+||+++ |+.||+|.+++ +. +..++... +++||+++|+|+++|.+++++.+|
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 58999999999999999999995 69999999999 43 22233333 379999999999999999988764
No 112
>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=98.64 E-value=1.5e-07 Score=75.61 Aligned_cols=62 Identities=24% Similarity=0.396 Sum_probs=53.5
Q ss_pred CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEE
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLS 443 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LS 443 (514)
+.|++|+|+|.++.++|+||+++ +++|+||.++++. .+.+++||+|+|+|++++ ++ ..|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 47999999999999999999997 4899999999973 467899999999999997 32 357776
No 113
>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=98.64 E-value=2.1e-07 Score=104.87 Aligned_cols=95 Identities=18% Similarity=0.237 Sum_probs=74.8
Q ss_pred EEcCCCcEEEEe-hHHHHHhhhhHHHhh-----hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc----c-cccCC
Q 010232 267 GRTLSGRPLLST-RRLFRKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL----L-SRVNN 334 (514)
Q Consensus 267 ~~d~~grliLS~-kk~~~~~~w~~l~~~-----~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel----~-~~i~~ 334 (514)
.++.+|.+.++. .+.....+.+.+... .+.|+++.|+|+++.++|+||++. |++||||.|++ | .++.+
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 356788886554 344444444444432 469999999999999999999995 89999999998 2 57788
Q ss_pred hhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 335 FTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 335 ~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
+.++. ++||+|+|+|+++|+ ++||.|+
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 7788876
No 114
>PRK08059 general stress protein 13; Validated
Probab=98.62 E-value=1.5e-07 Score=84.78 Aligned_cols=73 Identities=16% Similarity=0.293 Sum_probs=64.2
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
++.|+++.|+|+++.++|++|+++ ++.||+|.+++ ..++.++.+.. .+|+.+.|+|+++|.+++++.+|+|..
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~-~vGD~I~vkI~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFL-SVGDEVKVKVLSVDEEKGKISLSIRAT 79 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcC-CCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence 568999999999999999999996 69999999999 55565555543 799999999999999999999999865
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=75.49 Aligned_cols=64 Identities=20% Similarity=0.342 Sum_probs=54.2
Q ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCC--CceEeeh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSE 364 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rIiLS~ 364 (514)
+.|++++|+|.+++++|++|++++.+||||.+++... +. +++|++++++|+++++++ .+|++|+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~-----~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG-----ES-YRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC-----Cc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 4799999999999999999999889999999999421 11 269999999999998654 4688886
No 116
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.62 E-value=7.4e-08 Score=95.76 Aligned_cols=71 Identities=17% Similarity=0.276 Sum_probs=66.4
Q ss_pred cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
..|++|-|+|..+.++|+||.+ +|++||||.||+ ..++++.+++. ++||++-|+|++||++++.|-||+|.
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~v-kegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYV-KEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHh-hcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 4899999999999999999999 589999999999 67889999887 89999999999999999999999983
No 117
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.61 E-value=2.1e-07 Score=73.58 Aligned_cols=66 Identities=23% Similarity=0.327 Sum_probs=57.1
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
|+++.|+|+++.++|+||+++ +..||+|.+++ +.++.++.+.. .+||.+.|+|.++|+ ++++.+|+
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 59999999999 55555555543 799999999999998 88999885
No 118
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.60 E-value=1.8e-07 Score=107.29 Aligned_cols=99 Identities=17% Similarity=0.180 Sum_probs=76.1
Q ss_pred CCCcEE-EEehHHHHHhhhhHHHh---hhcCCCEEE-EEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhc
Q 010232 270 LSGRPL-LSTRRLFRKMAWHRVRQ---IKQLNEPIE-VKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKV 342 (514)
Q Consensus 270 ~~grli-LS~kk~~~~~~w~~l~~---~~k~GeiV~-GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~V 342 (514)
++|.+. ++........+.+.+.+ ..+.|+++. |+|+++.++|+||++. |++||||+|++ +.++.++.+.. ++
T Consensus 723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~-kv 801 (891)
T PLN00207 723 DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAF-KV 801 (891)
T ss_pred CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhc-CC
Confidence 455553 33333333334333333 357999996 6999999999999995 79999999999 77788888765 89
Q ss_pred CCEEEEEEEEEeCCCCceEeehhh----hhhh
Q 010232 343 GRRMYVQITRINEDTNDLILSERE----AWAT 370 (514)
Q Consensus 343 Gq~V~vkVl~vD~e~~rIiLS~K~----~~~~ 370 (514)
||.|+|+|+++|+ +++|.||+|. +|+.
T Consensus 802 GD~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~ 832 (891)
T PLN00207 802 GDRIDVKLIEVND-KGQLRLSRRALLPEANSE 832 (891)
T ss_pred CCEEEEEEEEECC-CCcEEEEEeccccCchhh
Confidence 9999999999997 7899999985 6764
No 119
>PHA02945 interferon resistance protein; Provisional
Probab=98.57 E-value=1.7e-07 Score=78.86 Aligned_cols=69 Identities=14% Similarity=0.176 Sum_probs=60.8
Q ss_pred cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc---ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL---LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel---~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
+.|+++-|+|.. .++|+||.+ +|++||||.|+. ..++++ ++.. +||++.|+|+++|+.++.|-||.|+.
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 589999999999 999999999 489999999955 456677 6664 99999999999999999999999853
No 120
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.52 E-value=3.9e-07 Score=95.97 Aligned_cols=109 Identities=17% Similarity=0.238 Sum_probs=78.5
Q ss_pred CcccCCCEEEEEEEEEcCCCcEEEEehHHHH----HhhhhHHHhhh--cCCCEEEEEEEEEECCeEEEEECCEEEEEecc
Q 010232 253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFR----KMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA 326 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~----~~~w~~l~~~~--k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~s 326 (514)
+..++||.+...+...+.+...+.+.++... +...+.+.+.+ +.|++++|+|.++.++|++|+++|++||||.+
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 3478999998876533333323333333322 23344455555 79999999999999999999999999999998
Q ss_pred ccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeehhhh
Q 010232 327 ELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA 367 (514)
Q Consensus 327 el~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~K~~ 367 (514)
++... +. +++|++++|+|++++.+++ .|+||+..+
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 2699999999999996554 699999754
No 121
>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=98.49 E-value=4.2e-07 Score=77.87 Aligned_cols=74 Identities=19% Similarity=0.259 Sum_probs=66.2
Q ss_pred CCCCceEEEEEEEEecceEEEEE--------CCCceEEEEEeecccccccc--CcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRI--------GDSNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMFPDKISL 442 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I--------~~~gi~GLvh~Sels~~~v~--~~~~~~kvGd~VkvkVi~vde~~rI~L 442 (514)
.++|++|.|+|++++...+.|+| .. ...|++|++++...++. ++.+.|++||.|+|+|+++.+...+.|
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 48999999999999999999999 66 58999999999887776 788999999999999999877678999
Q ss_pred EEecC
Q 010232 443 SIADL 447 (514)
Q Consensus 443 SlK~l 447 (514)
|+++-
T Consensus 83 st~~~ 87 (92)
T cd05791 83 STAEN 87 (92)
T ss_pred EecCC
Confidence 99753
No 122
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.48 E-value=8.6e-07 Score=84.71 Aligned_cols=81 Identities=25% Similarity=0.405 Sum_probs=67.9
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe------
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM------ 435 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd------ 435 (514)
..+|+++.|+|++++++|+||+++ .++|++|.+++.+.+.. +....+++||.|+++|++++
T Consensus 79 p~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 156 (179)
T TIGR00448 79 PELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP 156 (179)
T ss_pred ccCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence 467999999999999999999996 48999999999866432 23478999999999999996
Q ss_pred CCCeEEEEEecCcCCCCccc
Q 010232 436 FPDKISLSIADLESEPGLFV 455 (514)
Q Consensus 436 e~~rI~LSlK~l~~~P~~~~ 455 (514)
+..+|.||+|+.-.-|++.+
T Consensus 157 ~~~~I~lt~k~~~LG~~~w~ 176 (179)
T TIGR00448 157 EGSKIGLTMRQPLLGKLEWI 176 (179)
T ss_pred CcceEEEEeccCcCCccccc
Confidence 24689999999877777655
No 123
>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=98.47 E-value=5.2e-07 Score=102.94 Aligned_cols=73 Identities=26% Similarity=0.446 Sum_probs=64.0
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK 439 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r 439 (514)
.-++|+++.|+|++|++||+||++.+.+++||+|+++++++++ .+....|++||+|+|+|+++| .+++
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 4578999999999999999999998656999999999986643 344567999999999999998 7899
Q ss_pred EEEEE
Q 010232 440 ISLSI 444 (514)
Q Consensus 440 I~LSl 444 (514)
|.+++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99986
No 124
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.46 E-value=6e-07 Score=90.84 Aligned_cols=70 Identities=19% Similarity=0.302 Sum_probs=63.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
+.|+++.|+|+++.++|+||++. |++||||.+++ +.++.++.+.. .+|+.+.|+|+++|.+++++.||.|
T Consensus 7 ~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~-kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHV-KEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhC-CCCCEEEEEEEEEecccCeEEEEEE
Confidence 58999999999999999999994 79999999999 56677776654 8999999999999999999999997
No 125
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.45 E-value=5.4e-07 Score=69.42 Aligned_cols=63 Identities=22% Similarity=0.347 Sum_probs=52.9
Q ss_pred EEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 300 V~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
+.|+|+++.++|++|+++ +..||+|.+++ ..+..++.+. ..+|+.+.|+|+++|++++++.+|
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~-~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV-FKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhE-eCCCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999997 79999999999 4434444443 379999999999999988888876
No 126
>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=98.42 E-value=1e-06 Score=74.81 Aligned_cols=71 Identities=17% Similarity=0.232 Sum_probs=58.7
Q ss_pred hcCCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccc-c---cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 294 KQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-L---SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel-~---~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
.+.|+++.|+|+++.++ |+||+++ |.+||||.+++ + .++.++.+.. .+|+.|.|+|++....++-..+|.+
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~-~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL-KEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC-CCCCEEEEEEEEecCCCCCceEEEE
Confidence 46899999999999996 9999996 79999999999 4 4566666644 7999999999998776666666543
No 127
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.38 E-value=1.5e-06 Score=98.86 Aligned_cols=98 Identities=18% Similarity=0.202 Sum_probs=76.2
Q ss_pred EcCCCcEEEEe-hHHHHHhhhhH---HHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232 268 RTLSGRPLLST-RRLFRKMAWHR---VRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK 341 (514)
Q Consensus 268 ~d~~grliLS~-kk~~~~~~w~~---l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~ 341 (514)
.+.+|.+.++. .+...+.+... +....+.|+++.|+|+++.++|+||++. |.+||+|++++ +.++.++.+.. +
T Consensus 589 i~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~-k 667 (693)
T PRK11824 589 IEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL-K 667 (693)
T ss_pred cCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee-C
Confidence 34578876554 33333333332 2234589999999999999999999995 79999999999 67777777654 8
Q ss_pred cCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 342 VGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 342 VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
+||.|+|+|+++|.+ +++.||+|..
T Consensus 668 vGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 668 EGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CCCEEEEEEEEECCC-CcEEEEEEec
Confidence 999999999999987 9999999753
No 128
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=98.38 E-value=1.4e-06 Score=69.06 Aligned_cols=61 Identities=21% Similarity=0.115 Sum_probs=38.9
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCCCCCC
Q 010232 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG 251 (514)
Q Consensus 172 ~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~~~~~ 251 (514)
+|++++.+|+++++.|+|++.|...+.+||.+|+.
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 48999999999999999999988889999988872
Q ss_pred CCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 010232 252 RPVVETGTVLFAEVLGRTLSGRPLLSTR 279 (514)
Q Consensus 252 ~~~~~vGd~V~v~Vl~~d~~grliLS~k 279 (514)
..+++||.|.++|| .|.++|+++|++
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 22689999999999 788999999974
No 129
>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=98.33 E-value=2.1e-06 Score=70.64 Aligned_cols=68 Identities=12% Similarity=0.238 Sum_probs=54.8
Q ss_pred CCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc-cccC-----------ChhhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRVN-----------NFTELKEKVGRRMYVQITRINEDTNDLI 361 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~-~~i~-----------~~~el~~~VGq~V~vkVl~vD~e~~rIi 361 (514)
.|+++.|+|++++++|+||+++ |++||+|.+++. .++. ..... .++|+.++|+|+++|.+++++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEE
Confidence 3889999999999999999997 699999999983 3211 11122 2689999999999999888988
Q ss_pred eeh
Q 010232 362 LSE 364 (514)
Q Consensus 362 LS~ 364 (514)
++.
T Consensus 80 ~~l 82 (83)
T cd04471 80 FEL 82 (83)
T ss_pred EEE
Confidence 874
No 130
>PRK11642 exoribonuclease R; Provisional
Probab=98.33 E-value=2.2e-06 Score=98.88 Aligned_cols=77 Identities=25% Similarity=0.366 Sum_probs=65.6
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CCCeE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKI 440 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~~rI 440 (514)
-++|++++|+|++|+++|+||+|.+.+++||||.+++.+++.. +....|++||+|+|+|+.+| ++++|
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI 720 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence 3789999999999999999999987469999999999876321 23567999999999999998 88999
Q ss_pred EEEEecCcC
Q 010232 441 SLSIADLES 449 (514)
Q Consensus 441 ~LSlK~l~~ 449 (514)
.|++-....
T Consensus 721 ~f~l~~~~~ 729 (813)
T PRK11642 721 DFSLISSER 729 (813)
T ss_pred EEEEecccc
Confidence 999954443
No 131
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.31 E-value=1.6e-06 Score=82.55 Aligned_cols=75 Identities=27% Similarity=0.461 Sum_probs=62.9
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----------cC-cccccCCCCEEEEEEEEEe--CC--
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----------TS-VSDLLNEGERVKVLVVKSM--FP-- 437 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----------~~-~~~~~kvGd~VkvkVi~vd--e~-- 437 (514)
...|++|.|.|.++.++|+||.|++ .+||+|+|++.++++ .+ -..++++||.|++||+.+. ..
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 5679999999999999999999997 799999999998843 22 3347999999999999885 32
Q ss_pred --CeEEEEEecCcC
Q 010232 438 --DKISLSIADLES 449 (514)
Q Consensus 438 --~rI~LSlK~l~~ 449 (514)
.+|.|+||+.-.
T Consensus 157 ~~~~I~lTmrq~~L 170 (183)
T COG1095 157 RESKIGLTMRQPGL 170 (183)
T ss_pred ccceEEEEeccccC
Confidence 689999987654
No 132
>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=98.30 E-value=2.5e-06 Score=96.56 Aligned_cols=73 Identities=22% Similarity=0.386 Sum_probs=63.5
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK 439 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r 439 (514)
.-++|++++|+|++|+++|+||+|.+.+++||||++++.+++. .+....|++||+|+|+|+++| ++++
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~ 648 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS 648 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 3468999999999999999999998548999999999988641 234577999999999999998 8899
Q ss_pred EEEEE
Q 010232 440 ISLSI 444 (514)
Q Consensus 440 I~LSl 444 (514)
|.+++
T Consensus 649 I~f~l 653 (654)
T TIGR00358 649 IIFEL 653 (654)
T ss_pred EEEEE
Confidence 99986
No 133
>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=98.28 E-value=3.8e-06 Score=67.75 Aligned_cols=61 Identities=10% Similarity=0.167 Sum_probs=51.7
Q ss_pred CCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-c--ccCChhhHhhhcCCEEEEEEEEEeCCCC
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-S--RVNNFTELKEKVGRRMYVQITRINEDTN 358 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~--~i~~~~el~~~VGq~V~vkVl~vD~e~~ 358 (514)
|+++.|+|+++.+.|++|+++ |++|++|.+++. . ...++.+.. .+||.+.|+|+++|.++.
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 799999999994 4 255565543 799999999999987653
No 134
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.28 E-value=3.9e-06 Score=80.90 Aligned_cols=103 Identities=15% Similarity=0.215 Sum_probs=78.4
Q ss_pred CCcccCCCEEEEEEEEE---cCCC-cEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC----------
Q 010232 252 RPVVETGTVLFAEVLGR---TLSG-RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE---------- 317 (514)
Q Consensus 252 ~~~~~vGd~V~v~Vl~~---d~~g-rliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~---------- 317 (514)
...+..+..|.+-+.+. |.++ ++.+. .|.......+.|++|.|+|+++.+.|++|++.
T Consensus 24 ~Gty~~~~~i~as~~G~~~id~~~~~Isv~--------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~ 95 (189)
T PRK09521 24 EGTYEDNGEVYASVVGKVFIDDINRKISVI--------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELA 95 (189)
T ss_pred CCEEeeCCEEEEEeeEEEEEcCCCCEEEEe--------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccC
Confidence 44567788899888883 4433 34442 45543445679999999999999999999994
Q ss_pred -CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 318 -GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 318 -Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
++.||+|.+++ +.+..+..+.. ++|+.|.|+|++++ +++.||.|.
T Consensus 96 ~~~~G~l~~s~i~~~~~~~~~~~~-~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 96 TSKLAYIHISQVSDGYVESLTDAF-KIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred CCceeeEEhhHcChhhhhhHHhcc-CCCCEEEEEEEecC---CcEEEEEec
Confidence 47899999999 44444444443 89999999999997 689999874
No 135
>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=6.3e-06 Score=67.93 Aligned_cols=62 Identities=19% Similarity=0.334 Sum_probs=54.5
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
++.|+.+.|+|+++.++|+||+++ +..||+|.+++...+ ++||+++++|.++ .+++++.+|.
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 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCcC--------CCCCEEEEEEEEE-CCCCcEEEEE
Confidence 579999999999999999999996 599999999984322 5999999999999 7889988874
No 136
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.24 E-value=1.8e-06 Score=97.08 Aligned_cols=74 Identities=18% Similarity=0.131 Sum_probs=67.7
Q ss_pred hhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 293 IKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 293 ~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
.++.|+++.|+|.++.++|+||+|+ ..+|+||+|++ ...+.+|.++. .+|+.|+|+|+++|..++||.||++..
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv-~vGdiV~v~V~~vD~~r~rI~Lsmr~~ 730 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVV-KVGDIVKVKVIEVDTARKRIALSMRLD 730 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhc-ccCCEEEEEEEEEecccCeeeeEeecc
Confidence 5689999999999999999999995 47999999999 56688888876 899999999999999999999999865
No 137
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.22 E-value=6.2e-06 Score=79.19 Aligned_cols=77 Identities=27% Similarity=0.416 Sum_probs=63.9
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CC---
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP--- 437 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~--- 437 (514)
..+|+++.|+|++++++|+||+++. ++|++|.+++.+++.. +....+++||.|+++|++++ ++
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 4689999999999999999999984 8999999999876432 34677999999999999997 33
Q ss_pred --CeEEEEEecCcCCC
Q 010232 438 --DKISLSIADLESEP 451 (514)
Q Consensus 438 --~rI~LSlK~l~~~P 451 (514)
.+|.+|+|+--.-+
T Consensus 157 ~~~~I~ls~~~~~LG~ 172 (187)
T PRK08563 157 RGSKIGLTMRQPGLGK 172 (187)
T ss_pred CCCEEEEEecCCCCCc
Confidence 38999998754433
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=8.2e-06 Score=92.80 Aligned_cols=93 Identities=16% Similarity=0.176 Sum_probs=70.9
Q ss_pred EcCCCcEEEEe-hHHHHHhhh---hHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232 268 RTLSGRPLLST-RRLFRKMAW---HRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK 341 (514)
Q Consensus 268 ~d~~grliLS~-kk~~~~~~w---~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~ 341 (514)
++.+|++.++. .+.....+- ..+....+.|+++.|+|+++.++|+||++. |++||+|.|++ +.++.++.+.. +
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 45678885443 333333332 233344578999999999999999999994 79999999999 67787777764 8
Q ss_pred cCCEEEEEEEEEeCCCCceEe
Q 010232 342 VGRRMYVQITRINEDTNDLIL 362 (514)
Q Consensus 342 VGq~V~vkVl~vD~e~~rIiL 362 (514)
+||.|.|+|+++|. ++++.|
T Consensus 665 vGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 665 EGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred CCCEEEEEEEEECC-CCCccC
Confidence 99999999999997 666643
No 139
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.17 E-value=4.5e-06 Score=69.75 Aligned_cols=71 Identities=13% Similarity=0.132 Sum_probs=66.3
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEE-eeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLH-ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh-~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
-.++|+++. .|..+.+.|++|.+-++|++|+|. .++++.+++.++++.+ +|..+.|+|+.+| +++-|+||.
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 358899999 899999999999998888999999 9999999999999999 9999999999999 899999985
No 140
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.15 E-value=6.3e-06 Score=86.36 Aligned_cols=96 Identities=21% Similarity=0.356 Sum_probs=73.2
Q ss_pred hcCCEEEEEEEEEeCCCCceEeehh-hhh----h-------hccC--CCCceEEEEEEEEecce-EEEEECCCceEEEEE
Q 010232 341 KVGRRMYVQITRINEDTNDLILSER-EAW----A-------TLNL--REGTLLEGTVKKIYPYG-AQIRIGDSNRSGLLH 405 (514)
Q Consensus 341 ~VGq~V~vkVl~vD~e~~rIiLS~K-~~~----~-------~~~l--~~G~iV~G~V~~I~~~G-aFV~I~~~gi~GLvh 405 (514)
.+|+.+.+.|.. .+-+|+.++.. +.+ . ...+ +.|++|+|+|.++.+.| ++|+++ +++|+||
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 QIGDEVKKEIPP--ENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILP 160 (341)
T ss_pred ccCCEEEEEecc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEec
Confidence 599999998853 23445544443 321 0 0234 69999999999999988 699996 6899999
Q ss_pred eeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEEEec
Q 010232 406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLSIAD 446 (514)
Q Consensus 406 ~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LSlK~ 446 (514)
.+++. |.+.|++||+|+|+|++++ .. ..|.||.+.
T Consensus 161 ~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 161 KKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred HHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 99987 4567999999999999997 32 478999853
No 141
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.13 E-value=2.4e-05 Score=78.11 Aligned_cols=159 Identities=18% Similarity=0.269 Sum_probs=100.2
Q ss_pred CCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-
Q 010232 252 RPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL- 328 (514)
Q Consensus 252 ~~~~~vGd~V~v~Vl~~-d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel- 328 (514)
...+..+..+.+-+.+. ..+++ .++.+..... -.-+.|++|.|+|+++...|++|+++ ++.|+||.+++
T Consensus 26 ~Gty~~~g~i~As~~G~~~~~~~-~i~V~p~~~~-------y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~ 97 (235)
T PRK04163 26 RGTYKENGKIYSTVVGLVDIKDD-KVRVIPLEGK-------YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVL 97 (235)
T ss_pred CceEEeCCEEEEEEeEEEEEECC-EEEEEECCCc-------ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcC
Confidence 33456677788877772 22222 3333322111 11269999999999999999999997 58999999999
Q ss_pred cccc----CChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCceEEEEEEEEecceEEEEECCCceEEEE
Q 010232 329 LSRV----NNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLL 404 (514)
Q Consensus 329 ~~~i----~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLv 404 (514)
+.+. .+.++.. .+|+.|.|+|+++++++ .+.||.|.. .-|.+..|.+..|.+.-+---|+. .|.+
T Consensus 98 ~~~~~~d~~~~~~~~-~~GDlV~akV~~i~~~~-~~~LS~k~~------~lG~L~~G~~~~V~~~~i~~lig~---~g~~ 166 (235)
T PRK04163 98 GRPVNVEGTDLRKYL-DIGDYIIAKVKDVDRTR-DVVLTLKGK------GLGKIEGGTIVEIKPVKVPRVIGK---KGSM 166 (235)
T ss_pred CCccccchhhhHhhC-CCCCEEEEEEEEECCCC-cEEEEEcCC------CCCccCCCEEEEECHHHHHhhcCC---CChh
Confidence 4443 4455543 79999999999998654 599998743 235555555555554433222222 0100
Q ss_pred EeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232 405 HISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (514)
Q Consensus 405 h~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK 445 (514)
+. ..++...+.|. +..+++|.++-.
T Consensus 167 ---------i~------~l~~~~~~~I~-ig~NG~VwI~~~ 191 (235)
T PRK04163 167 ---------IN------MLKEETGCDII-VGQNGRIWIKGP 191 (235)
T ss_pred ---------Hh------hhhhhhCcEEE-EcCCcEEEEeeC
Confidence 00 12334445553 567899998884
No 142
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.11 E-value=5.4e-06 Score=87.41 Aligned_cols=95 Identities=19% Similarity=0.254 Sum_probs=71.2
Q ss_pred hcCCEEEEEEEEEeCCCCceEeehhhhhh-----------hccC--CCCceEEEEEEEEecceEEEEECCCceEEEEEee
Q 010232 341 KVGRRMYVQITRINEDTNDLILSEREAWA-----------TLNL--REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS 407 (514)
Q Consensus 341 ~VGq~V~vkVl~vD~e~~rIiLS~K~~~~-----------~~~l--~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S 407 (514)
.+|+.+.+.+...+-.+..+.. .|+.+. ...+ +.|+++.|+|.++.+.|+||+++ +++|+||.+
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 ELGDVIEIEVTPKDFGRIAAQT-AKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPA 164 (362)
T ss_pred cCCCEEEEecCcCCCChHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHH
Confidence 5999999988754433222222 222111 1244 99999999999999999999997 589999998
Q ss_pred ccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEE
Q 010232 408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSI 444 (514)
Q Consensus 408 els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LSl 444 (514)
++. |.+.|++||+|+|+|++++ +.+ .|.||.
T Consensus 165 E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSR 198 (362)
T PRK12327 165 EQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSR 198 (362)
T ss_pred HcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence 875 3688999999999999997 333 577777
No 143
>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=98.02 E-value=1.4e-05 Score=68.92 Aligned_cols=69 Identities=19% Similarity=0.213 Sum_probs=55.3
Q ss_pred CEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCCh-----------hhHhhhcCCEEEEEEEEEeCCC-----Cce
Q 010232 298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNF-----------TELKEKVGRRMYVQITRINEDT-----NDL 360 (514)
Q Consensus 298 eiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~-----------~el~~~VGq~V~vkVl~vD~e~-----~rI 360 (514)
+++.|+|++++++|+||+++++.||+|.+++ ..+.... ... +.+|+.+.++|.++|.+. .++
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 3333211 122 379999999999999764 479
Q ss_pred Eeehhhh
Q 010232 361 ILSEREA 367 (514)
Q Consensus 361 iLS~K~~ 367 (514)
.||.|..
T Consensus 80 ~ls~k~~ 86 (99)
T cd04460 80 GLTMRQP 86 (99)
T ss_pred EEEEecC
Confidence 9999863
No 144
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.00 E-value=2.3e-05 Score=87.20 Aligned_cols=98 Identities=15% Similarity=0.177 Sum_probs=76.6
Q ss_pred EcCCCcEEEEeh-HHHHHh---hhhHHHhhhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-ccccCChhhHhhh
Q 010232 268 RTLSGRPLLSTR-RLFRKM---AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK 341 (514)
Q Consensus 268 ~d~~grliLS~k-k~~~~~---~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-~~~i~~~~el~~~ 341 (514)
++++|.+..+.. ...... ....+....+.|+++.|+|+++.++|+||.+ +|-+|++|.|++ +.++.+..+.. +
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 457888854433 233333 3344455668999999999999999999999 578999999999 66777666665 8
Q ss_pred cCCEEEEEEEEEeCCCCceEeehhhh
Q 010232 342 VGRRMYVQITRINEDTNDLILSEREA 367 (514)
Q Consensus 342 VGq~V~vkVl~vD~e~~rIiLS~K~~ 367 (514)
+||.+.|+|+.+|+ .+++.+|++..
T Consensus 666 ~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 666 EGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred cCceEEEEEeeecc-cCCccceehhc
Confidence 99999999999985 68899998753
No 145
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.92 E-value=1e-05 Score=77.21 Aligned_cols=107 Identities=17% Similarity=0.173 Sum_probs=70.7
Q ss_pred EEEEEEEE-c-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccC----
Q 010232 261 LFAEVLGR-T-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN---- 333 (514)
Q Consensus 261 V~v~Vl~~-d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~---- 333 (514)
+.+.|+.. + .+|+++...-....+..+..|.-.-..|++|.|.|++++++|+||.++-++||+|.+|+ +.++.
T Consensus 44 ~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~ 123 (183)
T COG1095 44 LVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEK 123 (183)
T ss_pred EEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcc
Confidence 33444542 2 56666633222222222222222235899999999999999999999889999999999 33221
Q ss_pred ------ChhhHhhhcCCEEEEEEEEEeCCC-----CceEeehhhh
Q 010232 334 ------NFTELKEKVGRRMYVQITRINEDT-----NDLILSEREA 367 (514)
Q Consensus 334 ------~~~el~~~VGq~V~vkVl~vD~e~-----~rIiLS~K~~ 367 (514)
.-......+|+.|+++|+.+.... .+|.+++|++
T Consensus 124 ~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq~ 168 (183)
T COG1095 124 NKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQP 168 (183)
T ss_pred cceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEeccc
Confidence 111122368999999999987655 4788888875
No 146
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.92 E-value=4.3e-05 Score=80.54 Aligned_cols=108 Identities=19% Similarity=0.180 Sum_probs=74.7
Q ss_pred CcccCCCEEEEEEEEEcCCCcEE-EEehHHHHH----hhhhHHHhhh--cCCCEEEEEEEEEEC-CeEEEEECCEEEEEe
Q 010232 253 PVVETGTVLFAEVLGRTLSGRPL-LSTRRLFRK----MAWHRVRQIK--QLNEPIEVKFTEWNT-GGLLTRIEGLRAFLP 324 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~d~~grli-LS~kk~~~~----~~w~~l~~~~--k~GeiV~GkV~~v~~-~G~fVdi~Gi~gFVP 324 (514)
+.+++||.+...+-- ..=||+. -+.++...+ ...+.+.+.+ +.|++++|+|.++.. ++++|++++..|+||
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 PSVEIGDELTYELSL-ENMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLP 167 (374)
T ss_pred CCCCCCCEEEEecCh-hhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeC
Confidence 457899999876542 2234443 233333211 1112222222 699999999999996 569999999999999
Q ss_pred ccccccccCChhhHhhhcCCEEEEEEEEEeCCCC---ceEeehhhh
Q 010232 325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDTN---DLILSEREA 367 (514)
Q Consensus 325 ~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~---rIiLS~K~~ 367 (514)
.+++...- . +.+|++++|+|.+|+...+ .|+|||..+
T Consensus 168 ~~eqip~E-----~-~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p 207 (374)
T PRK12328 168 MKNRIKGE-----K-FKVGDVVKAVLKRVKIDKNNGILIELSRTSP 207 (374)
T ss_pred HHHcCCCC-----c-CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence 99984221 1 2599999999999988765 899999753
No 147
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.81 E-value=8.3e-06 Score=81.20 Aligned_cols=88 Identities=22% Similarity=0.283 Sum_probs=78.3
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES 449 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~ 449 (514)
-.+++++|-+.|.+|...|+||.+-.+ +++|+|-.|+||..|+.++.+..++|..=.|.|+.+| +++-|+||.+.+.+
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 468999999999999999999999443 7999999999999999999999999999999999999 89999999999988
Q ss_pred CCCccccchh
Q 010232 450 EPGLFVSDKE 459 (514)
Q Consensus 450 ~P~~~~~~k~ 459 (514)
+.-....+++
T Consensus 93 ed~~kC~Er~ 102 (304)
T KOG2916|consen 93 EDKEKCEERF 102 (304)
T ss_pred HHHHHHHHHH
Confidence 6655544443
No 148
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.78 E-value=0.00013 Score=62.45 Aligned_cols=77 Identities=21% Similarity=0.257 Sum_probs=59.0
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEe--------CCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdI--------G~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~ 239 (514)
+-+++||+|.|+|+++....+.|+| .....|++|.+++.+.+-.+
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 4578999999999999999999999 66778999988875331000
Q ss_pred ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (514)
Q Consensus 240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk 280 (514)
..+ ...|++||.|.|+|++.+....+.||++.
T Consensus 55 --~~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~ 86 (92)
T cd05791 55 --VEM-------YKCFRPGDIVRAKVISLGDASSYYLSTAE 86 (92)
T ss_pred --HHH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence 001 23489999999999987666778899864
No 149
>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=97.74 E-value=0.00021 Score=60.82 Aligned_cols=59 Identities=10% Similarity=0.180 Sum_probs=49.3
Q ss_pred CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc-----------ccccCCCCEEEEEEEEEe
Q 010232 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV-----------SDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~-----------~~~~kvGd~VkvkVi~vd 435 (514)
+|++++|+|++++++|+||.+++ +.+|+|.+.+......++ ...+++|+.|++||+.+.
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 58999999999999999999996 799999988865433332 345889999999999885
No 150
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.74 E-value=0.00014 Score=57.66 Aligned_cols=61 Identities=20% Similarity=0.235 Sum_probs=37.9
Q ss_pred CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA 445 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK 445 (514)
+|++...+|.+++++|+|++.+. +-.-|+|.+++. ..+++||.|.|.|. .|.++|+..|+|
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 58899999999999999999887 689999999986 45899999999997 477789999885
No 151
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=97.73 E-value=8.1e-05 Score=71.18 Aligned_cols=73 Identities=12% Similarity=0.172 Sum_probs=58.8
Q ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc-cccC-Chh---------hHhhhcCCEEEEEEEEEe-----CCCC
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NFT---------ELKEKVGRRMYVQITRIN-----EDTN 358 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~-~~i~-~~~---------el~~~VGq~V~vkVl~vD-----~e~~ 358 (514)
..|+++.|+|++++++|+||+++.++|++|.+++. .+.. ++. .....+|+.|+++|.++| ++..
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 48999999999999999999997799999999983 3221 111 123479999999999998 5667
Q ss_pred ceEeehhhh
Q 010232 359 DLILSEREA 367 (514)
Q Consensus 359 rIiLS~K~~ 367 (514)
+|.+|+|++
T Consensus 160 ~I~lt~k~~ 168 (179)
T TIGR00448 160 KIGLTMRQP 168 (179)
T ss_pred eEEEEeccC
Confidence 899999975
No 152
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.70 E-value=0.00024 Score=67.97 Aligned_cols=88 Identities=22% Similarity=0.288 Sum_probs=68.8
Q ss_pred CCceEeehhhhhh-hccCCCCceEEEEEEEEecceEEEEECCC---------ceEEEEEeeccccccccCcccccCCCCE
Q 010232 357 TNDLILSEREAWA-TLNLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGER 426 (514)
Q Consensus 357 ~~rIiLS~K~~~~-~~~l~~G~iV~G~V~~I~~~GaFV~I~~~---------gi~GLvh~Sels~~~v~~~~~~~kvGd~ 426 (514)
.++..+|.+.... ..-++.|++|-|+|+++....+.|+|-.. -..|-+|+|+++..++.+.++.|++||.
T Consensus 45 ~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDi 124 (188)
T COG1096 45 DKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI 124 (188)
T ss_pred ccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccE
Confidence 3444555543322 23578999999999999999999988521 1467899999999999999999999999
Q ss_pred EEEEEEEEeCCCeEEEEEec
Q 010232 427 VKVLVVKSMFPDKISLSIAD 446 (514)
Q Consensus 427 VkvkVi~vde~~rI~LSlK~ 446 (514)
|+|+|++.- ..+.||++.
T Consensus 125 vrA~Vis~~--~~~~Lst~~ 142 (188)
T COG1096 125 VRARVISTG--DPIQLSTKG 142 (188)
T ss_pred EEEEEEecC--CCeEEEecC
Confidence 999999753 667888754
No 153
>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=97.66 E-value=0.00034 Score=59.44 Aligned_cols=73 Identities=26% Similarity=0.416 Sum_probs=58.6
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~ 247 (514)
|.+++||+|-|+|+.+....+.|||+....|+||..++.-.
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 57889999999999999999999999888999887665211
Q ss_pred CCCCCCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 010232 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR 279 (514)
Q Consensus 248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~k 279 (514)
..+.++.+++||.|.|+|...+.+..+.||..
T Consensus 43 tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~ 74 (86)
T cd05790 43 TKRNRPNLNVGDLVYARVVKANRDMEPELSCV 74 (86)
T ss_pred cccccccCCCCCEEEEEEEecCCCCCeEEEEe
Confidence 01114678999999999998887777777764
No 154
>PRK05054 exoribonuclease II; Provisional
Probab=97.65 E-value=0.00017 Score=81.82 Aligned_cols=71 Identities=14% Similarity=0.173 Sum_probs=58.7
Q ss_pred CCC--ceEEEEEEEEecceEEEEECCCceEEEEEeeccccc---ccc--C-------cccccCCCCEEEEEEEEEe-CCC
Q 010232 374 REG--TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT---RVT--S-------VSDLLNEGERVKVLVVKSM-FPD 438 (514)
Q Consensus 374 ~~G--~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~---~v~--~-------~~~~~kvGd~VkvkVi~vd-e~~ 438 (514)
++| +.+.|+|++|+++|+||+|.+.+++||||.+.|.+. +.- + -...|++||+|+|+|.++| +++
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 465 599999999999999999987789999999999653 111 1 1246999999999999998 888
Q ss_pred eEEEEE
Q 010232 439 KISLSI 444 (514)
Q Consensus 439 rI~LSl 444 (514)
+|.+++
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 998875
No 155
>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=97.55 E-value=0.00026 Score=58.02 Aligned_cols=67 Identities=21% Similarity=0.356 Sum_probs=56.5
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccC---cccccCCCCEE-EEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS---VSDLLNEGERV-KVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~---~~~~~kvGd~V-kvkVi~vd-e~~rI~LSlK 445 (514)
|++|+|+|..-++.+++|++.+.|+.|++|..++++ ++.+ .-..+++||++ .+.|+ + ..+.|.||.|
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 4432 33458999999 89998 5 5667788765
No 156
>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=97.53 E-value=0.00023 Score=76.64 Aligned_cols=62 Identities=35% Similarity=0.568 Sum_probs=53.8
Q ss_pred cCCCCceEEEEEEEEecc--eEEEEECCCceEEEEEeeccccc------------cccCcccccCCCCEEEEEEEEE
Q 010232 372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~--GaFV~I~~~gi~GLvh~Sels~~------------~v~~~~~~~kvGd~VkvkVi~v 434 (514)
...+|+++.|+|.+|.|. ||||+|+. +..||+|.+++.+. +..++.+.+++||.|.|.|++-
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 457999999999999999 99999998 89999999998753 2445667899999999999973
No 157
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.47 E-value=0.00042 Score=68.82 Aligned_cols=76 Identities=24% Similarity=0.360 Sum_probs=68.0
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
-.++||+|-|+|..+.+.++.|+|+. -+.+++|.|++.+..+ .+++.+|++||-|.|+|..++..+...|++|+.
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 46899999999999999999999998 5999999999966653 478889999999999999999999999999765
Q ss_pred c
Q 010232 448 E 448 (514)
Q Consensus 448 ~ 448 (514)
.
T Consensus 140 ~ 140 (239)
T COG1097 140 G 140 (239)
T ss_pred C
Confidence 4
No 158
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.43 E-value=0.00066 Score=65.00 Aligned_cols=73 Identities=10% Similarity=0.024 Sum_probs=57.2
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccc-----------c-cCcccccCCCCEEEEEEEEEe-C--C
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-----------V-TSVSDLLNEGERVKVLVVKSM-F--P 437 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~-----------v-~~~~~~~kvGd~VkvkVi~vd-e--~ 437 (514)
.-.|++++|+|++++++|+||.++. .++|||.++|.+.. . .+-...++.|+.|++||..+. + +
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 5789999999999999999999987 67999999997431 1 122456999999999999885 2 2
Q ss_pred CeEEEEEecC
Q 010232 438 DKISLSIADL 447 (514)
Q Consensus 438 ~rI~LSlK~l 447 (514)
.++..|||+-
T Consensus 157 ~~~i~T~~~~ 166 (176)
T PTZ00162 157 LFAIATINSD 166 (176)
T ss_pred cEEEEEecCC
Confidence 3566677653
No 159
>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=97.42 E-value=0.00052 Score=78.64 Aligned_cols=69 Identities=16% Similarity=0.247 Sum_probs=56.5
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc-ccc-----------CChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL 360 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~-~~i-----------~~~~el~~~VGq~V~vkVl~vD~e~~rI 360 (514)
+.|+++.|+|++++++|+||++. |++|+||++++. .++ .+... .+++||+|+|+|.++|..+++|
T Consensus 626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~-~~~lGd~V~Vkv~~vd~~~~~I 704 (709)
T TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGK-VFRLGDRVKVRVVKADLDTGKI 704 (709)
T ss_pred cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCc-EECCCCEEEEEEEEEecccCeE
Confidence 68999999999999999999996 699999999993 221 11111 1369999999999999999999
Q ss_pred Eeeh
Q 010232 361 ILSE 364 (514)
Q Consensus 361 iLS~ 364 (514)
.++.
T Consensus 705 ~~~l 708 (709)
T TIGR02063 705 DFEL 708 (709)
T ss_pred EEEE
Confidence 8874
No 160
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.41 E-value=0.00074 Score=67.12 Aligned_cols=80 Identities=21% Similarity=0.383 Sum_probs=64.7
Q ss_pred ccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (514)
Q Consensus 167 ~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~ 246 (514)
-|.+++||+|-|.|+.+...++.|||++...++||.++++.+. + ..
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 4789999999999999999999999999999999999884321 0 00
Q ss_pred CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (514)
Q Consensus 247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk 280 (514)
...+-++.+++||.|.|+|...|.++.+.|+.|.
T Consensus 105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~ 138 (239)
T COG1097 105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD 138 (239)
T ss_pred cccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence 0011256789999999999999999999998843
No 161
>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=97.40 E-value=0.00094 Score=56.72 Aligned_cols=72 Identities=22% Similarity=0.128 Sum_probs=62.0
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD 446 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~ 446 (514)
.++||.|-|+|+.++..+.+|+|+. -..|++|.+.+... .++.+..|++||-|-|+|..++......||+.+
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~ 75 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVD 75 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeC
Confidence 4789999999999999999999998 58999999887533 344567899999999999998877789999976
No 162
>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=97.39 E-value=0.00068 Score=55.63 Aligned_cols=65 Identities=23% Similarity=0.390 Sum_probs=53.5
Q ss_pred CCEEEEEEEEEECCeEEEEEC--CEEEEEeccccccccCC----hhhHhhhcCCEE-EEEEEEEeCCCCceEeehh
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNN----FTELKEKVGRRM-YVQITRINEDTNDLILSER 365 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~~i~~----~~el~~~VGq~V-~vkVl~vD~e~~rIiLS~K 365 (514)
|..|+|+|...++.+++|+++ |++|++|..|+.+...+ ++.+ .+|+++ .+.|+ |...+.+.+|.|
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 688999999999999999995 69999999999544332 2334 599999 88888 788888888875
No 163
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.37 E-value=0.00038 Score=66.87 Aligned_cols=72 Identities=19% Similarity=0.264 Sum_probs=56.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc-cccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCC-----
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NF---------TELKEKVGRRMYVQITRINEDTN----- 358 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~-~~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~----- 358 (514)
..|+++.|+|+++++.|++|+++.++||++.+++. .+.. ++ ......+|+.++++|.+++....
T Consensus 80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~ 159 (187)
T PRK08563 80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS 159 (187)
T ss_pred cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence 58999999999999999999998899999999983 3221 00 01123689999999999987543
Q ss_pred ceEeehhh
Q 010232 359 DLILSERE 366 (514)
Q Consensus 359 rIiLS~K~ 366 (514)
+|.+|++.
T Consensus 160 ~I~ls~~~ 167 (187)
T PRK08563 160 KIGLTMRQ 167 (187)
T ss_pred EEEEEecC
Confidence 78889885
No 164
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.35 E-value=0.00085 Score=72.14 Aligned_cols=109 Identities=15% Similarity=0.195 Sum_probs=74.0
Q ss_pred CcccCCCEEEEEEEEE-cCCCcEEE-EehHHHH----HhhhhHHHhhh--cCCCEEEEEEEEEECCeEEEEE----CC--
Q 010232 253 PVVETGTVLFAEVLGR-TLSGRPLL-STRRLFR----KMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRI----EG-- 318 (514)
Q Consensus 253 ~~~~vGd~V~v~Vl~~-d~~grliL-S~kk~~~----~~~w~~l~~~~--k~GeiV~GkV~~v~~~G~fVdi----~G-- 318 (514)
+.+++||.|...|.-. ..=||+.+ +.|+... ....+.+.+.+ +.|+++.|+|.++.+.+++|++ +.
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 4578999998765321 12355532 2333221 11222233322 6999999999999999999998 42
Q ss_pred EEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCC---CceEeehhhh
Q 010232 319 LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT---NDLILSEREA 367 (514)
Q Consensus 319 i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~---~rIiLS~K~~ 367 (514)
++|+||.+++...- . +++|++++|+|.+|+... -.|+|||..+
T Consensus 181 ~EaiLP~~Eqip~E-----~-y~~Gdrika~i~~V~~~~~kGpqIilSRt~p 226 (449)
T PRK12329 181 VEAELPKREQLPND-----N-YRANATFKVFLKEVSEGPRRGPQLFVSRANA 226 (449)
T ss_pred eEEEecHHHcCCCC-----c-CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence 89999999983221 1 269999999999997753 3799999753
No 165
>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=97.28 E-value=0.00076 Score=56.80 Aligned_cols=61 Identities=18% Similarity=0.310 Sum_probs=41.6
Q ss_pred CCCceEEEEEEEEecceEEEEECCC-----------------ceEEEEEeeccccccccC--cccccCCCCEEEEEEEEE
Q 010232 374 REGTLLEGTVKKIYPYGAQIRIGDS-----------------NRSGLLHISNMSRTRVTS--VSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaFV~I~~~-----------------gi~GLvh~Sels~~~v~~--~~~~~kvGd~VkvkVi~v 434 (514)
++|++|.|+|+++++.-|+++|-.. ...|+||.+++....... +.+.|++||.|+|+|+++
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 6788999999999888887777321 478999999988765543 578899999999999864
No 166
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.15 E-value=0.001 Score=70.41 Aligned_cols=94 Identities=16% Similarity=0.199 Sum_probs=69.0
Q ss_pred hcCCEEEEEEEEEeCCCCceEee-hhhhh-------------hhccCCCCceEEEEEEEEecc-eEEEEECCCceEEEEE
Q 010232 341 KVGRRMYVQITRINEDTNDLILS-EREAW-------------ATLNLREGTLLEGTVKKIYPY-GAQIRIGDSNRSGLLH 405 (514)
Q Consensus 341 ~VGq~V~vkVl~vD~e~~rIiLS-~K~~~-------------~~~~l~~G~iV~G~V~~I~~~-GaFV~I~~~gi~GLvh 405 (514)
.+|+.+...+.-- +-+|+.+. .|+.+ +...-+.|+++.|+|.++... +++|+++ +.+|++|
T Consensus 92 ~vGd~i~~~i~~~--~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP 167 (374)
T PRK12328 92 EIGDELTYELSLE--NMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEID--EIRAVLP 167 (374)
T ss_pred CCCCEEEEecChh--hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcC--CeEEEeC
Confidence 5899998766521 22333222 22221 123568999999999999875 5999998 5899999
Q ss_pred eeccccccccCcccccCCCCEEEEEEEEEe-CCC---eEEEEE
Q 010232 406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD---KISLSI 444 (514)
Q Consensus 406 ~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~---rI~LSl 444 (514)
.++.. |.+.|++||+++|+|.+|. ..+ +|.||.
T Consensus 168 ~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSR 204 (374)
T PRK12328 168 MKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSR 204 (374)
T ss_pred HHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEc
Confidence 99976 5688999999999999996 332 677887
No 167
>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=97.12 E-value=0.0014 Score=74.45 Aligned_cols=68 Identities=12% Similarity=0.191 Sum_probs=55.0
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeecccc--c-cc--c-----Cc--ccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--T-RV--T-----SV--SDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~--~-~v--~-----~~--~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
|+.+.|+|++++++|+||++.+.|++||||.+.+.. + +. . .+ ...|++||+|+|+|.++| ++++|.+
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 458999999999999999996658999999999965 2 21 1 11 125999999999999998 7888876
Q ss_pred E
Q 010232 443 S 443 (514)
Q Consensus 443 S 443 (514)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 168
>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=97.12 E-value=0.0021 Score=73.12 Aligned_cols=69 Identities=16% Similarity=0.333 Sum_probs=56.1
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-cccc-----------CChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL 360 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i-----------~~~~el~~~VGq~V~vkVl~vD~e~~rI 360 (514)
+.|+.+.|+|++++++|+||++. |++||||++++ +.+. ++... .+.+|++|+|+|.++|..+++|
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 68999999999999999999995 69999999999 3321 11111 2369999999999999999998
Q ss_pred Eeeh
Q 010232 361 ILSE 364 (514)
Q Consensus 361 iLS~ 364 (514)
.++.
T Consensus 650 ~f~l 653 (654)
T TIGR00358 650 IFEL 653 (654)
T ss_pred EEEE
Confidence 8763
No 169
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.08 E-value=0.0015 Score=74.98 Aligned_cols=74 Identities=23% Similarity=0.363 Sum_probs=63.2
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK 439 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r 439 (514)
.-++|+...|+|.+++.+|+||.+.+.+++|++|++.+...+. ......++.||.|+|+|.+++ ..++
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 5689999999999999999999998867999999999986422 233446999999999999998 7889
Q ss_pred EEEEEe
Q 010232 440 ISLSIA 445 (514)
Q Consensus 440 I~LSlK 445 (514)
|.+++-
T Consensus 699 i~~~~v 704 (706)
T COG0557 699 IDFELV 704 (706)
T ss_pred eEEEec
Confidence 988873
No 170
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.07 E-value=0.0025 Score=54.21 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=31.1
Q ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEecccc
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel 328 (514)
.|+++.|+|+++++.|++|.++.+++|++.+++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~i 33 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLI 33 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeec
Confidence 489999999999999999999889999998888
No 171
>PRK11642 exoribonuclease R; Provisional
Probab=97.03 E-value=0.002 Score=74.83 Aligned_cols=71 Identities=14% Similarity=0.196 Sum_probs=57.2
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-ccccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-NF---------TELKEKVGRRMYVQITRINEDTNDLI 361 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~rIi 361 (514)
+.|+++.|+|++++++|+||++. +++||||.+++ +.++. +. ..-.+.+|+.|+|+|..+|..+++|.
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 68999999999999999999995 49999999999 33211 00 00123699999999999999999999
Q ss_pred eehh
Q 010232 362 LSER 365 (514)
Q Consensus 362 LS~K 365 (514)
++.-
T Consensus 722 f~l~ 725 (813)
T PRK11642 722 FSLI 725 (813)
T ss_pred EEEe
Confidence 9863
No 172
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.02 E-value=0.0022 Score=53.87 Aligned_cols=67 Identities=16% Similarity=0.255 Sum_probs=57.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEE--CCEEEEEe-cccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLP-KAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE 364 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP-~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~ 364 (514)
+.|+.+. .|+.+.+.|++|.+ -|++|+|+ .+++ .+++++..++. +|....++|+++|+.++-|-||.
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 5788888 89999999999998 25999888 9999 56677777764 99999999999999999888774
No 173
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.95 E-value=0.004 Score=68.12 Aligned_cols=72 Identities=17% Similarity=0.298 Sum_probs=60.5
Q ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~ 368 (514)
..|-+.+++|+++.+.|++|.+. +..|++|.+|| ..++.+|.++. .|||.|.++.++.|+.. .+.+|.|+.+
T Consensus 667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~l-evGq~I~vk~ie~d~~g-~~~ls~ralL 740 (760)
T KOG1067|consen 667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLL-EVGQEIQVKYIERDPRG-GIMLSSRALL 740 (760)
T ss_pred EeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHH-hhcceeEEEEEeecCcc-ceeehhhhhc
Confidence 45778899999999999999995 57999999999 57788998884 89999999999999755 4566666544
No 174
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.85 E-value=0.0051 Score=66.31 Aligned_cols=72 Identities=10% Similarity=0.064 Sum_probs=57.9
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEe----CC-ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccc
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI 242 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdI----G~-k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~ 242 (514)
|.-+.|++|+|+|.+++.++++|++ |. +.+|+||.+|..|.
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 4566899999999999999999998 33 38999999887643
Q ss_pred cccCCCCCCCCcccCCCEEEEEEEEEcC---C-CcEEEEehHHHH
Q 010232 243 AMSGGSGPGRPVVETGTVLFAEVLGRTL---S-GRPLLSTRRLFR 283 (514)
Q Consensus 243 ~l~~~~~~~~~~~~vGd~V~v~Vl~~d~---~-grliLS~kk~~~ 283 (514)
..|++|+.|.|+|..+.. . -+++||+..+..
T Consensus 194 ----------E~y~~Gdrika~i~~V~~~~~kGpqIilSRt~p~l 228 (449)
T PRK12329 194 ----------DNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGL 228 (449)
T ss_pred ----------CcCCCCCEEEEEEEEeecCCCCCCEEEEEcCCHHH
Confidence 348999999999999642 2 368899877754
No 175
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.84 E-value=0.001 Score=73.03 Aligned_cols=72 Identities=18% Similarity=0.343 Sum_probs=61.9
Q ss_pred hccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 370 TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 370 ~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
+.+++.|.++.|+|.++..||+||+++. .+.||+|.++++.. ..+.+|+.+-|.|..+. +++.|++....+.
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecCh-hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 3479999999999999999999999999 79999999999852 45889999999999987 5578877665544
No 176
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.79 E-value=0.0014 Score=76.46 Aligned_cols=76 Identities=21% Similarity=0.256 Sum_probs=68.2
Q ss_pred cCCCCceEEEEEEEEecce---EEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232 372 NLREGTLLEGTVKKIYPYG---AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL 447 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~G---aFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l 447 (514)
.+..|.+|.++|++|+..- +-|.+.+ |+.|+||.+++|+..+.+|...+++||+|.++|++++ ++=-+.||+|..
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 5889999999999998765 5678888 9999999999999999999999999999999999998 666788888865
Q ss_pred c
Q 010232 448 E 448 (514)
Q Consensus 448 ~ 448 (514)
.
T Consensus 1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred H
Confidence 4
No 177
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.73 E-value=0.0049 Score=59.06 Aligned_cols=35 Identities=20% Similarity=0.355 Sum_probs=32.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL 329 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~ 329 (514)
-.|+++.|+|+++++.|++|.+|-+++|||.++|.
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~ 114 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIP 114 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCC
Confidence 38999999999999999999997799999999994
No 178
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.83 E-value=0.02 Score=66.62 Aligned_cols=60 Identities=27% Similarity=0.543 Sum_probs=50.2
Q ss_pred CCCceEEEEEEEEec--ceEEEEECCCceEEEEEeecccccccc---------CcccccCCCCEEEEEEEEE
Q 010232 374 REGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVT---------SVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~~v~---------~~~~~~kvGd~VkvkVi~v 434 (514)
.+|.||.|+|.+|.+ .++||+|+. |..||+|.+++...... .....+++||.|-|.|.+-
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 589999999999987 689999999 89999999998643321 2345699999999999874
No 179
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.80 E-value=0.011 Score=59.41 Aligned_cols=71 Identities=21% Similarity=0.376 Sum_probs=63.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEE---CCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
+.+++|-+.|..+..-|++|.+ +.++|+|-+|+|+ +|+++...+- +||..=.|.|++||++++-|-||.|+
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kli-rVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLI-RVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHH-hcCCcceEEEEEEcCCCCceechhcc
Confidence 5899999999999999999988 5799999999994 6677777765 89999999999999999999999873
No 180
>PRK11712 ribonuclease G; Provisional
Probab=95.58 E-value=0.03 Score=61.69 Aligned_cols=62 Identities=29% Similarity=0.516 Sum_probs=50.3
Q ss_pred cCCCCceEEEEEEEEec--ceEEEEECCCceEEEEEeeccccc------------cccCcccccCCCCEEEEEEEEE
Q 010232 372 NLREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~------------~v~~~~~~~kvGd~VkvkVi~v 434 (514)
...+|.++.|+|.+|.| .+|||+|+. +..||+|.+++... ....+.+.+++||.|-|.|.+-
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 35689999999999988 689999999 89999999997321 1123355699999999999874
No 181
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=95.55 E-value=0.035 Score=59.98 Aligned_cols=57 Identities=16% Similarity=0.202 Sum_probs=45.5
Q ss_pred cCCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccccc-------------ccCChhhHhhhcCCEEEEEEEE
Q 010232 295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-------------RVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~-------------~i~~~~el~~~VGq~V~vkVl~ 352 (514)
..|.++.|+|.++.++ |+||+++ |-.||+|++++.. +..+..+.. .+||.|.|.|.+
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 4899999999999999 9999996 5799999999832 122233333 689999999986
No 182
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=95.36 E-value=0.062 Score=45.33 Aligned_cols=23 Identities=39% Similarity=0.564 Sum_probs=18.1
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe
Q 010232 170 PKPGDFVIGVVVSGNENKLDVNV 192 (514)
Q Consensus 170 ik~GdiV~G~Vv~v~~~Gv~VdI 192 (514)
+++|++|.|+|+++++..++++|
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 57899999999999999999987
No 183
>PRK05054 exoribonuclease II; Provisional
Probab=95.20 E-value=0.071 Score=60.80 Aligned_cols=67 Identities=21% Similarity=0.346 Sum_probs=51.5
Q ss_pred CCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-cc--ccC---C------hhhHhhhcCCEEEEEEEEEeCCCCceEe
Q 010232 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LS--RVN---N------FTELKEKVGRRMYVQITRINEDTNDLIL 362 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~--~i~---~------~~el~~~VGq~V~vkVl~vD~e~~rIiL 362 (514)
|+.+.|.|++++++|+||.+. |+.||||.+.| .. ... + ...-.+.+||+|+|+|.++|..+++|.+
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 0011236899999999999998888866
Q ss_pred e
Q 010232 363 S 363 (514)
Q Consensus 363 S 363 (514)
+
T Consensus 642 ~ 642 (644)
T PRK05054 642 R 642 (644)
T ss_pred E
Confidence 4
No 184
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=95.07 E-value=0.15 Score=49.24 Aligned_cols=105 Identities=15% Similarity=0.193 Sum_probs=66.3
Q ss_pred CCCcccCCCEEEEEEEEE-c-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECCE---------
Q 010232 251 GRPVVETGTVLFAEVLGR-T-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGL--------- 319 (514)
Q Consensus 251 ~~~~~~vGd~V~v~Vl~~-d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~Gi--------- 319 (514)
+...+..|..|.+-+.+. . ...+.++|.+.... .-...+.|++|.|+|+++....+.|++-++
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 355677788888877762 2 23344445443322 224457999999999999999999999333
Q ss_pred --EEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 320 --RAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 320 --~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
.|-+|.|+. ....++.++.+ .+|+.|+++|++.- ..+.||.+
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 456777777 44444444443 66777777776542 34555554
No 185
>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=94.67 E-value=0.13 Score=58.58 Aligned_cols=67 Identities=27% Similarity=0.420 Sum_probs=50.6
Q ss_pred CCEEEEEEEEEECCeEEEEE--CCEEEEEecccccc---cc-CChh--------hHhhhcCCEEEEEEEEEeCCCCceEe
Q 010232 297 NEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELLS---RV-NNFT--------ELKEKVGRRMYVQITRINEDTNDLIL 362 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel~~---~i-~~~~--------el~~~VGq~V~vkVl~vD~e~~rIiL 362 (514)
|+...|.|+.++++|+||.+ .|+.||||.+.+.. .. -+.. .-.+.+|++|+|+|.++|..+++|.+
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 37999999998822 11 0100 10246899999999999988888765
Q ss_pred e
Q 010232 363 S 363 (514)
Q Consensus 363 S 363 (514)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 186
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=94.59 E-value=0.18 Score=56.02 Aligned_cols=149 Identities=14% Similarity=0.181 Sum_probs=95.1
Q ss_pred cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccccccc
Q 010232 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS 245 (514)
Q Consensus 166 ~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~ 245 (514)
.++++..|.+-.|+|.++...|+||++.....|+|+.+.+..
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~-------------------------------------- 157 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG-------------------------------------- 157 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccCC--------------------------------------
Confidence 468999999999999999999999999999999988777631
Q ss_pred CCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHH------HHHh-----hhhHHHhhhcCCC--EEEEEEEEEEC-C
Q 010232 246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRL------FRKM-----AWHRVRQIKQLNE--PIEVKFTEWNT-G 310 (514)
Q Consensus 246 ~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~------~~~~-----~w~~l~~~~k~Ge--iV~GkV~~v~~-~ 310 (514)
.+.+.+|+++.+.|..+. ..|.+-+....+ ...+ ....|.+ ..|+ .++|+|+.+.. .
T Consensus 158 ------~~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~~~~~~ke~~r~~i~~id~--~ig~tV~I~GeV~qikqT~ 229 (715)
T COG1107 158 ------DPDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYREVQVEKELPRTLIDDLDE--MIGKTVRIEGEVTQIKQTS 229 (715)
T ss_pred ------CCCCCCCCeEEEEeeccCCCCCccceeecCCccchhhhhhhhcccccHHHHHh--hcCceEEEEEEEEEEEEcC
Confidence 234678999998888754 346653332221 1111 1233433 3555 46788998864 3
Q ss_pred e-EEEEECCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 311 G-LLTRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 311 G-~fVdi~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
| -+..+-.=.|++|..-+. .-++-.-++ .+|+.|.+.= .++...+++.+-
T Consensus 230 GPTVFtltDetg~i~aAAFe~aGvRAyP~I--evGdiV~ViG-~V~~r~g~lQiE 281 (715)
T COG1107 230 GPTVFTLTDETGAIWAAAFEEAGVRAYPEI--EVGDIVEVIG-EVTRRDGRLQIE 281 (715)
T ss_pred CCEEEEEecCCCceehhhhccCCcccCCCC--CCCceEEEEE-EEeecCCcEEEe
Confidence 4 333443346777766552 222222223 4899887643 366677777554
No 187
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=94.50 E-value=0.062 Score=63.27 Aligned_cols=72 Identities=21% Similarity=0.244 Sum_probs=58.7
Q ss_pred hcCCCEEEEEEEEEECC--eE-EEEE-CCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232 294 KQLNEPIEVKFTEWNTG--GL-LTRI-EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE 366 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~--G~-fVdi-~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~ 366 (514)
+..|.+|.++|++++.+ +| -|.+ .|+.||||...++ ..+.+|.... ++|+.|.|+|+++|.++-.+-||.|.
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 46899999999999754 44 3455 4899999999995 4677776665 79999999999999998888888873
No 188
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.76 E-value=0.29 Score=46.14 Aligned_cols=61 Identities=15% Similarity=0.214 Sum_probs=43.8
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccc----cccccC-------cccccCCCCEEEEEEEEEe
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTS-------VSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels----~~~v~~-------~~~~~kvGd~VkvkVi~vd 435 (514)
.-.|++|+|+|+++...|+|+++++ ++-++..-.+. ...-++ -...+++|.+|+++|+..+
T Consensus 79 pfKGEVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 79 PFKGEVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred ecCCcEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 4579999999999999999999997 55555332222 111111 1226899999999999875
No 189
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=93.61 E-value=0.099 Score=52.60 Aligned_cols=97 Identities=24% Similarity=0.365 Sum_probs=68.0
Q ss_pred hhhhhchhc----cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcc
Q 010232 157 KVGEDKVSV----EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK 232 (514)
Q Consensus 157 ~~~~~~~~~----~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~ 232 (514)
....|++.+ .-|..+.||+|.|+|+.|....+=||++.+.++.|+.+-+.- .|.
T Consensus 66 ~rvNkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNL----------------------PGg 123 (301)
T KOG3013|consen 66 QRVNKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNL----------------------PGG 123 (301)
T ss_pred hhhcceEEEeehhhhcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccC----------------------Cch
Confidence 334444443 347899999999999999999999999999999988766521 011
Q ss_pred cee-eeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHH
Q 010232 233 MGI-VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282 (514)
Q Consensus 233 ~~v-~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~ 282 (514)
+.. -.+.|+..|+. .++.||.|.+.|-..-.+|-+.|-+|...
T Consensus 124 ~~RRk~~~DEl~MR~-------fl~egDLi~AEVQ~v~~dGs~sLhTRS~K 167 (301)
T KOG3013|consen 124 IQRRKSEEDELQMRS-------FLKEGDLIVAEVQNVFHDGSLSLHTRSLK 167 (301)
T ss_pred hhhccchhhHHHHHH-------HhhccCeehHHHHHhccCCeEEEEecchh
Confidence 111 12234444543 37899999988876667888887776554
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=93.56 E-value=0.32 Score=42.63 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=36.1
Q ss_pred hhhhhchhccc----cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecc
Q 010232 157 KVGEDKVSVEY----YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTK 203 (514)
Q Consensus 157 ~~~~~~~~~~~----~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~s 203 (514)
..|+.++-.+- -+ ..|.+|.|+|.++.++-+|||+|.|..++++..
T Consensus 5 ~sFaslLR~S~fi~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp 54 (104)
T PF10246_consen 5 ESFASLLRNSPFIQLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRP 54 (104)
T ss_pred ccHHHHhcCChhhhcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecc
Confidence 45666665542 23 369999999999999999999999999987643
No 191
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=93.21 E-value=0.5 Score=45.09 Aligned_cols=73 Identities=19% Similarity=0.136 Sum_probs=52.8
Q ss_pred cCCCCceEEEEEEEEecceEEEEEC--------CCceEEEEEeeccccc--cccCcccccCCCCEEEEEEEEEeCCCeEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIG--------DSNRSGLLHISNMSRT--RVTSVSDLLNEGERVKVLVVKSMFPDKIS 441 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~--------~~gi~GLvh~Sels~~--~v~~~~~~~kvGd~VkvkVi~vde~~rI~ 441 (514)
-...|++|.++|..+...=|-|+|- . ...|+||..++... .--++-+.|++||.|.|+|++........
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~-~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~ 143 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKK-SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYL 143 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhh-hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEE
Confidence 3467888888888877766666552 3 58999999887542 22345566999999999999866666777
Q ss_pred EEEe
Q 010232 442 LSIA 445 (514)
Q Consensus 442 LSlK 445 (514)
||.-
T Consensus 144 LTtA 147 (193)
T KOG3409|consen 144 LTTA 147 (193)
T ss_pred EEEe
Confidence 7773
No 192
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=92.88 E-value=0.3 Score=44.17 Aligned_cols=36 Identities=14% Similarity=0.079 Sum_probs=31.6
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccc
Q 010232 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (514)
Q Consensus 172 ~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p 207 (514)
+|+++.|+|.+.+..|+.|.+|.=-+.+||...|.+
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ 38 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPE 38 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-T
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCC
Confidence 699999999999999999999988889999988863
No 193
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=91.20 E-value=0.77 Score=53.03 Aligned_cols=71 Identities=15% Similarity=0.244 Sum_probs=54.0
Q ss_pred hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccccc-ccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCCce
Q 010232 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS-RVN-NF---------TELKEKVGRRMYVQITRINEDTNDL 360 (514)
Q Consensus 294 ~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~-~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~rI 360 (514)
...|+...|.|+++..+|+||.+. |++|+||.+.+.. ++. +. ....+.+|+.|+++|.++|...+++
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 369999999999999999999995 4899999999842 211 00 0112368999999999998887777
Q ss_pred Eeeh
Q 010232 361 ILSE 364 (514)
Q Consensus 361 iLS~ 364 (514)
.++.
T Consensus 700 ~~~~ 703 (706)
T COG0557 700 DFEL 703 (706)
T ss_pred EEEe
Confidence 6653
No 194
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=90.92 E-value=0.95 Score=43.24 Aligned_cols=75 Identities=23% Similarity=0.285 Sum_probs=51.5
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe---CCc-----eeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232 170 PKPGDFVIGVVVSGNENKLDVNV---GAD-----LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (514)
Q Consensus 170 ik~GdiV~G~Vv~v~~~Gv~VdI---G~k-----~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~ 241 (514)
+..|++|+.+|.+++...+-|+| |.+ ..|+|+..++-+.. ++ .
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tE------------kd-----------------r 116 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATE------------KD-----------------R 116 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccc------------cc-----------------h
Confidence 56899999999999998877765 433 45777776664321 00 0
Q ss_pred ccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232 242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (514)
Q Consensus 242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk 280 (514)
+++ -+-|++||.|.+.|++.......+||+.+
T Consensus 117 v~v-------~ksFrPgDiVlAkVis~~~~~~y~LTtAe 148 (193)
T KOG3409|consen 117 VKV-------YKSFRPGDIVLAKVISLGDGSNYLLTTAE 148 (193)
T ss_pred hhh-------hhccCCCcEEEEEEeecCCCCcEEEEEec
Confidence 111 23488999999999985555667777654
No 195
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=90.82 E-value=0.36 Score=53.34 Aligned_cols=62 Identities=29% Similarity=0.453 Sum_probs=52.3
Q ss_pred cCCCCceEEEEEEEEec--ceEEEEECCCceEEEEEeeccccccccC-----cccccCCCCEEEEEEEEEe
Q 010232 372 NLREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVTS-----VSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~~v~~-----~~~~~kvGd~VkvkVi~vd 435 (514)
...+|.++.|+|++|.| -.+||+|+. +-.||+|.+++.+ +... +...++.||.+-|.|++-.
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 45689999999999988 578999999 8999999999998 4333 3458999999999998753
No 196
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=90.30 E-value=1.6 Score=37.29 Aligned_cols=64 Identities=17% Similarity=0.160 Sum_probs=50.4
Q ss_pred eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD 446 (514)
Q Consensus 378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~ 446 (514)
.++|+|+.+.+.+.| |.+.+ |..-+.|+|-=-. .-.-.+.+||.|.|.+-..| .++||..-.|.
T Consensus 8 e~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR----~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMR----KHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEecccee----eeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 589999999999988 68888 8888888875221 11223778999999998777 88999988874
No 197
>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=89.68 E-value=1.7 Score=39.41 Aligned_cols=60 Identities=17% Similarity=0.231 Sum_probs=44.0
Q ss_pred CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-------------cccCcccccCCCCEEEEEEEEEe
Q 010232 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-------------RVTSVSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-------------~v~~~~~~~kvGd~VkvkVi~vd 435 (514)
+|+++.|+|++-+..|+.|.++= =-+-+||.+.|... +-.+-.-++..|+.|+.||..+.
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 69999999999999999999975 36778888887522 11344455789999999999764
No 198
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=89.67 E-value=1.4 Score=41.67 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=27.5
Q ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEec
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK 325 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~ 325 (514)
.|++++|.|+.+++.|+|+++|.++.|+-.
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~ss 110 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSS 110 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeec
Confidence 899999999999999999999888888763
No 199
>PRK10811 rne ribonuclease E; Reviewed
Probab=88.77 E-value=0.82 Score=53.84 Aligned_cols=62 Identities=16% Similarity=0.233 Sum_probs=45.6
Q ss_pred CCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccccccc-CC---------hhhHhhhcCCEEEEEEEEEeCCCC
Q 010232 296 LNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSRV-NN---------FTELKEKVGRRMYVQITRINEDTN 358 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~~i-~~---------~~el~~~VGq~V~vkVl~vD~e~~ 358 (514)
.|.|+.|+|.++.++ ++||+|+ |..||+|+++....+ .+ ..... ..||.|.|.|.+-...++
T Consensus 38 vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~L-k~GqeILVQV~KEa~gtK 112 (1068)
T PRK10811 38 KANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVL-REGQEVIVQIDKEERGNK 112 (1068)
T ss_pred ccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccccccccccccc-CCCCEEEEEEeecccCCC
Confidence 799999999999985 9999996 579999999883211 11 11111 579999999987443333
No 200
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=88.45 E-value=2.5 Score=34.47 Aligned_cols=59 Identities=24% Similarity=0.266 Sum_probs=44.9
Q ss_pred eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEE
Q 010232 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKIS 441 (514)
Q Consensus 378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~ 441 (514)
.+.|+|+...+.+.| |.+.+ |..-+.|++-=-. .-.-.+.+||.|.|.+-..+ +++||.
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 588999999999988 68888 8899998876221 11234788999999887666 666764
No 201
>PRK11712 ribonuclease G; Provisional
Probab=88.27 E-value=1.3 Score=49.00 Aligned_cols=57 Identities=19% Similarity=0.364 Sum_probs=43.4
Q ss_pred cCCCEEEEEEEEEECC--eEEEEEC-CEEEEEeccccccc-------------cCChhhHhhhcCCEEEEEEEE
Q 010232 295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSR-------------VNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~~-------------i~~~~el~~~VGq~V~vkVl~ 352 (514)
..|.++.|+|.++.++ ++||+|| +-.||+|++++... ..+..++. +.||.+.|.|.+
T Consensus 37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l-~~Gq~iLVQV~K 109 (489)
T PRK11712 37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELV-RQGQDIMVQVVK 109 (489)
T ss_pred ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhc-cCCCEEEEEEEe
Confidence 3899999999999986 8999996 58999999987210 11122222 589999998886
No 202
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=87.98 E-value=2.7 Score=41.45 Aligned_cols=63 Identities=27% Similarity=0.513 Sum_probs=47.7
Q ss_pred cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~ 247 (514)
|-+.+||.|-|.|+....+...||||....+.||.--+. +.
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 678899999999999999999999998667766543331 00
Q ss_pred CCCCCCcccCCCEEEEEEEEEc
Q 010232 248 SGPGRPVVETGTVLFAEVLGRT 269 (514)
Q Consensus 248 ~~~~~~~~~vGd~V~v~Vl~~d 269 (514)
....++.+++||.|.|+|...+
T Consensus 102 tkrNrPnl~vGdliyakv~~a~ 123 (230)
T KOG1004|consen 102 TKRNRPNLQVGDLIYAKVVDAN 123 (230)
T ss_pred cccCCCccccccEEEEEEEecC
Confidence 1112567899999999998644
No 203
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=86.27 E-value=2.8 Score=36.82 Aligned_cols=54 Identities=15% Similarity=0.196 Sum_probs=45.8
Q ss_pred CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
-..|.+|.|+|.+|...-+||++++ ...+.++...... +.|..|.+|.+++...
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~-KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGG-KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL 74 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCC-ceeEEEecccccc-------cccccCCEEEEEECCH
Confidence 3589999999999999999999999 7999998777542 4588899999988753
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=83.11 E-value=13 Score=29.26 Aligned_cols=59 Identities=31% Similarity=0.374 Sum_probs=39.9
Q ss_pred EEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 010232 379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443 (514)
Q Consensus 379 V~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LS 443 (514)
..|+|+...+ || |+.-.+.+-+-++|.+++.... -..++.|+.|...+.. .+++-....
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g~~A~~ 62 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKGPQAVN 62 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTSEEEEE
T ss_pred CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCCCEEEE
Confidence 4799999875 66 5555553558999999998653 2458899999999875 444433333
No 205
>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=80.41 E-value=5.7 Score=31.71 Aligned_cols=64 Identities=19% Similarity=0.282 Sum_probs=43.8
Q ss_pred CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
|+.++-+|..+++.|--+--++ .+.|+. +...|...-...+.+||++++.|+.|| -+-.+.+||
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 6778888999888776665555 466662 112222233456889999999999998 566666654
No 206
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=77.28 E-value=16 Score=30.48 Aligned_cols=65 Identities=23% Similarity=0.249 Sum_probs=48.4
Q ss_pred CceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232 376 GTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA 445 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK 445 (514)
.-.+.|+|....+.+-| |.+.+ |+.-+.|++-=-.. -.-.+.+||.|.|..-..+ ++++|..-.+
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 45688999999998876 88888 88888888763222 1234789999999998776 6677766543
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=76.91 E-value=6.3 Score=39.10 Aligned_cols=97 Identities=19% Similarity=0.297 Sum_probs=62.2
Q ss_pred hhhchhccccCCCC--CCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232 159 GEDKVSVEYYEPKP--GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (514)
Q Consensus 159 ~~~~~~~~~~~ik~--GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~ 236 (514)
....|+..-+++.. |+...|++.+..+.|+.|+++ +...-+|.++|.|++.. .++++. -+.+.+
T Consensus 59 l~eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~g-----------~~~Qi~--~rFG~V 124 (225)
T PF09883_consen 59 LREEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGPG-----------SPRQIR--RRFGLV 124 (225)
T ss_pred HHHHhCCCCchhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCCC-----------CHHHHH--HHhCcc
Confidence 34445544455555 999999999999999999997 67788899999777421 222211 011111
Q ss_pred eccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhH
Q 010232 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR 289 (514)
Q Consensus 237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~ 289 (514)
..-.|+++|+..+......+|-++......|.+
T Consensus 125 --------------------~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~ 157 (225)
T PF09883_consen 125 --------------------QHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTR 157 (225)
T ss_pred --------------------cCCceEEEEEEcccCcccccCHHHHHHHHHHhh
Confidence 123456676655544566777777777667755
No 208
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=76.69 E-value=4.5 Score=37.51 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=38.1
Q ss_pred cchhhhhchhccc---cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEee
Q 010232 155 DDKVGEDKVSVEY---YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTML 201 (514)
Q Consensus 155 ~~~~~~~~~~~~~---~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp 201 (514)
+|+.||.+|--+- -.-..|..|.|+|..+-.+-+|+|.|.|...++.
T Consensus 62 ~nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~ 111 (173)
T KOG4078|consen 62 PNQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCK 111 (173)
T ss_pred chhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEc
Confidence 3578999887653 2345699999999999999999999999887654
No 209
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=73.46 E-value=27 Score=28.79 Aligned_cols=63 Identities=21% Similarity=0.126 Sum_probs=43.9
Q ss_pred EEEEEEEec-ceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
.|+|+-... .|. ||...+.+-+-|+|+|.+...- ...++.||.|...+.. +++++-...+..+
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 478888755 343 6655543689999999996432 1458899999998864 4667766666554
No 210
>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=68.98 E-value=33 Score=26.86 Aligned_cols=48 Identities=23% Similarity=0.233 Sum_probs=37.0
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
-+.|+|..+.+.-+.++.++.|+.-+++.+.++ .+..++++++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~---------~l~~~~~v~l~t~~~ 51 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLS---------ELPEGGEVKLYTYLI 51 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHH---------TS-TTSEEEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHH---------hCCCCCEEEEEEEEE
Confidence 478999999999999999987788888777654 366677888777655
No 211
>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=68.35 E-value=34 Score=26.71 Aligned_cols=58 Identities=26% Similarity=0.306 Sum_probs=39.6
Q ss_pred EEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 010232 380 EGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443 (514)
Q Consensus 380 ~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LS 443 (514)
.|+|+...+ || |+...+.+-+-|+|.+++...- ...+++||.|...+.. +..+.....
T Consensus 2 ~G~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~-~~~g~~A~~ 62 (65)
T cd04458 2 TGTVKWFDDEKGFG-FITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEE-GDKGPQAVN 62 (65)
T ss_pred cEEEEEEECCCCeE-EEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEE-CCCCCeEEE
Confidence 578888765 66 5545443689999999997531 2568999999998864 344444433
No 212
>PRK15464 cold shock-like protein CspH; Provisional
Probab=66.81 E-value=37 Score=27.70 Aligned_cols=58 Identities=24% Similarity=0.291 Sum_probs=40.5
Q ss_pred EEEEEEEEec-ceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEE
Q 010232 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKIS 441 (514)
Q Consensus 379 V~G~V~~I~~-~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~ 441 (514)
+.|+|+...+ .|. ||.-.+.+-+-|+|+|.+.... ...+.+||+|...|.. ++++.-.
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~-~~kG~~A 64 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVN-GLRGPTA 64 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC----CCCCCCCCEEEEEEEE-CCCCcee
Confidence 4799998865 444 6766553679999999996332 2358899999998864 3444433
No 213
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=66.30 E-value=69 Score=33.64 Aligned_cols=113 Identities=19% Similarity=0.247 Sum_probs=72.2
Q ss_pred cCCCEEEEEEEEEEC-CeEE-EEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhcc
Q 010232 295 QLNEPIEVKFTEWNT-GGLL-TRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLN 372 (514)
Q Consensus 295 k~GeiV~GkV~~v~~-~G~f-Vdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~ 372 (514)
+.|.+++|+|.+-.+ +|+. +.+++....||.-.+ .+|+.+.++|-.-| +.++.+++- .
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 467888888888765 4544 344444444443322 48999999987533 566666552 2
Q ss_pred CCCCceEEEEEEEEecceE----EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232 373 LREGTLLEGTVKKIYPYGA----QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 373 l~~G~iV~G~V~~I~~~Ga----FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
...-.++.|+|+.+.+-+- .++++ |-.-...++..+.+. -.+++||.|-|.|+.+
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 3445677888888876543 34444 345555666665432 3489999999999876
No 214
>PRK10943 cold shock-like protein CspC; Provisional
Probab=65.84 E-value=47 Score=26.85 Aligned_cols=51 Identities=24% Similarity=0.378 Sum_probs=37.3
Q ss_pred eEEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 378 LLEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 378 iV~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
.+.|+|+...+ || |+.-.+.+-+-|+|+|.+.... ...+.+||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFG-FITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEhhHccccC----CCCCCCCCEEEEEEEE
Confidence 46799998765 55 6655442679999999997432 1457899999998764
No 215
>PRK09890 cold shock protein CspG; Provisional
Probab=65.41 E-value=58 Score=26.41 Aligned_cols=58 Identities=19% Similarity=0.314 Sum_probs=39.8
Q ss_pred EEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232 379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442 (514)
Q Consensus 379 V~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~L 442 (514)
+.|+|+...+ || |+.-.+.+-+-|+|+|.+...-. ..+++||+|...+.. .+++....
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~-~~~G~~A~ 65 (70)
T PRK09890 5 MTGLVKWFNADKGFG-FITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ-GQRGPAAA 65 (70)
T ss_pred ceEEEEEEECCCCcE-EEecCCCCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE-CCCCceeE
Confidence 4799998764 55 66665535799999999974321 357899999997754 34444333
No 216
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=64.65 E-value=51 Score=26.63 Aligned_cols=51 Identities=25% Similarity=0.418 Sum_probs=36.9
Q ss_pred eEEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 378 LLEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 378 iV~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
.+.|+|+...+ || ||.-.+.+-+-|+|+|.+.... ...+.+||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGyG-FI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFG-FITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEeecccccC----CCCCCCCCEEEEEEEE
Confidence 36789998764 55 6666443579999999996432 1457899999998764
No 217
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=63.34 E-value=8.5 Score=42.71 Aligned_cols=69 Identities=16% Similarity=0.172 Sum_probs=49.1
Q ss_pred cCCCEEEEEEEEEECC--eEEEEECC-EEEEEeccccccccCChhh----HhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 295 QLNEPIEVKFTEWNTG--GLLTRIEG-LRAFLPKAELLSRVNNFTE----LKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~--G~fVdi~G-i~gFVP~sel~~~i~~~~e----l~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
..|.++.|+|+++.++ .+||+++. -.||+|.+++..+.+.+.+ .....|+.+-+.|+.-...++-..+|
T Consensus 36 ~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 36 IVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred eecCceEEEecccCccchhheeeccCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeecCccccccce
Confidence 4899999999999987 79999963 6899999999544332222 12257888888888654444433333
No 218
>PRK14998 cold shock-like protein CspD; Provisional
Probab=62.98 E-value=53 Score=26.95 Aligned_cols=63 Identities=21% Similarity=0.131 Sum_probs=42.9
Q ss_pred EEEEEEEec-ceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL 447 (514)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l 447 (514)
.|+|+-... .|. ||.-.+.+-+-|+|+|.|.... ...+..|++|...+.. +++++-...+..+
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~-~~~G~~A~~V~~~ 67 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQ-GPKGNHASVIVPI 67 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC----CCCCCCCCEEEEEEEE-CCCCceeEEEEEC
Confidence 488888755 333 6666543689999999996432 2458899999998865 4666655555443
No 219
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=62.34 E-value=67 Score=25.96 Aligned_cols=54 Identities=22% Similarity=0.355 Sum_probs=38.0
Q ss_pred EEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCC
Q 010232 379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD 438 (514)
Q Consensus 379 V~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~ 438 (514)
+.|+|+...+ || |+.-.+.+-+-|+|+|.+.... ...+++||.|...+.. ++++
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~-~~~G 61 (70)
T PRK10354 5 MTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES-GAKG 61 (70)
T ss_pred ceEEEEEEeCCCCcE-EEecCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEE-CCCC
Confidence 4799988754 56 5665542579999999997431 1458899999998764 3444
No 220
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=61.24 E-value=8.8 Score=39.04 Aligned_cols=75 Identities=17% Similarity=0.287 Sum_probs=60.5
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc----c------ccCcccccCCCCEEEEEEEEEeCCCeEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----R------VTSVSDLLNEGERVKVLVVKSMFPDKIS 441 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~----~------v~~~~~~~kvGd~VkvkVi~vde~~rI~ 441 (514)
.-++||+|-|+|..|.+.-+-|+++. ..++.+..|-+.-- | -...+.+|+.||-|.+-|-++-.++.+.
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 56899999999999999999999998 78888888776421 1 1245678999999999998877888888
Q ss_pred EEEecC
Q 010232 442 LSIADL 447 (514)
Q Consensus 442 LSlK~l 447 (514)
|-.+-+
T Consensus 161 LhTRS~ 166 (301)
T KOG3013|consen 161 LHTRSL 166 (301)
T ss_pred EEecch
Confidence 877544
No 221
>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=61.14 E-value=31 Score=28.23 Aligned_cols=57 Identities=14% Similarity=0.223 Sum_probs=39.8
Q ss_pred EEEEEEEEEECCeEE-EEE-CCE--EEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232 299 PIEVKFTEWNTGGLL-TRI-EGL--RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLI 361 (514)
Q Consensus 299 iV~GkV~~v~~~G~f-Vdi-~Gi--~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIi 361 (514)
.+.|+|++...+|.| |.+ +|. .|.++-.--..++. + ..|+.|.+.+..+|..+++|+
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 578999999998876 576 464 45555322222221 2 489999999999998888876
No 222
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=60.69 E-value=30 Score=29.69 Aligned_cols=62 Identities=11% Similarity=0.205 Sum_probs=43.4
Q ss_pred CEEEEEEEEEECCeEE-EEEC-CE--EEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232 298 EPIEVKFTEWNTGGLL-TRIE-GL--RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365 (514)
Q Consensus 298 eiV~GkV~~v~~~G~f-Vdi~-Gi--~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K 365 (514)
-.++|+|+....++.| |.++ |. .|.++-.--..++. + .+|+.|.+.+.-+|..+++|+--.+
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 4688999999998877 5774 54 44444221122222 2 4899999999999999999887665
No 223
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=58.07 E-value=36 Score=26.23 Aligned_cols=49 Identities=20% Similarity=0.282 Sum_probs=31.8
Q ss_pred ceEEEEEEEEecce----EEEEECCCc-eEEEEEeeccccccccCcccccCCCCEEEEEEE
Q 010232 377 TLLEGTVKKIYPYG----AQIRIGDSN-RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (514)
Q Consensus 377 ~iV~G~V~~I~~~G----aFV~I~~~g-i~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi 432 (514)
-.+.|+|..+.+.| +.+.+++.. +...++..... .-.+++||+|.+.+.
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 46889999999999 666667633 55555544432 123789999998774
No 224
>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=57.98 E-value=77 Score=24.75 Aligned_cols=49 Identities=20% Similarity=0.331 Sum_probs=35.1
Q ss_pred EEEEEEEEEC---CeEEEEECC-EEEEEeccccccccCChhhHhhhcCCEEEEEEEE
Q 010232 300 IEVKFTEWNT---GGLLTRIEG-LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 300 V~GkV~~v~~---~G~fVdi~G-i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
.+|+|+.++. +|.+..-++ -+.|+|.+.+.... +..+ ..|+.|.+.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~--~~~l--~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG--FRSL--KEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS--STS----TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc--cccC--CCCCEEEEEEEE
Confidence 3799999986 477666554 49999999994322 1223 489999999886
No 225
>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=57.07 E-value=58 Score=26.17 Aligned_cols=60 Identities=22% Similarity=0.137 Sum_probs=39.2
Q ss_pred EEEEEEEec-ceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232 380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (514)
Q Consensus 380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl 444 (514)
.|+|+.... .|. |+.-.+.+-+-|+|+|.+.... ...+++||+|...+.. .+++.-...+
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~-~~~G~~A~~V 64 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQ-GPKGAHATHI 64 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEE-CCCCceeEEE
Confidence 488888754 333 6655443689999999996432 1458899999998764 3444433333
No 226
>PRK10943 cold shock-like protein CspC; Provisional
Probab=56.90 E-value=43 Score=27.09 Aligned_cols=49 Identities=14% Similarity=0.235 Sum_probs=35.6
Q ss_pred EEEEEEEEEEC---CeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 299 PIEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 299 iV~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
.++|+|+..+. +|.+-.-+ |-+.|+|++.+. .....+ ..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l-----~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTL-----AEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCC-----CCCCEEEEEEEE
Confidence 46899999986 46655544 579999999994 222322 489999998874
No 227
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=56.45 E-value=59 Score=28.52 Aligned_cols=64 Identities=17% Similarity=0.096 Sum_probs=46.0
Q ss_pred CCceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 375 EGTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
....+.|+|+.....+.| |.+.+ |..-++|++-=... .-.++.||.|.|.+...+ .+++|..-+
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-GVERMGRIPGKMKK-----RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhhcc-----cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 344588999999999987 57777 78888888763322 345889999999887665 444554433
No 228
>PRK15463 cold shock-like protein CspF; Provisional
Probab=55.60 E-value=43 Score=27.27 Aligned_cols=51 Identities=25% Similarity=0.352 Sum_probs=37.3
Q ss_pred EEEEEEEEec-ceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 379 LEGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 379 V~G~V~~I~~-~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
+.|+|+.... .|. |+.-.+.+-+-|+|++.+.... ...+++||.|...+..
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 4799998865 443 6666553679999999997432 1358899999998764
No 229
>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=55.08 E-value=43 Score=27.84 Aligned_cols=58 Identities=26% Similarity=0.214 Sum_probs=41.7
Q ss_pred EEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 379 V~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
+.|+|++..+.+.| |.+.+ |..-++|++-=... .-.++.||.|.|.....+ .+++|.-
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-GKKRLCRIRGKMRK-----RVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-CCEEEEEEchhhcc-----cEEEcCCCEEEEEeccccCCEEEEEE
Confidence 57899999998887 67777 78888887663322 345889999999876554 3445543
No 230
>PRK15463 cold shock-like protein CspF; Provisional
Probab=54.38 E-value=42 Score=27.29 Aligned_cols=48 Identities=17% Similarity=0.162 Sum_probs=34.7
Q ss_pred EEEEEEEEEC---CeEEEEEC-CEEEEEeccccccc-cCChhhHhhhcCCEEEEEEEE
Q 010232 300 IEVKFTEWNT---GGLLTRIE-GLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 300 V~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~~~-i~~~~el~~~VGq~V~vkVl~ 352 (514)
..|+|+..+. +|.+-.-+ +-+.|+|++.+... ... + ..|++|.+.+..
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 35554444 47999999999432 333 2 489999998764
No 231
>PRK15464 cold shock-like protein CspH; Provisional
Probab=53.49 E-value=44 Score=27.29 Aligned_cols=48 Identities=8% Similarity=0.079 Sum_probs=34.0
Q ss_pred EEEEEEEEEC-C--eEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 300 IEVKFTEWNT-G--GLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 300 V~GkV~~v~~-~--G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
+.|+|+.++. . |.+..-+ |-+.|+|++.+. ...+. + ..|++|.+.|..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~---l--~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEV---L--IPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCC---C--CCCCEEEEEEEE
Confidence 4799999986 3 4443333 479999999993 32222 2 489999999875
No 232
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=52.78 E-value=88 Score=28.87 Aligned_cols=55 Identities=22% Similarity=0.216 Sum_probs=33.6
Q ss_pred CCceEEEEEEEEecce---------EEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCC
Q 010232 375 EGTLLEGTVKKIYPYG---------AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFP 437 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~G---------aFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~ 437 (514)
.|.+.+-+|..+.+.| +.|++++ +-..+.|+.. .+| +.+++|++|++.+....++
T Consensus 63 ~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~-~~~i~~~i~~------~~p-~~v~iGm~V~~v~~~~~~~ 126 (140)
T COG1545 63 EGKVETYTVVYVKPPGFSLEEPYVIAIVELEE-GGRILGQLVD------VDP-DDVEIGMKVEAVFRKREED 126 (140)
T ss_pred CeEEEEEEEEeeCCCCcccCCCEEEEEEEeCC-CCceEEEEEe------cCc-ccccCCCEEEEEEEEcccc
Confidence 4445555555555543 4666765 3456666655 123 3489999999999876533
No 233
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=52.21 E-value=59 Score=26.29 Aligned_cols=49 Identities=20% Similarity=0.282 Sum_probs=35.3
Q ss_pred EEEEEEEEEEC---CeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 299 PIEVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 299 iV~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
.++|+|+..+. +|.+..-+ |-+.|+|++.+. ..... + ..|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~---l--~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKT---L--AEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCC---C--CCCCEEEEEEEE
Confidence 46799999986 46655544 479999999994 22222 2 489999998875
No 234
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=49.67 E-value=55 Score=27.00 Aligned_cols=47 Identities=15% Similarity=0.216 Sum_probs=34.0
Q ss_pred EEEEEEEEC---CeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 301 ~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
+|+|+..+. +|.+..-+ |-+.|+|++.+. ...+. + ..|+.|.+.+..
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 589999986 35554444 589999999994 22232 2 489999999875
No 235
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=49.54 E-value=41 Score=31.38 Aligned_cols=56 Identities=16% Similarity=0.252 Sum_probs=46.8
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd 435 (514)
.--.|..|.|+|-.|...-+|+++++ ...+.+....+. .+.|+.|-+|..+++...
T Consensus 79 g~a~gklV~GkIfhiV~~DlYIDFG~-KFhcVC~rP~~n-------~e~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 79 GDAKGKLVIGKIFHIVEEDLYIDFGG-KFHCVCKRPALN-------GEAYQKGARVRLRLIDLE 134 (173)
T ss_pred cCcCCcEEEeeeeeeeccceEEecCC-eEEEEEcCcCcC-------HHHhhcCceEEEEEcChh
Confidence 34578899999999999999999998 788998877765 356889999999988543
No 236
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.20 E-value=53 Score=32.06 Aligned_cols=52 Identities=12% Similarity=-0.013 Sum_probs=40.5
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE-eCC
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-MFP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v-de~ 437 (514)
.+.|+|..+.+..+.+++++.|+.-+++.+.+. +..++|+.+++++..+ +++
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~--------~l~~~g~~v~l~t~~~vrEd 56 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLA--------AIGAIGDEVFLYTHLIVRED 56 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHH--------HhccCCCeEEEEEEEEEecC
Confidence 478999999999999999987777777766653 3336799999998866 344
No 237
>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=47.66 E-value=1.1e+02 Score=23.81 Aligned_cols=46 Identities=20% Similarity=0.242 Sum_probs=33.2
Q ss_pred EEEEEEEEEECCeEEEEECC--EEEEEeccccccccCChhhHhhhcCCEEEEEEEEE
Q 010232 299 PIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRI 353 (514)
Q Consensus 299 iV~GkV~~v~~~G~fVdi~G--i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~v 353 (514)
.+.|+|..+.+.-++++.+| .+.++|.+.+..- ..++++++.+.-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~~l---------~~~~~v~l~t~~~ 51 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLSEL---------PEGGEVKLYTYLI 51 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHHTS----------TTSEEEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHHhC---------CCCCEEEEEEEEE
Confidence 57999999999999999987 5899997766311 2455666666544
No 238
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.38 E-value=63 Score=31.46 Aligned_cols=52 Identities=15% Similarity=0.080 Sum_probs=40.2
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~ 437 (514)
.+.|+|..+.+..+.+++++.|+.-+++.+.+. ...+.|+.+++.+..+- ++
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~--------~l~~~g~~~~l~t~~~vrEd 56 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPA--------LIGGLGQRVRVFTHLHVRED 56 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHH--------hcccCCCeEEEEEEEEEecC
Confidence 478999999999999999877777777766653 22357999999988663 44
No 239
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.85 E-value=64 Score=31.30 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=37.7
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
.+.|+|..+.+..+.+++++.|++-.++.+.+. . ++.|+.+++.+..
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 478999999999999999877777777765553 2 5789999998764
No 240
>PRK09890 cold shock protein CspG; Provisional
Probab=45.62 E-value=90 Score=25.28 Aligned_cols=48 Identities=15% Similarity=0.227 Sum_probs=34.6
Q ss_pred EEEEEEEEEC---CeEEEEECC-EEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 300 IEVKFTEWNT---GGLLTRIEG-LRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 300 V~GkV~~v~~---~G~fVdi~G-i~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
..|+|+..+. +|.+..-+| -+.|+|++.+. ..... + ..|+.|.+.+..
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 466655544 79999999994 22232 2 489999998764
No 241
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=45.32 E-value=81 Score=25.48 Aligned_cols=48 Identities=17% Similarity=0.249 Sum_probs=34.5
Q ss_pred EEEEEEEEEC---CeEEEEECC-EEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 300 IEVKFTEWNT---GGLLTRIEG-LRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 300 V~GkV~~v~~---~G~fVdi~G-i~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
..|+|+..+. +|.+-.-+| -+.|+|++.+. ..... + .+|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~---l--~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKS---L--DEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCC---C--CCCCEEEEEEEE
Confidence 3799999975 466555444 79999999994 22222 2 489999998764
No 242
>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=44.84 E-value=66 Score=31.26 Aligned_cols=51 Identities=14% Similarity=0.066 Sum_probs=40.4
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~ 437 (514)
.+.|+|..+.+..+.|+.++.|+.-+++.+.++ .++.|+.|++.+..+- ++
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~---------~l~~g~~v~l~t~~~vred 55 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAY---------ELNLEQKAQVFTHLVVRED 55 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHH---------hcCCCCeEEEEEEEEEecC
Confidence 478999999999999999987788777776664 2455999999988663 44
No 243
>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=44.62 E-value=1e+02 Score=30.83 Aligned_cols=82 Identities=12% Similarity=0.250 Sum_probs=55.6
Q ss_pred HhhhhHHHhhhcC--CCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhh----cCCEEEEEEEEEeCC
Q 010232 284 KMAWHRVRQIKQL--NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEK----VGRRMYVQITRINED 356 (514)
Q Consensus 284 ~~~w~~l~~~~k~--GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~----VGq~V~vkVl~vD~e 356 (514)
...|-.+...++. |+++.|++.++.+-|+.++++|+..-+|..+| .-...+++.+... ..-.|.++|+.++..
T Consensus 60 ~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 60 REEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVDGIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDG 139 (225)
T ss_pred HHHhCCCCchhcccCCceEEEEEEeecccceEEEeecccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccC
Confidence 3456666555566 99999999999999999999888888898888 3222344333211 233455788877553
Q ss_pred CCceEeehhh
Q 010232 357 TNDLILSERE 366 (514)
Q Consensus 357 ~~rIiLS~K~ 366 (514)
....+|-++
T Consensus 140 -~~~rltd~q 148 (225)
T PF09883_consen 140 -IEARLTDEQ 148 (225)
T ss_pred -cccccCHHH
Confidence 556666653
No 244
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.94 E-value=67 Score=31.41 Aligned_cols=51 Identities=16% Similarity=0.078 Sum_probs=39.4
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~ 437 (514)
.+.|+|..+.+..+.++.++.|+.-+++.+.+. .++.|+.|++.+..+- ++
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~---------~l~~g~~v~l~t~~~vrEd 55 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLA---------RLVEGQEAELHTRLVVRED 55 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHHHH---------HcCCCCeEEEEEEEEEccC
Confidence 478999999999999999876777777655543 2467999999988663 54
No 245
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.74 E-value=1.1e+02 Score=29.79 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=22.5
Q ss_pred CEEEEEEEEEeCCeEEEEeCC-ceeEEeec
Q 010232 174 DFVIGVVVSGNENKLDVNVGA-DLLGTMLT 202 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp~ 202 (514)
.++.|+|+.+.++.+.+++|+ +.+.++|.
T Consensus 3 ~~i~G~i~~~~~~~viie~~GvGY~v~vs~ 32 (195)
T PRK14604 3 ASIRGIIQSIGNDHLIVETGGVGLLIYAPR 32 (195)
T ss_pred ceEEEEEEEEcCCEEEEEECCEEEEEEeCH
Confidence 368999999999999999854 45565553
No 246
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=40.91 E-value=1.3e+02 Score=25.05 Aligned_cols=47 Identities=32% Similarity=0.572 Sum_probs=33.8
Q ss_pred cCCCEEEEEEEEEECCe-EEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeC
Q 010232 295 QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINE 355 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G-~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~ 355 (514)
++|++.+.+|..+.+.| =+.+++|+-.|+|-. .+|++++++|.++-.
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 57888888888887654 233344888888833 379999999998744
No 247
>PRK14998 cold shock-like protein CspD; Provisional
Probab=39.57 E-value=1.1e+02 Score=25.03 Aligned_cols=47 Identities=15% Similarity=0.206 Sum_probs=33.8
Q ss_pred EEEEEEEEC---CeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 301 ~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
.|+|+..+. +|.+..-+ |-+.|+|++.+. ...+. + ..|++|.+.+..
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~---l--~~G~~V~f~~~~ 54 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT---L--KAGQSVRFDVHQ 54 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCC---C--CCCCEEEEEEEE
Confidence 589999886 35554444 479999999994 22232 2 489999999875
No 248
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.52 E-value=90 Score=30.64 Aligned_cols=51 Identities=14% Similarity=-0.053 Sum_probs=38.9
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE-eCC
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-MFP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v-de~ 437 (514)
.+.|+|..+.+-.+.|+.++.|+.-.++.+.+. .++.|+.+++.+.-+ +++
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~~---------~l~~g~~v~l~t~~~vrED 55 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCLA---------ELRLLEDVEILTYLHTRED 55 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHHH---------hcCCCCcEEEEEEEEEecC
Confidence 478999999999999999877777777765543 245799999988654 444
No 249
>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=39.35 E-value=79 Score=25.38 Aligned_cols=47 Identities=13% Similarity=0.144 Sum_probs=33.6
Q ss_pred EEEEEEEEC---CeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEE
Q 010232 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 301 ~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
+|+|+..+. +|.+..-+ |-+.|+|++.+. ..... + ..|++|.+.+..
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 589999885 45555544 589999999994 22222 2 489999998764
No 250
>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=38.61 E-value=1.5e+02 Score=25.52 Aligned_cols=67 Identities=12% Similarity=0.160 Sum_probs=37.9
Q ss_pred eEEEEEEEEecce--EEEEECCC--ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 378 LLEGTVKKIYPYG--AQIRIGDS--NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 378 iV~G~V~~I~~~G--aFV~I~~~--gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
.+.|.|.++...| +|++|.+. .+..++...+.......+....++.|+.|.|.=.=.. ..+.+.|..
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~ 74 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFV 74 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEe
Confidence 4789999998766 79999652 3444554443322222222333889999876532112 334444433
No 251
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.88 E-value=88 Score=30.31 Aligned_cols=51 Identities=12% Similarity=0.185 Sum_probs=38.7
Q ss_pred eEEEEEEEEecceEEEE-ECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE-eCC
Q 010232 378 LLEGTVKKIYPYGAQIR-IGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-MFP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~-I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v-de~ 437 (514)
.+.|+|..+.+..+.|+ .++.|+.-+++.+.+. .++.|+.|+..+..+ +++
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~~~~~~---------~l~~g~~v~l~t~~~vrEd 56 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFISLFCSA---------KIQKGEKHELFITQIIKED 56 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEecHHHHH---------HcCCCCeEEEEEEEEEecC
Confidence 47899999999999998 5876777777665543 246899999988765 344
No 252
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.21 E-value=1.6e+02 Score=28.62 Aligned_cols=29 Identities=14% Similarity=0.156 Sum_probs=22.5
Q ss_pred CEEEEEEEEEeCCeEEEEeC-CceeEEeec
Q 010232 174 DFVIGVVVSGNENKLDVNVG-ADLLGTMLT 202 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv~VdIG-~k~~G~Lp~ 202 (514)
.++.|+|+.+.++.+.++++ -+.+.++|.
T Consensus 3 ~~l~G~v~~~~~~~vvi~~~GvGY~v~~s~ 32 (194)
T PRK14605 3 SSLNGILEASGKDWAVINVSGVGFRCYMPA 32 (194)
T ss_pred ceEEEEEEEecCCEEEEEECCEEEEEEeCH
Confidence 36899999999999999984 345665553
No 253
>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=36.04 E-value=1.4e+02 Score=23.20 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=34.7
Q ss_pred EEEEEEEEC---CeEEEEEC-CEEEEEeccccccc-cCChhhHhhhcCCEEEEEEEE
Q 010232 301 EVKFTEWNT---GGLLTRIE-GLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 301 ~GkV~~v~~---~G~fVdi~-Gi~gFVP~sel~~~-i~~~~el~~~VGq~V~vkVl~ 352 (514)
.|+|+.++. +|.+..-+ |-+.|+|.+.+... ... + .+|+.|.+.+..
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~---~--~~G~~V~f~~~~ 53 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRS---L--EEGDRVEFELEE 53 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCc---C--CCCCEEEEEEEE
Confidence 588888876 47666665 68999999999432 222 2 489999998875
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=35.56 E-value=99 Score=23.93 Aligned_cols=42 Identities=21% Similarity=0.230 Sum_probs=25.8
Q ss_pred EEEEEEECCeEEEEEC--CEEEEEeccccccccCChhhHhhhcCCEEEEEEEE
Q 010232 302 VKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 302 GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
|++....++=.||... +-+.|||..+|..- .-|++|.|+++.
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 3444444444566564 57999999988432 369999999997
No 255
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=34.74 E-value=61 Score=31.57 Aligned_cols=33 Identities=30% Similarity=0.405 Sum_probs=29.0
Q ss_pred CCCEEEEEEEEEECCeEEEEECCE-EEEEecccc
Q 010232 296 LNEPIEVKFTEWNTGGLLTRIEGL-RAFLPKAEL 328 (514)
Q Consensus 296 ~GeiV~GkV~~v~~~G~fVdi~Gi-~gFVP~sel 328 (514)
.|+++.|+|.+....|+-|-++-. +.|||.+-|
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L 114 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEML 114 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhC
Confidence 899999999999999999999533 789998777
No 256
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=34.74 E-value=74 Score=31.01 Aligned_cols=84 Identities=13% Similarity=0.069 Sum_probs=54.3
Q ss_pred hccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccccc
Q 010232 164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA 243 (514)
Q Consensus 164 ~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~ 243 (514)
......+-.|+++.|+|......|+-|.+|.=-+.++|..-+.+-. .|--.+.+=|+.-+.+-
T Consensus 73 R~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~----------------~f~~~e~vWVWey~~Ed- 135 (202)
T KOG3297|consen 73 RVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPC----------------VFEPDEQVWVWEYEQED- 135 (202)
T ss_pred EEEEEecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCc----------------ccccccEEEEEEecccC-
Confidence 3344677789999999999999999999997778888877665321 11111223333222100
Q ss_pred ccCCCCCCCCcccCCCEEEEEEEEE
Q 010232 244 MSGGSGPGRPVVETGTVLFAEVLGR 268 (514)
Q Consensus 244 l~~~~~~~~~~~~vGd~V~v~Vl~~ 268 (514)
-+ .....+.+|..|+++|.+.
T Consensus 136 g~----~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 136 GP----GTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred CC----CceeEecCCCeEEEEEeee
Confidence 00 1134578999999999874
No 257
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=34.46 E-value=1.8e+02 Score=24.52 Aligned_cols=60 Identities=18% Similarity=0.118 Sum_probs=42.1
Q ss_pred ceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 377 TLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 377 ~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
..+.|+|+.....+.| |.+.+ |..-++|++-=... .-.++.||.|.|.....+ .+++|..
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK~Rk-----~iwI~~GD~VlVe~~~~~~~kg~Iv~ 66 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-GKERLARIPGKMRK-----KVWIRRGDIVLVDPWDFQDVKADIIY 66 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEchhhcc-----cEEEcCCCEEEEEecCCCCCEEEEEE
Confidence 3477999999998887 67777 78888887664322 345889999998776443 3344443
No 258
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=34.22 E-value=3.4e+02 Score=27.54 Aligned_cols=112 Identities=14% Similarity=0.110 Sum_probs=64.0
Q ss_pred EEEEEEEEEECC--eEEEE--E--CC--EEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhh
Q 010232 299 PIEVKFTEWNTG--GLLTR--I--EG--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWAT 370 (514)
Q Consensus 299 iV~GkV~~v~~~--G~fVd--i--~G--i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~ 370 (514)
.+.|+|+++... +..|+ + ++ +.+.|...-+ +++...+|+.+.+.|-. ..|.++.-.+
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~-------~~L~l~~G~~v~~~Ika-----~~V~l~~~~~--- 193 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSA-------ERLGLDEGKEVLVLIKA-----PWVGITQDPA--- 193 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHH-------hhcCCCCCCeEEEEEEC-----CEEEEEcCCC---
Confidence 789999999866 44444 3 22 4555543332 11222589998888764 2355553211
Q ss_pred ccCCCCceEEEEEEEEecceEEEE----ECCCc--eEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 371 LNLREGTLLEGTVKKIYPYGAQIR----IGDSN--RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 371 ~~l~~G~iV~G~V~~I~~~GaFV~----I~~~g--i~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
.....-..+.|+|.++...|..++ +++ | +...|+...+. .-.+++|+.|.+.+..
T Consensus 194 ~~~SarN~l~g~V~~i~~~~~~~~V~l~l~~-g~~l~A~IT~~s~~-------~L~L~~G~~V~a~iKa 254 (263)
T PRK10676 194 VAQAADNQLPGTISHIERGAEQSEVLMALPD-GQTLCATVPNNEAA-------RLSLQQGDAVTAYFNA 254 (263)
T ss_pred CCCChhheEEEEEEEEEeCCCcEEEEEEeCC-CCEEEEEecHHHHH-------hcCCCCCCEEEEEEEc
Confidence 123344679999999987665443 323 2 22223222111 1238899999998863
No 259
>COG1278 CspC Cold shock proteins [Transcription]
Probab=34.13 E-value=76 Score=25.92 Aligned_cols=47 Identities=15% Similarity=0.298 Sum_probs=33.3
Q ss_pred EEEEEEEEC---CeEEEEECC-EEEEEecccc-ccccCChhhHhhhcCCEEEEEEEE
Q 010232 301 EVKFTEWNT---GGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITR 352 (514)
Q Consensus 301 ~GkV~~v~~---~G~fVdi~G-i~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~ 352 (514)
.|+|+..+. +|.+--=+| -+.|+|+|.+ ...++. + ..||+|.+.+..
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 578888875 355444344 7999999999 444443 3 489999998874
No 260
>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=33.81 E-value=2e+02 Score=27.91 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=22.2
Q ss_pred EEEEEEEEEeCCeEEEEeCC-ceeEEeec
Q 010232 175 FVIGVVVSGNENKLDVNVGA-DLLGTMLT 202 (514)
Q Consensus 175 iV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp~ 202 (514)
++.|+|+.+.++.+.|++++ +.+.++|.
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~ 32 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPM 32 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecH
Confidence 68999999999999999853 45665553
No 261
>COG1278 CspC Cold shock proteins [Transcription]
Probab=33.70 E-value=1.6e+02 Score=24.12 Aligned_cols=59 Identities=27% Similarity=0.375 Sum_probs=37.2
Q ss_pred EEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232 380 EGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444 (514)
Q Consensus 380 ~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl 444 (514)
.|+|+-..+ || |+.=.+.+-+-|+|+|.+..... ..|..||+|...+.. +.++.....+
T Consensus 3 ~GtVKwfn~~KGfG-FI~p~~G~~DvFVH~Sai~~~g~----~~L~eGQ~V~f~~~~-g~kgp~A~nv 64 (67)
T COG1278 3 TGTVKWFNATKGFG-FITPEDGGKDVFVHISAIQRAGF----RTLREGQKVEFEVEQ-GRKGPSAANV 64 (67)
T ss_pred cceEEEeeCCCcce-EcCCCCCCcCEEEEeeeeccCCC----cccCCCCEEEEEEec-CCCCCceeEE
Confidence 466766543 44 54444424799999999964332 347889999998864 3444444433
No 262
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.46 E-value=2e+02 Score=28.08 Aligned_cols=27 Identities=22% Similarity=0.255 Sum_probs=21.4
Q ss_pred EEEEEEEEEeCCeEEEEeCC-ceeEEee
Q 010232 175 FVIGVVVSGNENKLDVNVGA-DLLGTML 201 (514)
Q Consensus 175 iV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp 201 (514)
++.|+|+.+.++.+.|++++ +.+.++|
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs 31 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCP 31 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcC
Confidence 68999999999999999843 4555554
No 263
>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=33.29 E-value=67 Score=26.12 Aligned_cols=56 Identities=13% Similarity=0.081 Sum_probs=37.2
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEee-ccccccccCcccccCCCCEEEEEEEEE
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S-els~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
...++|..+..-=+.|.+.+++.-..+|.+ .+.+. ...-++.+++||.+.|.++..
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdt-frf~seklkvG~~l~v~lk~~ 59 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDT-FRFDSEKLSVGQCLDVTLKDP 59 (69)
T ss_pred ccchhhhhhhhceEEEEeeccccEEEEEchhhcccc-ccccceeeeccceEEEEEecC
Confidence 356677777776678888776666666654 33332 222346699999999988753
No 264
>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=32.95 E-value=1.9e+02 Score=22.18 Aligned_cols=53 Identities=13% Similarity=0.005 Sum_probs=32.1
Q ss_pred hcCCEEEEEEEEEeCCCCceEeehhhh----hhhccCCCCceEEEEEEEEecceEEEE
Q 010232 341 KVGRRMYVQITRINEDTNDLILSEREA----WATLNLREGTLLEGTVKKIYPYGAQIR 394 (514)
Q Consensus 341 ~VGq~V~vkVl~vD~e~~rIiLS~K~~----~~~~~l~~G~iV~G~V~~I~~~GaFV~ 394 (514)
++|+++.+.|.+.. ..+..+.-...- +.......|+.+..+|++..++-++=+
T Consensus 3 ~~G~~~~VlVe~~~-~~g~~~gr~~~~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 3 YVGKTLEVLVEELG-DEGQGIGRTDNGKVVFVPGGLPLIGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -TTEEEEEEEEEE--TTSEEEEEET-TEEEEETT--T--TEEEEEEEEEE-SSEEEEE
T ss_pred cCCcEEEEEEEEec-CCCEEEEEeCCCeEEEECCCCCCCCCEEEEEEEEeeCCcEEEE
Confidence 58999999999887 445554444321 111111269999999999998776643
No 265
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=32.90 E-value=3e+02 Score=23.62 Aligned_cols=70 Identities=19% Similarity=0.250 Sum_probs=46.1
Q ss_pred CCceEEEEEEEEec--ce-EEEEECCC--ceEEEEEeeccccccccCcc-cccCCCCEEEEEEE-EEe-CCCeEEEEEec
Q 010232 375 EGTLLEGTVKKIYP--YG-AQIRIGDS--NRSGLLHISNMSRTRVTSVS-DLLNEGERVKVLVV-KSM-FPDKISLSIAD 446 (514)
Q Consensus 375 ~G~iV~G~V~~I~~--~G-aFV~I~~~--gi~GLvh~Sels~~~v~~~~-~~~kvGd~VkvkVi-~vd-e~~rI~LSlK~ 446 (514)
..--|+|.|.+++. .| +|..|-+. .+.+.+..+... .+. ..++.|++|.|+.- .+- ..++++|...+
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~-----~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~ 96 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRAR-----RIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVED 96 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHh-----hCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEE
Confidence 55668999998876 33 46777542 355555544432 333 56899999998874 222 67889999887
Q ss_pred CcC
Q 010232 447 LES 449 (514)
Q Consensus 447 l~~ 449 (514)
+.|
T Consensus 97 i~P 99 (99)
T PF13742_consen 97 IDP 99 (99)
T ss_pred eEC
Confidence 654
No 266
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=32.46 E-value=4.7e+02 Score=27.68 Aligned_cols=203 Identities=18% Similarity=0.207 Sum_probs=103.7
Q ss_pred ccccccccccchhhHhHHhhhhhceeeecCCcccccccc--------CCCCcccccCCccccce------eecccCCccc
Q 010232 34 KYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSS--------AQFPENVENEGLEGNEE------LELLNKPNLV 99 (514)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 99 (514)
-|-||.-|-|.-+..-+. ++||..+. ..+-||.+-. ...|.+ ..|+|- -.||-+|-..
T Consensus 79 GYVFQDARLFpH~tVrgN--L~YG~~~~-~~~~fd~iv~lLGI~hLL~R~P~~-----LSGGEkQRVAIGRALLt~P~LL 150 (352)
T COG4148 79 GYVFQDARLFPHYTVRGN--LRYGMWKS-MRAQFDQLVALLGIEHLLDRYPGT-----LSGGEKQRVAIGRALLTAPELL 150 (352)
T ss_pred eeEeeccccccceEEecc--hhhhhccc-chHhHHHHHHHhCcHHHHhhCCCc-----cCcchhhHHHHHHHHhcCCCee
Confidence 477888888877766554 34666665 3444555431 223432 222221 1356666655
Q ss_pred cCCCCCccccccCCCCCChhhhhhhhhccccCCC---------ChHHHhhhccccccccccccccc-hhhhhchhcccc-
Q 010232 100 PISNGVASEVDKKSEKPDEEEALAPFLKFFKPRD---------SAEEVEEEGSEVGVSRESIDVDD-KVGEDKVSVEYY- 168 (514)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~- 168 (514)
-..+.++|=++ +-+.|.| |||.=-.-+- |-+++.--. +.=|+-+++..-+ +..++-|+....
T Consensus 151 LmDEPLaSLD~-----~RK~Eil-pylERL~~e~~IPIlYVSHS~~Ev~RLA-d~vV~le~GkV~A~g~~e~v~~~~~~~ 223 (352)
T COG4148 151 LMDEPLASLDL-----PRKREIL-PYLERLRDEINIPILYVSHSLDEVLRLA-DRVVVLENGKVKASGPLEEVWGSPDFP 223 (352)
T ss_pred eecCchhhccc-----chhhHHH-HHHHHHHHhcCCCEEEEecCHHHHHhhh-heEEEecCCeEEecCcHHHHhcCcccC
Confidence 43333333332 4455544 8886432221 223232110 1112222222233 455555555421
Q ss_pred ----CCCCCCEEEEEEEEEeCCeEE--EEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccc
Q 010232 169 ----EPKPGDFVIGVVVSGNENKLD--VNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI 242 (514)
Q Consensus 169 ----~ik~GdiV~G~Vv~v~~~Gv~--VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~ 242 (514)
.=+.|.++.|+|.+-++..-. |.+|+ ..+-..
T Consensus 224 p~~~~~e~~~vl~~~V~~hd~~y~lt~l~l~~---~~l~v~--------------------------------------- 261 (352)
T COG4148 224 PWLPREEQSSVLEGTVLEHDPRYGLTALALGD---QHLWVP--------------------------------------- 261 (352)
T ss_pred cccCccccceEEEEEehhcCCCcceEEEecCc---eEEEee---------------------------------------
Confidence 224588899999998775433 33442 111000
Q ss_pred cccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE
Q 010232 243 AMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI 316 (514)
Q Consensus 243 ~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi 316 (514)
.....+|..++++|...| +.++++++..... --++.|+|+.+.+.+--|++
T Consensus 262 ---------~~~a~~g~~~R~~I~a~D----Vslal~~P~~~Si----------rNiLp~~v~~i~~~~~~V~v 312 (352)
T COG4148 262 ---------KLDAPVGARLRIRIQARD----VSLALQKPEQTSI----------RNILPGKVVGIEDDDGQVDV 312 (352)
T ss_pred ---------ccCCCCCCcEEEEEEccc----eEEEecCccccch----------hhccceeEEEEEcCCCcEEE
Confidence 122468999998887533 6677777654422 23678899998876544433
No 267
>PRK14646 hypothetical protein; Provisional
Probab=31.80 E-value=2.2e+02 Score=26.81 Aligned_cols=66 Identities=11% Similarity=0.122 Sum_probs=46.9
Q ss_pred ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeec
Q 010232 329 LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISN 408 (514)
Q Consensus 329 ~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Se 408 (514)
.+++.+++++..++|+.++++...- .++ -..+.|++.++.+-++.+.+.+ -.--+|.++
T Consensus 86 dRpL~~~~df~r~~G~~v~V~l~~~--~~~-----------------~~~~~G~L~~~~~~~v~l~~~g--~~~~i~~~~ 144 (155)
T PRK14646 86 SDELTSERDFKTFKGFPVNVELNQK--NSK-----------------IKFLNGLLYEKSKDYLAINIKG--KIKKIPFNE 144 (155)
T ss_pred CCcCCCHHHHHHhCCCEEEEEEecC--cCC-----------------eEEEEEEEEEEeCCEEEEEECC--EEEEEEHHH
Confidence 3556778888788999999887642 111 2457899999999999988864 455577777
Q ss_pred ccccccc
Q 010232 409 MSRTRVT 415 (514)
Q Consensus 409 ls~~~v~ 415 (514)
+...++.
T Consensus 145 I~ka~L~ 151 (155)
T PRK14646 145 VLKISLC 151 (155)
T ss_pred eeeEEeC
Confidence 7654443
No 268
>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=31.65 E-value=2.3e+02 Score=23.57 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=42.0
Q ss_pred EEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE-e-CCCeEEEEE
Q 010232 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-M-FPDKISLSI 444 (514)
Q Consensus 379 V~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v-d-e~~rI~LSl 444 (514)
+-|+|......+.| |.+.+ |..-|+|++-=...+ -.++.||.|.|..... + .+++|..-+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~Rk~-----iwI~~GD~VlV~~~~~~~~~kg~Iv~r~ 64 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD-GQRRLVSIPGKLRKN-----IWIKRGDFLIVDPIEEGEDVKADIIFVY 64 (78)
T ss_pred eEEEEEEECCCCEEEEEECC-CCEEEEEEchhhccC-----EEEcCCCEEEEEecccCCCceEEEEEEe
Confidence 45889999998887 67777 788888887643322 4488999999987765 3 334444333
No 269
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.50 E-value=2.3e+02 Score=27.52 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=21.5
Q ss_pred EEEEEEEEEeCCeEEEEeCC-ceeEEee
Q 010232 175 FVIGVVVSGNENKLDVNVGA-DLLGTML 201 (514)
Q Consensus 175 iV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp 201 (514)
++.|+|+.++++.+.|++++ +.+.++|
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~ 31 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLS 31 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEec
Confidence 68999999999999999843 4555554
No 270
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.10 E-value=58 Score=32.36 Aligned_cols=48 Identities=19% Similarity=0.303 Sum_probs=31.5
Q ss_pred hhhhhchhccccCCCCCCEEEEEEEEEeCCe--EEEEeCCceeEEeeccccccc
Q 010232 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENK--LDVNVGADLLGTMLTKEVLPL 208 (514)
Q Consensus 157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~G--v~VdIG~k~~G~Lp~sEl~p~ 208 (514)
++|...- ++.+++.|++..|+.+...+.| +||||| ..|-=|...+.|+
T Consensus 62 eefgei~--sl~~~~~Gdv~vGrl~~l~~vgyg~yvdig--V~~p~~~dalvpl 111 (247)
T COG4044 62 EEFGEIP--SLSKVEEGDVYVGRLIDLGKVGYGAYVDIG--VLGPRPKDALVPL 111 (247)
T ss_pred HHhCCCC--ccccCCCCcEEEEEEeeeccceeEEEcccc--ccCCCcccccccH
Confidence 4555444 6789999999999999998765 556654 3333333344443
No 271
>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=31.02 E-value=1.8e+02 Score=22.23 Aligned_cols=45 Identities=22% Similarity=0.264 Sum_probs=29.6
Q ss_pred EEEEEEEEEECCe----EEEEECC---EEEEEeccccccccCChhhHhhhcCCEEEEEE
Q 010232 299 PIEVKFTEWNTGG----LLTRIEG---LRAFLPKAELLSRVNNFTELKEKVGRRMYVQI 350 (514)
Q Consensus 299 iV~GkV~~v~~~G----~fVdi~G---i~gFVP~sel~~~i~~~~el~~~VGq~V~vkV 350 (514)
.+.|+|..+...| +.+++++ +.+.++..... ++...+|+++.+.|
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 5555554 56777755441 11124899998865
No 272
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.78 E-value=3.1e+02 Score=23.96 Aligned_cols=52 Identities=19% Similarity=0.223 Sum_probs=38.5
Q ss_pred CceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 376 GTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 376 G~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
-..+.|+|+.....+.| |.+.+ |..-++|++-=... .-.++.||.|.|....
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~Rk-----~iwI~~GD~VlVsp~d 70 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLD-GKTRLGRIPGKLKK-----RIWIREGDVVIVKPWE 70 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhhcc-----cEEecCCCEEEEEEcc
Confidence 45588999999998887 67777 78888887763322 3458899999985443
No 273
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=30.52 E-value=96 Score=24.67 Aligned_cols=49 Identities=20% Similarity=0.192 Sum_probs=33.1
Q ss_pred eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEE
Q 010232 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (514)
Q Consensus 378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi 432 (514)
.+.|+|.+....+.| |.+.+ |..-+++++-=...+ -.++.||.|.|-+-
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~r~~-----iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGKFRKR-----IWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HHHHTC-----C---TTEEEEEEES
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceeee-----EecCCCCEEEEEec
Confidence 567999999988887 77777 788887776543222 24788999988663
No 274
>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=30.46 E-value=88 Score=23.54 Aligned_cols=35 Identities=17% Similarity=0.116 Sum_probs=23.6
Q ss_pred cCCCCCCEEEEEEE-EEeCCe-EEEEeCCceeEEeecccc
Q 010232 168 YEPKPGDFVIGVVV-SGNENK-LDVNVGADLLGTMLTKEV 205 (514)
Q Consensus 168 ~~ik~GdiV~G~Vv-~v~~~G-v~VdIG~k~~G~Lp~sEl 205 (514)
-.++.||+|. |+ ..++++ +++.. .+..|++|.+.+
T Consensus 16 Ls~~~Gd~i~--v~~~~~~~~ww~~~~-~g~~G~~P~~~v 52 (55)
T PF07653_consen 16 LSFKKGDVIE--VLGEKDDDGWWLGEN-NGRRGWFPSSYV 52 (55)
T ss_dssp -EB-TTEEEE--EEEEECSTSEEEEEE-TTEEEEEEGGGE
T ss_pred eEEecCCEEE--EEEeecCCCEEEEEE-CCcEEEEcHHHE
Confidence 4678999986 55 444444 55666 678899998876
No 275
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=30.06 E-value=1.9e+02 Score=27.42 Aligned_cols=64 Identities=20% Similarity=0.152 Sum_probs=43.8
Q ss_pred CCCceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232 374 REGTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI 444 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl 444 (514)
+.|+ +-|+|+...+.|.| |.+.+ |..-|+|++-=... .-.+++||.|.|.+-..+ .+++|..-+
T Consensus 30 eegq-~~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GKmRK-----~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 30 EEGQ-EYAQVLRMLGNGRLEAYCFD-GVKRLCHIRGKMRK-----RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred CCCc-EEEEEEEEcCCCEEEEEECC-CCEEEEEeecccee-----eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 3455 56899999999887 67777 88899988764332 245788999998764433 344554433
No 276
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.04 E-value=1.3e+02 Score=29.56 Aligned_cols=52 Identities=19% Similarity=0.223 Sum_probs=36.9
Q ss_pred eEEEEEEEEecce-EEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC
Q 010232 378 LLEGTVKKIYPYG-AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP 437 (514)
Q Consensus 378 iV~G~V~~I~~~G-aFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~ 437 (514)
.+.|+|..+.+-. +.+++++.|+.-.++.+.+. ...+.|+.++..+..+- ++
T Consensus 4 ~l~G~v~~~~~~~~vviev~GvGY~v~i~~~~~~--------~l~~~g~~v~l~t~~~vrEd 57 (203)
T PRK14602 4 YLEGRVAERRENSCVVLTPGGVGYEVFLPAHTLA--------RLPEKGGQVSFFVHTVVRED 57 (203)
T ss_pred eEEEEEEEEcCCcEEEEEeCCEEEEEEcCHHHHH--------HhccCCCeEEEEEEEEEecC
Confidence 4789999997764 46899876777666655442 22367999999988663 44
No 277
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=29.60 E-value=2.8e+02 Score=28.16 Aligned_cols=76 Identities=12% Similarity=0.201 Sum_probs=44.3
Q ss_pred ccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE----EE-CC--EEEEEeccc
Q 010232 255 VETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT----RI-EG--LRAFLPKAE 327 (514)
Q Consensus 255 ~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV----di-~G--i~gFVP~se 327 (514)
+.+|+.+.+.|-. ..+.++...+... ...-.+.|+|.++..+|..+ ++ +| +.+.|+...
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----PWVGITQDPAVAQ----------AADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNE 236 (263)
T ss_pred CCCCCeEEEEEEC----CEEEEEcCCCCCC----------ChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHH
Confidence 5789999888663 3455543221100 12237899999998776543 33 23 455555433
Q ss_pred cccccCChhhHhhhcCCEEEEEEE
Q 010232 328 LLSRVNNFTELKEKVGRRMYVQIT 351 (514)
Q Consensus 328 l~~~i~~~~el~~~VGq~V~vkVl 351 (514)
+ .++...+|+.|.+.|-
T Consensus 237 ~-------~~L~L~~G~~V~a~iK 253 (263)
T PRK10676 237 A-------ARLSLQQGDAVTAYFN 253 (263)
T ss_pred H-------HhcCCCCCCEEEEEEE
Confidence 2 2222358999998774
No 278
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.17 E-value=2.6e+02 Score=27.47 Aligned_cols=28 Identities=7% Similarity=0.122 Sum_probs=21.8
Q ss_pred CEEEEEEEEEeCCeEEEEeC-CceeEEee
Q 010232 174 DFVIGVVVSGNENKLDVNVG-ADLLGTML 201 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv~VdIG-~k~~G~Lp 201 (514)
.+++|+|+.+.++.+.|++| -+.+.++|
T Consensus 3 ~~l~G~v~~~~~~~vvidv~GVGY~v~vs 31 (196)
T PRK13901 3 NKIYGKIIEKKESSIVIMATPFEFELLVS 31 (196)
T ss_pred cEEEEEEEEEeCCEEEEEeCCEEEEEEec
Confidence 36899999999999999984 34555554
No 279
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.16 E-value=3.5e+02 Score=27.09 Aligned_cols=98 Identities=11% Similarity=0.085 Sum_probs=58.3
Q ss_pred EcCCCcEEEEehHHHH-------HhhhhHHH--hhhcCCCEEEEEEEEEECC--eEEEEEC--C---EEEEEecccccc-
Q 010232 268 RTLSGRPLLSTRRLFR-------KMAWHRVR--QIKQLNEPIEVKFTEWNTG--GLLTRIE--G---LRAFLPKAELLS- 330 (514)
Q Consensus 268 ~d~~grliLS~kk~~~-------~~~w~~l~--~~~k~GeiV~GkV~~v~~~--G~fVdi~--G---i~gFVP~sel~~- 330 (514)
++.+.-..++..-... ...|..+. ...+.|+++-|++.+..+- |++|+++ | .++++|.-+|..
T Consensus 38 vt~~~w~~itleGed~e~sanli~eefgei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~ 117 (247)
T COG4044 38 VTKKQWAKITLEGEDEEVSANLIVEEFGEIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRT 117 (247)
T ss_pred eecccceEEEEECccHHHHHHHHHHHhCCCCccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhc
Confidence 4445555666544432 34566666 4568999999999999875 5566662 1 478999888832
Q ss_pred ccCCh-hhHhh----hcCCEEEEEEEEEeCCCCce--Eeehh
Q 010232 331 RVNNF-TELKE----KVGRRMYVQITRINEDTNDL--ILSER 365 (514)
Q Consensus 331 ~i~~~-~el~~----~VGq~V~vkVl~vD~e~~rI--iLS~K 365 (514)
.-.+| +.+.. -..-.+.|.|.++|+..+.| .|+-+
T Consensus 118 ~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~EIea~ltd~ 159 (247)
T COG4044 118 FGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQEIEARLTDK 159 (247)
T ss_pred cCCCcHHHHHHHcCCcccCceEEEEEeccchhhhhhhhhhHH
Confidence 22233 32211 12345677777777655444 44443
No 280
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.63 E-value=2.4e+02 Score=27.41 Aligned_cols=28 Identities=21% Similarity=0.058 Sum_probs=22.0
Q ss_pred CEEEEEEEEEeCCeEEEEe--CCceeEEee
Q 010232 174 DFVIGVVVSGNENKLDVNV--GADLLGTML 201 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv~VdI--G~k~~G~Lp 201 (514)
.++.|+|+.++++.+.|+. |-+.+.++|
T Consensus 3 ~~l~G~v~~~~~~~vvie~~~GvGY~v~~~ 32 (188)
T PRK14606 3 AGISGRVLKKSGNVLLVETKSGVVFEIVCD 32 (188)
T ss_pred ceEEEEEEEecCCEEEEEeCCcEEEEEEeC
Confidence 3689999999999999994 555666655
No 281
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.49 E-value=2.6e+02 Score=27.13 Aligned_cols=27 Identities=4% Similarity=0.007 Sum_probs=21.0
Q ss_pred EEEEEEEEEeCCeEEEE-eC-CceeEEee
Q 010232 175 FVIGVVVSGNENKLDVN-VG-ADLLGTML 201 (514)
Q Consensus 175 iV~G~Vv~v~~~Gv~Vd-IG-~k~~G~Lp 201 (514)
++.|+|..+.++.+.|| ++ -+.+.++|
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~ 32 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFIS 32 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEec
Confidence 68999999999999999 44 34555554
No 282
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=27.85 E-value=1.1e+02 Score=22.79 Aligned_cols=34 Identities=15% Similarity=0.104 Sum_probs=23.1
Q ss_pred CCCCCCEEEEEEEEEeCCe-EEEEeCCceeEEeecccc
Q 010232 169 EPKPGDFVIGVVVSGNENK-LDVNVGADLLGTMLTKEV 205 (514)
Q Consensus 169 ~ik~GdiV~G~Vv~v~~~G-v~VdIG~k~~G~Lp~sEl 205 (514)
.++.|++|.. +.-.+.+ +++.. .+..|++|.+.+
T Consensus 14 s~~~Gd~i~v--~~~~~~~W~~g~~-~g~~G~~P~~yV 48 (49)
T PF14604_consen 14 SFKKGDVITV--LEKSDDGWWYGRN-TGRTGLFPANYV 48 (49)
T ss_dssp EB-TTEEEEE--EEESSTSEEEEEE-TTEEEEEEGGGE
T ss_pred eEcCCCEEEE--EEeCCCCEEEEEE-CCEEEEECHHhC
Confidence 5788999974 3444445 55665 568999998765
No 283
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=26.61 E-value=3.8e+02 Score=27.88 Aligned_cols=14 Identities=36% Similarity=0.377 Sum_probs=10.4
Q ss_pred CCceEEEEEEEEec
Q 010232 375 EGTLLEGTVKKIYP 388 (514)
Q Consensus 375 ~G~iV~G~V~~I~~ 388 (514)
+|..++|+|..|.+
T Consensus 273 ~~~~~~G~V~~Is~ 286 (346)
T PRK10476 273 RGRPFEGKVDSIGW 286 (346)
T ss_pred CCceEEEEEEEECC
Confidence 45668888888876
No 284
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=25.88 E-value=17 Score=39.93 Aligned_cols=67 Identities=25% Similarity=0.421 Sum_probs=45.7
Q ss_pred cCCCEEEEEEEEEECCeEEEEE--CCEEEEEecccc-ccc--cC-Ch--------hhHhhhcCCEEEEEEEEEeCCCCce
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAEL-LSR--VN-NF--------TELKEKVGRRMYVQITRINEDTNDL 360 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel-~~~--i~-~~--------~el~~~VGq~V~vkVl~vD~e~~rI 360 (514)
..+....+.|..+.++|+-|++ +|.-+|||..-+ ..+ +. +. .+...++|+.+.|++.+|..+++.|
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 4677889999999999999999 789999998877 222 10 00 0112256777777777666555554
Q ss_pred E
Q 010232 361 I 361 (514)
Q Consensus 361 i 361 (514)
+
T Consensus 640 i 640 (645)
T COG4776 640 I 640 (645)
T ss_pred h
Confidence 4
No 285
>CHL00010 infA translation initiation factor 1
Probab=25.77 E-value=3.8e+02 Score=22.13 Aligned_cols=65 Identities=26% Similarity=0.280 Sum_probs=38.6
Q ss_pred EEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232 379 LEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE 448 (514)
Q Consensus 379 V~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~ 448 (514)
+.|+|.++.+.|.| |.+.+ |..-.+++.--.. .-.-.+.+||.|.+.+...+ .+++|..-.+...
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGklr----~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~~ 75 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDN-GCQVLGYISGKIR----RNSIRILPGDRVKVELSPYDLTKGRIIYRLRNKD 75 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCC-CCEEEEEecccee----cCCcccCCCCEEEEEEcccCCCeEEEEEEecCCC
Confidence 67999998865554 45544 4444444333221 11233678999999875444 4567776665443
No 286
>PLN00208 translation initiation factor (eIF); Provisional
Probab=25.77 E-value=2.6e+02 Score=26.31 Aligned_cols=62 Identities=18% Similarity=0.140 Sum_probs=42.8
Q ss_pred CCCceEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 374 REGTLLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 374 ~~G~iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
..|+ +-|+|+.....|.| |.+.+ |..-|+|++-=... .-.+++||.|.|.+-..+ .+++|..
T Consensus 30 ~egq-~~g~V~~~lGn~~~~V~c~d-G~~rLa~IpGKmRK-----rIWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 30 EDGQ-EYAQVLRMLGNGRCEALCID-GTKRLCHIRGKMRK-----KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred CCCc-EEEEEEEEcCCCEEEEEECC-CCEEEEEEecccee-----eEEecCCCEEEEEccCCCCCEEEEEE
Confidence 3444 66899999998887 67777 88999988764332 245889999999865443 3334433
No 287
>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=25.59 E-value=1.2e+02 Score=23.35 Aligned_cols=49 Identities=16% Similarity=0.272 Sum_probs=30.4
Q ss_pred ceEEEEEEEEecceEEEEE----CCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEE
Q 010232 377 TLLEGTVKKIYPYGAQIRI----GDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432 (514)
Q Consensus 377 ~iV~G~V~~I~~~GaFV~I----~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi 432 (514)
..+.|+|.++.+.|.++++ ++. -+...++...+. .-.+++|+.|.+.+.
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 4688999999887776554 331 133333332221 134789999998875
No 288
>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=25.29 E-value=2.3e+02 Score=21.79 Aligned_cols=46 Identities=24% Similarity=0.386 Sum_probs=29.7
Q ss_pred EEEEEEEEEECCeEEEEE----C-C--EEEEEeccccccccCChhhHhhhcCCEEEEEEE
Q 010232 299 PIEVKFTEWNTGGLLTRI----E-G--LRAFLPKAELLSRVNNFTELKEKVGRRMYVQIT 351 (514)
Q Consensus 299 iV~GkV~~v~~~G~fVdi----~-G--i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl 351 (514)
.+.|+|.++...|..+++ + + +.+.+|...+. ++...+|+.+.+.+-
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~-------~l~l~~G~~v~~~ik 60 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA-------ELGLKPGKEVYAVIK 60 (69)
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh-------hCCCCCCCEEEEEEE
Confidence 578999999887755444 3 2 45566654441 122258999988764
No 289
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=25.15 E-value=2.1e+02 Score=28.59 Aligned_cols=58 Identities=19% Similarity=0.157 Sum_probs=43.4
Q ss_pred cCCCEEEEEEEEEECCeEEEEECC-EEEEEeccccc--cccCChhhHhhhcCCEEEEEEEEEeC
Q 010232 295 QLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELL--SRVNNFTELKEKVGRRMYVQITRINE 355 (514)
Q Consensus 295 k~GeiV~GkV~~v~~~G~fVdi~G-i~gFVP~sel~--~~i~~~~el~~~VGq~V~vkVl~vD~ 355 (514)
..|+.|-|.|+.....+.-|+++| -.+.+|.-... .+-+.| ++ ++|+.|.++|...++
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP-nl--~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP-NL--QVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC-cc--ccccEEEEEEEecCC
Confidence 489999999999999999999988 56777765551 221222 23 599999999986554
No 290
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=25.01 E-value=1.4e+02 Score=30.85 Aligned_cols=49 Identities=27% Similarity=0.371 Sum_probs=39.0
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
....|.+-+|.|.+..+.|.+|+||. +.-+.++ ..+.+|.+|.++|...
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~-~~~~~l~-------------~~~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGK-DKLAKLS-------------SPAPPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecC-Ccceecc-------------CCCCCCceEEEEEEec
Confidence 57889999999999999999999986 3333332 2378999999999864
No 291
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.96 E-value=1.8e+02 Score=28.20 Aligned_cols=51 Identities=12% Similarity=-0.035 Sum_probs=37.7
Q ss_pred eEEEEEEEEecceEEEEE-CCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE-eCC
Q 010232 378 LLEGTVKKIYPYGAQIRI-GDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS-MFP 437 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I-~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v-de~ 437 (514)
.+.|+|..+.+.-+.++. ++.|+.-+++.+.+. .+..|+.+++++..+ +++
T Consensus 4 ~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~~---------~l~~g~~v~l~t~~~vrEd 56 (188)
T PRK14606 4 GISGRVLKKSGNVLLVETKSGVVFEIVCDVQTSE---------EVEEGGECFLHTFLSVSQD 56 (188)
T ss_pred eEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHHH---------HcCCCCeEEEEEEEEEecC
Confidence 478999999999899885 554677777655543 246799999998765 344
No 292
>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=24.90 E-value=2.2e+02 Score=22.00 Aligned_cols=34 Identities=15% Similarity=0.215 Sum_probs=22.8
Q ss_pred EEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232 391 AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433 (514)
Q Consensus 391 aFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~ 433 (514)
.||...+.+-+-|||..+|.. ..-||+|.|+++.
T Consensus 11 GFv~~~~~~~DifIp~~~l~~---------A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 11 GFVIPDDGGEDIFIPPRNLNG---------AMDGDKVLVRITP 44 (58)
T ss_dssp EEEEECT-TEEEEE-HHHHTT---------S-TT-EEEEEEEE
T ss_pred EEEEECCCCCCEEECHHHHCC---------CCCCCEEEEEEec
Confidence 366666436788899888752 3459999999987
No 293
>PRK14640 hypothetical protein; Provisional
Probab=24.37 E-value=4e+02 Score=24.88 Aligned_cols=61 Identities=11% Similarity=0.219 Sum_probs=44.0
Q ss_pred ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeec
Q 010232 329 LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISN 408 (514)
Q Consensus 329 ~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Se 408 (514)
.+++.+++++..++|+.++++... + +.-+..+.|++.++.+.++.+.+.+ -.--+|.++
T Consensus 83 ~RpL~~~~~f~r~~G~~v~V~l~~--~-----------------~~~~k~~~G~L~~v~~~~v~l~~~~--~~~~i~~~~ 141 (152)
T PRK14640 83 DRPLFKVAQFEKYVGQEAAVTLRM--A-----------------TNNRRKFKGVIKAVQGDMITLTVDG--KDEVLAFTN 141 (152)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEec--c-----------------cCCceEEEEEEEEEeCCEEEEEECC--eEEEEEhHH
Confidence 355677788877899999887753 1 2334678999999999999888764 345566666
Q ss_pred cc
Q 010232 409 MS 410 (514)
Q Consensus 409 ls 410 (514)
+.
T Consensus 142 I~ 143 (152)
T PRK14640 142 IQ 143 (152)
T ss_pred ee
Confidence 54
No 294
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.25 E-value=2e+02 Score=27.83 Aligned_cols=49 Identities=18% Similarity=0.200 Sum_probs=39.2
Q ss_pred eEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232 378 LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434 (514)
Q Consensus 378 iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v 434 (514)
.+.|+|..+.+..+.+++++.|++-+++.+.++ ..-+.|+.+...+...
T Consensus 4 ~i~G~i~~~~~~~~ii~~~gvGY~v~~~~~~~~--------~l~~~~~~~~l~~~~~ 52 (192)
T PRK00116 4 YLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLY--------ELPEVGEEVKLYTHLV 52 (192)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHH--------hccCCCCeEEEEEEEE
Confidence 478999999999999999987787777766654 2226799999998866
No 295
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=22.85 E-value=3.7e+02 Score=22.40 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=28.4
Q ss_pred cCCCCceEEEEEEEEecceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe
Q 010232 372 NLREGTLLEGTVKKIYPYGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd 435 (514)
-++.|++++-.|..+.+.|= ...+. |+.-|+|- ..+||+|+++|.++.
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 35677777777777766542 22222 23444431 456888888888764
No 296
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.78 E-value=2.9e+02 Score=23.14 Aligned_cols=61 Identities=13% Similarity=0.208 Sum_probs=40.5
Q ss_pred CCEEEEEEEEEECCeEE-EEE-CCE--EEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232 297 NEPIEVKFTEWNTGGLL-TRI-EGL--RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363 (514)
Q Consensus 297 GeiV~GkV~~v~~~G~f-Vdi-~Gi--~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS 363 (514)
.-.+.|+|.+...++-| |.+ +|. .|-||..--..++. + ..|+.|.+....+|..+++|+--
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~----I--~~GD~V~Ve~~~~d~~kg~I~~R 70 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIR----I--LPGDVVLVELSPYDLTKGRIVYR 70 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEE----e--CCCCEEEEEecccccccccEEEE
Confidence 45688999999988866 666 353 44444322111221 2 48999999999998888877643
No 297
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=22.36 E-value=1.9e+02 Score=25.60 Aligned_cols=37 Identities=22% Similarity=0.143 Sum_probs=28.5
Q ss_pred ccccCCCCCCEE------EEEEEEEeCCeEEEEeCCceeEEee
Q 010232 165 VEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLGTML 201 (514)
Q Consensus 165 ~~~~~ik~GdiV------~G~Vv~v~~~Gv~VdIG~k~~G~Lp 201 (514)
.....+++||.| -|+|++++++.+.|.++.+..-.+.
T Consensus 48 ~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~ 90 (106)
T PRK05585 48 KMLSSLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQ 90 (106)
T ss_pred HHHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEE
Confidence 344588999998 5999999999999999776544433
No 298
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.97 E-value=3.3e+02 Score=26.72 Aligned_cols=28 Identities=18% Similarity=0.170 Sum_probs=20.0
Q ss_pred CEEEEEEEEEeCCeE-EEEeC-CceeEEee
Q 010232 174 DFVIGVVVSGNENKL-DVNVG-ADLLGTML 201 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv-~VdIG-~k~~G~Lp 201 (514)
.++.|+|+.+..+.+ .|++| -+.+.++|
T Consensus 3 ~~l~G~v~~~~~~~~vviev~GvGY~v~i~ 32 (203)
T PRK14602 3 AYLEGRVAERRENSCVVLTPGGVGYEVFLP 32 (203)
T ss_pred ceEEEEEEEEcCCcEEEEEeCCEEEEEEcC
Confidence 368999999988865 67884 34555554
No 299
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.47 E-value=4.4e+02 Score=21.28 Aligned_cols=60 Identities=23% Similarity=0.264 Sum_probs=34.1
Q ss_pred eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232 378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISL 442 (514)
Q Consensus 378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~L 442 (514)
.+.|+|.+....+.| |.+.+ |..-.++..--.. .....+.+||.|.+.+...+ ++++|..
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~Gklr----~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELEN-GHEVLAHISGKMR----KNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-CCEEEEEEcccee----eCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 467899988866544 45544 4444444332211 11223778999999875444 3455543
No 300
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=21.45 E-value=65 Score=32.34 Aligned_cols=58 Identities=14% Similarity=0.181 Sum_probs=43.1
Q ss_pred cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe
Q 010232 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435 (514)
Q Consensus 372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd 435 (514)
..++|++++|.|..|.+.-+=.-|.+ -..+-||..+++.+|. .+..+|+.+..|.+.|
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 36899999999999977433222334 3577788888776553 5788999999998765
No 301
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=21.25 E-value=5.1e+02 Score=28.06 Aligned_cols=91 Identities=13% Similarity=0.138 Sum_probs=57.9
Q ss_pred CCceEEEEEEEEecc--e-EEEEECCC--ceEEEEEeeccccccccCcccccCCCCEEEEEEE-EEe-CCCeEEEEEecC
Q 010232 375 EGTLLEGTVKKIYPY--G-AQIRIGDS--NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV-KSM-FPDKISLSIADL 447 (514)
Q Consensus 375 ~G~iV~G~V~~I~~~--G-aFV~I~~~--gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi-~vd-e~~rI~LSlK~l 447 (514)
..-.|.|.|.+++.. | +|..|-+. .+.+.+..+... .+.-.++.|+.|.|..- ++- ..+++.|...++
T Consensus 24 ~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~-----~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~~i 98 (438)
T PRK00286 24 GQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR-----RLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVEEI 98 (438)
T ss_pred CcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh-----cCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEe
Confidence 345589999998754 5 78888652 356666555432 33355889999987764 233 678899999887
Q ss_pred cCCCCccccchhhhhhHHHHHHHHHHhhCccCC
Q 010232 448 ESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVS 480 (514)
Q Consensus 448 ~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~ 480 (514)
++.- . -.+...-++++++|.+.+
T Consensus 99 ~~~g---------~-G~l~~~~~~lk~~L~~eG 121 (438)
T PRK00286 99 EPAG---------I-GALAAAFEQLKEKLAAEG 121 (438)
T ss_pred eeCC---------c-cHHHHHHHHHHHHHHHCC
Confidence 6521 1 233344466666776654
No 302
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=21.23 E-value=2.6e+02 Score=27.03 Aligned_cols=28 Identities=11% Similarity=0.176 Sum_probs=22.0
Q ss_pred CEEEEEEEEEeCCeEEEEeCC-ceeEEee
Q 010232 174 DFVIGVVVSGNENKLDVNVGA-DLLGTML 201 (514)
Q Consensus 174 diV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp 201 (514)
.++.|+|..++++.+.+++++ +.+.++|
T Consensus 3 ~~i~G~i~~~~~~~~ii~~~gvGY~v~~~ 31 (192)
T PRK00116 3 GYLKGKLVEKGPDYVVIEVNGVGYEVQVP 31 (192)
T ss_pred ceEEEEEEEEcCCEEEEEECCEEEEEEeC
Confidence 368999999999999999853 4555555
No 303
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=20.84 E-value=2.3e+02 Score=23.84 Aligned_cols=33 Identities=27% Similarity=0.223 Sum_probs=26.0
Q ss_pred cccCCCCCCEE------EEEEEEEeCCeEEEEeCCceeE
Q 010232 166 EYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLG 198 (514)
Q Consensus 166 ~~~~ik~GdiV------~G~Vv~v~~~Gv~VdIG~k~~G 198 (514)
-..++++||.| -|+|++++++.+.|.+..+..-
T Consensus 34 m~~~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~i 72 (84)
T TIGR00739 34 LIESLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTEI 72 (84)
T ss_pred HHHhCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEE
Confidence 44588999987 4999999999888888765443
No 304
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=20.21 E-value=7.2e+02 Score=26.56 Aligned_cols=72 Identities=14% Similarity=0.231 Sum_probs=38.8
Q ss_pred cCCCEEEEEEEEEE-CCeEEEEEC-CEEEEEeccccccccC----ChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhh
Q 010232 295 QLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPKAELLSRVN----NFTELKEKVGRRMYVQITRINEDTNDLILSEREAW 368 (514)
Q Consensus 295 k~GeiV~GkV~~v~-~~G~fVdi~-Gi~gFVP~sel~~~i~----~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~ 368 (514)
..--++.|+|..+. .-|-+|.-+ .+--++|.+.+|-... +...+ ++|+.+.+++-.
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 34556778888764 345555442 1444566666542211 11122 489988776421
Q ss_pred hhccCCCCceEEEEEEEEec
Q 010232 369 ATLNLREGTLLEGTVKKIYP 388 (514)
Q Consensus 369 ~~~~l~~G~iV~G~V~~I~~ 388 (514)
+..+..+.|+|..|.+
T Consensus 279 ----~p~~~~~~G~V~~I~~ 294 (390)
T PRK15136 279 ----YGDDVVYTGKVVGLDM 294 (390)
T ss_pred ----CCCCceEEEEEEEECC
Confidence 1123467888888853
No 305
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=20.07 E-value=4.7e+02 Score=21.08 Aligned_cols=28 Identities=4% Similarity=-0.112 Sum_probs=19.8
Q ss_pred EEEEEEeCCeEEEEeCCce-eEEeecccc
Q 010232 178 GVVVSGNENKLDVNVGADL-LGTMLTKEV 205 (514)
Q Consensus 178 G~Vv~v~~~Gv~VdIG~k~-~G~Lp~sEl 205 (514)
++|-+++++.+.+-++.+. .-.+|.+.|
T Consensus 2 ~ivDRiE~~~AVl~~~~~~~~~~vp~~~L 30 (71)
T PF11213_consen 2 AIVDRIEGDYAVLELEDGEKEIDVPRSRL 30 (71)
T ss_pred eEEEEEeCCEEEEEECCCeEEEEEEHHHC
Confidence 6788888888888776654 566665555
Done!