Query 000449
Match_columns 1497
No_of_seqs 603 out of 3920
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 09:08:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000449hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1070 rRNA processing protei 100.0 2E-132 3E-137 1224.3 65.7 1207 43-1496 27-1280(1710)
2 KOG1070 rRNA processing protei 100.0 2.2E-89 4.7E-94 843.3 55.1 1130 121-1454 144-1329(1710)
3 COG0539 RpsA Ribosomal protein 100.0 3.5E-67 7.7E-72 625.2 43.4 491 314-835 14-516 (541)
4 COG0539 RpsA Ribosomal protein 100.0 3.9E-62 8.5E-67 582.0 46.1 495 402-944 16-517 (541)
5 PRK12269 bifunctional cytidyla 100.0 2.3E-59 5E-64 597.3 48.7 494 313-835 313-829 (863)
6 PRK06299 rpsA 30S ribosomal pr 100.0 4.5E-58 9.8E-63 582.2 48.6 496 317-835 26-534 (565)
7 TIGR00717 rpsA ribosomal prote 100.0 4.9E-58 1.1E-62 577.3 48.1 490 317-831 14-516 (516)
8 PRK12269 bifunctional cytidyla 100.0 3.9E-57 8.6E-62 576.9 51.7 489 402-943 316-829 (863)
9 PRK06299 rpsA 30S ribosomal pr 100.0 9.7E-57 2.1E-61 570.0 51.2 495 403-944 26-535 (565)
10 TIGR00717 rpsA ribosomal prote 100.0 2E-55 4.3E-60 553.6 47.1 496 126-655 11-516 (516)
11 PRK13806 rpsA 30S ribosomal pr 100.0 6.9E-50 1.5E-54 493.5 42.9 412 404-834 31-452 (491)
12 PRK13806 rpsA 30S ribosomal pr 100.0 1E-48 2.2E-53 483.1 45.1 402 494-941 30-451 (491)
13 PRK07899 rpsA 30S ribosomal pr 100.0 9.9E-44 2.1E-48 430.5 34.2 328 493-835 30-367 (486)
14 PRK06676 rpsA 30S ribosomal pr 100.0 7.1E-42 1.5E-46 415.3 35.7 334 488-835 7-351 (390)
15 PRK07899 rpsA 30S ribosomal pr 100.0 9.3E-41 2E-45 404.7 33.8 328 315-657 29-365 (486)
16 PRK06676 rpsA 30S ribosomal pr 100.0 5.1E-38 1.1E-42 381.6 33.9 335 315-663 11-356 (390)
17 PRK00087 4-hydroxy-3-methylbut 100.0 4.2E-38 9E-43 401.6 34.4 334 488-835 292-636 (647)
18 PRK00087 4-hydroxy-3-methylbut 100.0 3.1E-36 6.8E-41 384.4 32.4 330 314-657 295-634 (647)
19 PRK07400 30S ribosomal protein 100.0 1.8E-32 3.8E-37 319.1 28.0 244 576-835 21-269 (318)
20 PRK07400 30S ribosomal protein 100.0 3.1E-30 6.8E-35 300.3 26.8 243 495-751 28-274 (318)
21 COG2996 Predicted RNA-bindinin 99.7 2.6E-15 5.6E-20 162.6 22.3 215 667-945 3-222 (287)
22 COG1098 VacB Predicted RNA bin 99.6 2.7E-15 5.8E-20 143.5 5.0 79 1375-1454 2-80 (129)
23 PTZ00248 eukaryotic translatio 99.5 2.1E-14 4.4E-19 164.0 9.6 107 1377-1487 16-125 (319)
24 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 1.1E-13 2.4E-18 126.7 9.1 71 1376-1446 1-74 (74)
25 PTZ00248 eukaryotic translatio 99.4 4.1E-13 8.9E-18 153.5 11.2 110 757-893 12-125 (319)
26 COG2996 Predicted RNA-bindinin 99.4 2.1E-11 4.6E-16 132.6 22.2 229 584-849 4-236 (287)
27 COG1098 VacB Predicted RNA bin 99.4 1.7E-13 3.6E-18 131.3 5.3 77 758-835 2-78 (129)
28 cd05704 S1_Rrp5_repeat_hs13 S1 99.4 7.1E-13 1.5E-17 121.0 8.7 71 1376-1448 1-72 (72)
29 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 2E-12 4.4E-17 118.2 9.1 70 1379-1448 1-72 (73)
30 cd05706 S1_Rrp5_repeat_sc10 S1 99.3 5E-12 1.1E-16 116.0 10.4 73 1376-1448 1-73 (73)
31 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 3.3E-12 7.1E-17 120.3 8.8 79 1369-1447 5-83 (83)
32 cd05705 S1_Rrp5_repeat_hs14 S1 99.3 4.2E-12 9.1E-17 116.3 8.6 71 759-829 1-74 (74)
33 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 8.8E-12 1.9E-16 114.0 10.2 71 758-834 1-72 (74)
34 cd05693 S1_Rrp5_repeat_hs1_sc1 99.3 3.9E-12 8.6E-17 123.3 8.0 90 131-222 1-100 (100)
35 PRK08582 hypothetical protein; 99.3 1.6E-11 3.5E-16 126.1 11.4 79 1376-1455 3-81 (139)
36 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 2.7E-11 5.9E-16 110.8 10.9 72 1375-1452 1-73 (74)
37 PF00575 S1: S1 RNA binding do 99.3 1.6E-11 3.5E-16 113.0 9.4 73 1376-1448 2-74 (74)
38 cd05693 S1_Rrp5_repeat_hs1_sc1 99.3 8.1E-12 1.8E-16 121.1 7.0 77 1376-1452 1-99 (100)
39 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 1.6E-11 3.5E-16 115.6 8.6 79 752-830 5-83 (83)
40 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 2.2E-11 4.9E-16 110.7 8.9 70 1379-1448 1-70 (70)
41 cd05703 S1_Rrp5_repeat_hs12_sc 99.2 2.3E-11 5E-16 111.2 8.8 70 762-831 1-72 (73)
42 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 2.4E-11 5.2E-16 110.2 8.8 69 1379-1447 1-69 (69)
43 cd05707 S1_Rrp5_repeat_sc11 S1 99.2 2.8E-11 6E-16 109.4 8.3 68 1379-1446 1-68 (68)
44 PF00575 S1: S1 RNA binding do 99.2 5.6E-11 1.2E-15 109.4 10.5 73 759-831 2-74 (74)
45 cd05686 S1_pNO40 S1_pNO40: pNO 99.2 5.3E-11 1.2E-15 109.1 9.8 70 1377-1447 2-72 (73)
46 PRK07252 hypothetical protein; 99.2 9.1E-11 2E-15 117.3 12.3 77 1377-1453 2-78 (120)
47 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 4.9E-11 1.1E-15 108.5 9.1 69 1379-1447 1-71 (71)
48 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 4.7E-11 1E-15 108.6 8.6 70 762-831 1-70 (70)
49 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 7.1E-11 1.5E-15 107.5 8.7 69 586-654 1-71 (71)
50 cd04452 S1_IF2_alpha S1_IF2_al 99.2 1.2E-10 2.7E-15 107.6 9.8 74 1376-1449 1-76 (76)
51 cd05691 S1_RPS1_repeat_ec6 S1_ 99.2 1.4E-10 3E-15 106.4 10.0 72 1379-1450 1-72 (73)
52 PRK08059 general stress protei 99.2 1.8E-10 3.9E-15 116.5 11.6 82 1373-1454 2-83 (123)
53 cd05708 S1_Rrp5_repeat_sc12 S1 99.2 1.6E-10 3.5E-15 107.1 10.1 74 1377-1450 1-75 (77)
54 PRK05807 hypothetical protein; 99.1 2.2E-10 4.7E-15 117.4 11.0 74 1376-1451 3-76 (136)
55 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.1 1.4E-10 3E-15 105.1 8.6 69 586-654 1-69 (69)
56 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 1.8E-10 3.9E-15 104.1 8.0 68 762-829 1-68 (68)
57 cd05704 S1_Rrp5_repeat_hs13 S1 99.1 2.3E-10 5E-15 104.5 8.4 71 759-831 1-72 (72)
58 cd05687 S1_RPS1_repeat_ec1_hs1 99.1 3.2E-10 7E-15 103.1 9.3 70 1379-1448 1-70 (70)
59 cd05690 S1_RPS1_repeat_ec5 S1_ 99.1 2.9E-10 6.3E-15 103.0 8.4 68 1379-1446 1-69 (69)
60 cd05706 S1_Rrp5_repeat_sc10 S1 99.1 6.3E-10 1.4E-14 102.1 10.6 73 759-831 1-73 (73)
61 PRK08582 hypothetical protein; 99.1 5.2E-10 1.1E-14 115.0 10.9 76 759-835 3-78 (139)
62 COG2183 Tex Transcriptional ac 99.1 1.6E-10 3.4E-15 143.1 7.8 90 1364-1453 644-733 (780)
63 cd05692 S1_RPS1_repeat_hs4 S1_ 99.0 6.8E-10 1.5E-14 100.3 9.1 69 1379-1448 1-69 (69)
64 PRK07252 hypothetical protein; 99.0 9E-10 2E-14 110.2 10.6 76 760-835 2-77 (120)
65 PHA02945 interferon resistance 99.0 9.6E-10 2.1E-14 99.9 9.4 73 1376-1451 9-85 (88)
66 cd05684 S1_DHX8_helicase S1_DH 99.0 1.3E-09 2.9E-14 101.6 10.3 73 1379-1453 1-77 (79)
67 cd05690 S1_RPS1_repeat_ec5 S1_ 99.0 6.4E-10 1.4E-14 100.8 7.8 68 762-829 1-69 (69)
68 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 1E-09 2.2E-14 98.4 8.6 66 586-653 1-66 (66)
69 cd05689 S1_RPS1_repeat_ec4 S1_ 99.0 1.2E-09 2.6E-14 100.0 9.3 71 1376-1446 1-72 (72)
70 cd04452 S1_IF2_alpha S1_IF2_al 99.0 1.5E-09 3.2E-14 100.4 9.9 73 760-832 2-76 (76)
71 cd05686 S1_pNO40 S1_pNO40: pNO 99.0 1.4E-09 3E-14 99.8 9.5 70 760-830 2-72 (73)
72 cd05708 S1_Rrp5_repeat_sc12 S1 99.0 1.3E-09 2.8E-14 101.0 9.4 74 760-833 1-75 (77)
73 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 1.7E-09 3.8E-14 96.9 8.9 66 1379-1446 1-66 (66)
74 cd04465 S1_RPS1_repeat_ec2_hs2 99.0 1.8E-09 3.9E-14 97.2 8.9 67 586-655 1-67 (67)
75 cd05689 S1_RPS1_repeat_ec4 S1_ 99.0 1.8E-09 3.9E-14 98.8 8.8 71 759-829 1-72 (72)
76 cd05685 S1_Tex S1_Tex: The C-t 99.0 1.4E-09 3.1E-14 98.0 7.9 68 1379-1446 1-68 (68)
77 cd05691 S1_RPS1_repeat_ec6 S1_ 99.0 2.3E-09 5E-14 98.2 9.4 72 762-833 1-72 (73)
78 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 2.4E-09 5.2E-14 97.4 9.1 70 586-655 1-70 (70)
79 cd04472 S1_PNPase S1_PNPase: P 98.9 2.9E-09 6.4E-14 96.0 8.9 68 1379-1447 1-68 (68)
80 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.9 3.2E-09 6.9E-14 100.7 8.9 76 1376-1452 4-83 (86)
81 COG1093 SUI2 Translation initi 98.9 9.8E-10 2.1E-14 119.4 5.4 78 1376-1453 9-88 (269)
82 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.9 2.4E-09 5.1E-14 95.0 6.7 72 670-742 1-72 (72)
83 cd05692 S1_RPS1_repeat_hs4 S1_ 98.9 5.1E-09 1.1E-13 94.6 8.8 69 586-655 1-69 (69)
84 PRK08059 general stress protei 98.9 6.1E-09 1.3E-13 105.4 10.2 80 756-835 2-81 (123)
85 PLN00207 polyribonucleotide nu 98.9 2.8E-09 6E-14 136.5 9.3 82 1375-1457 750-832 (891)
86 smart00316 S1 Ribosomal protei 98.9 6E-09 1.3E-13 94.6 9.1 72 1377-1448 1-72 (72)
87 cd05688 S1_RPS1_repeat_ec3 S1_ 98.9 5.6E-09 1.2E-13 94.2 8.6 68 1378-1446 1-68 (68)
88 PRK05807 hypothetical protein; 98.9 7.7E-09 1.7E-13 106.1 10.6 74 759-834 3-76 (136)
89 cd04465 S1_RPS1_repeat_ec2_hs2 98.9 8.2E-09 1.8E-13 93.0 8.8 67 762-831 1-67 (67)
90 cd04471 S1_RNase_R S1_RNase_R: 98.8 1.3E-08 2.8E-13 95.8 10.0 70 1378-1447 1-82 (83)
91 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 1.1E-08 2.3E-13 96.3 9.1 76 1376-1452 4-79 (82)
92 cd04453 S1_RNase_E S1_RNase_E: 98.8 1.1E-08 2.4E-13 96.9 9.3 75 1375-1449 4-83 (88)
93 cd05685 S1_Tex S1_Tex: The C-t 98.8 7.4E-09 1.6E-13 93.3 7.7 68 762-829 1-68 (68)
94 cd05684 S1_DHX8_helicase S1_DH 98.8 1.4E-08 3.1E-13 94.7 9.6 72 762-835 1-76 (79)
95 PLN00207 polyribonucleotide nu 98.8 9.2E-09 2E-13 131.8 10.4 87 757-856 749-836 (891)
96 PRK03987 translation initiatio 98.8 1.3E-08 2.9E-13 115.5 10.3 78 1376-1453 6-85 (262)
97 cd05702 S1_Rrp5_repeat_hs11_sc 98.8 1.3E-08 2.9E-13 92.4 8.1 62 1379-1440 1-64 (70)
98 cd04472 S1_PNPase S1_PNPase: P 98.8 1.8E-08 3.9E-13 90.9 8.7 68 586-654 1-68 (68)
99 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2.4E-08 5.2E-13 90.0 8.5 68 585-653 1-68 (68)
100 PHA02945 interferon resistance 98.8 3.2E-08 7E-13 90.1 9.0 72 760-834 10-85 (88)
101 PRK09521 exosome complex RNA-b 98.8 6.1E-08 1.3E-12 105.9 12.6 111 1314-1452 24-145 (189)
102 smart00316 S1 Ribosomal protei 98.7 3.8E-08 8.1E-13 89.3 9.0 72 760-831 1-72 (72)
103 TIGR02696 pppGpp_PNP guanosine 98.7 2E-08 4.4E-13 126.2 9.2 71 1375-1446 644-718 (719)
104 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.7 4.7E-08 1E-12 92.8 8.6 75 759-834 4-82 (86)
105 cd04473 S1_RecJ_like S1_RecJ_l 98.7 1.1E-07 2.3E-12 88.2 10.5 68 1371-1447 9-76 (77)
106 PRK11824 polynucleotide phosph 98.7 4.8E-08 1E-12 126.2 10.9 76 1374-1450 617-692 (693)
107 cd04453 S1_RNase_E S1_RNase_E: 98.7 7.2E-08 1.6E-12 91.4 9.0 75 758-832 4-83 (88)
108 cd00164 S1_like S1_like: Ribos 98.7 5.6E-08 1.2E-12 86.3 7.5 65 1382-1446 1-65 (65)
109 PRK04163 exosome complex RNA-b 98.6 3.6E-07 7.7E-12 103.1 13.9 109 1316-1452 28-140 (235)
110 TIGR02696 pppGpp_PNP guanosine 98.6 7.5E-08 1.6E-12 121.2 8.3 71 758-829 644-718 (719)
111 cd04473 S1_RecJ_like S1_RecJ_l 98.6 2.3E-07 4.9E-12 86.0 9.4 71 575-654 6-76 (77)
112 cd04471 S1_RNase_R S1_RNase_R: 98.6 2.1E-07 4.6E-12 87.5 9.3 70 761-830 1-82 (83)
113 COG1093 SUI2 Translation initi 98.6 5.6E-08 1.2E-12 106.0 5.4 76 760-835 10-87 (269)
114 PRK03987 translation initiatio 98.6 1.8E-07 3.8E-12 106.4 9.4 76 760-835 7-84 (262)
115 cd00164 S1_like S1_like: Ribos 98.5 1.8E-07 3.9E-12 83.0 7.1 65 589-653 1-65 (65)
116 cd05702 S1_Rrp5_repeat_hs11_sc 98.5 2.5E-07 5.4E-12 84.1 8.0 63 762-824 1-65 (70)
117 cd04454 S1_Rrp4_like S1_Rrp4_l 98.5 3.9E-07 8.5E-12 85.6 9.2 74 760-834 5-78 (82)
118 cd04460 S1_RpoE S1_RpoE: RpoE, 98.5 3.8E-07 8.2E-12 89.0 9.1 74 1380-1454 1-90 (99)
119 COG2183 Tex Transcriptional ac 98.5 1.4E-07 3.1E-12 117.4 6.9 81 755-835 652-732 (780)
120 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.5 5.3E-07 1.2E-11 86.3 8.4 76 1376-1452 4-89 (92)
121 TIGR03591 polynuc_phos polyrib 98.5 2.8E-07 6E-12 118.9 8.4 71 1374-1445 614-684 (684)
122 PRK11824 polynucleotide phosph 98.4 5.8E-07 1.3E-11 116.3 10.4 76 757-833 617-692 (693)
123 PRK09202 nusA transcription el 98.4 4.1E-07 8.9E-12 111.3 8.0 119 437-568 72-201 (470)
124 COG1185 Pnp Polyribonucleotide 98.4 4.2E-07 9.2E-12 111.5 7.2 76 1374-1450 615-690 (692)
125 PRK09521 exosome complex RNA-b 98.4 1.6E-06 3.5E-11 94.8 10.8 96 727-835 40-145 (189)
126 PRK09202 nusA transcription el 98.4 5.7E-07 1.2E-11 110.1 8.0 122 524-657 73-201 (470)
127 cd04455 S1_NusA S1_NusA: N-uti 98.3 2.9E-06 6.3E-11 76.4 8.0 62 497-565 2-67 (67)
128 TIGR03591 polynuc_phos polyrib 98.2 2.9E-06 6.2E-11 109.7 10.2 70 582-652 615-684 (684)
129 TIGR00448 rpoE DNA-directed RN 98.2 4.7E-06 1E-10 90.3 10.3 77 1377-1454 80-172 (179)
130 cd04455 S1_NusA S1_NusA: N-uti 98.2 6.5E-06 1.4E-10 74.1 9.3 63 1377-1446 2-66 (67)
131 COG1185 Pnp Polyribonucleotide 98.2 1.8E-06 3.9E-11 106.1 6.9 77 756-833 614-690 (692)
132 PRK04163 exosome complex RNA-b 98.2 1.3E-05 2.8E-10 90.6 13.2 72 584-656 62-137 (235)
133 COG1095 RPB7 DNA-directed RNA 98.2 4.6E-06 9.9E-11 87.5 8.2 77 1377-1454 80-172 (183)
134 cd04460 S1_RpoE S1_RpoE: RpoE, 98.2 6.8E-06 1.5E-10 80.2 8.8 72 763-835 1-88 (99)
135 COG1096 Predicted RNA-binding 98.1 2.3E-05 4.9E-10 82.3 11.2 113 1314-1453 24-146 (188)
136 TIGR02063 RNase_R ribonuclease 98.1 8.6E-06 1.9E-10 106.9 10.1 72 1376-1447 625-708 (709)
137 TIGR01953 NusA transcription t 98.0 8.4E-06 1.8E-10 96.1 7.9 110 451-568 78-199 (341)
138 PRK11642 exoribonuclease R; Pr 98.0 2.3E-05 4.9E-10 102.9 10.3 76 1377-1452 642-729 (813)
139 TIGR01953 NusA transcription t 97.9 1.6E-05 3.4E-10 93.9 7.8 109 541-657 82-199 (341)
140 PRK08563 DNA-directed RNA poly 97.9 4.4E-05 9.5E-10 83.6 10.1 78 1376-1454 79-172 (187)
141 TIGR00358 3_prime_RNase VacB a 97.9 3.3E-05 7.2E-10 100.1 10.2 71 1377-1447 571-653 (654)
142 PRK12327 nusA transcription el 97.9 2.3E-05 5E-10 93.0 7.3 108 542-656 86-200 (362)
143 PRK12327 nusA transcription el 97.8 3.6E-05 7.8E-10 91.4 7.6 106 454-567 84-200 (362)
144 TIGR00448 rpoE DNA-directed RN 97.8 9.2E-05 2E-09 80.4 9.4 73 761-834 81-169 (179)
145 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.8 7.3E-05 1.6E-09 66.9 6.9 67 499-566 1-72 (72)
146 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.8 8.3E-05 1.8E-09 71.3 7.8 76 1258-1348 5-88 (92)
147 KOG1067 Predicted RNA-binding 97.7 3.3E-05 7E-10 91.7 4.8 78 582-659 665-742 (760)
148 cd05701 S1_Rrp5_repeat_hs10 S1 97.7 4.9E-05 1.1E-09 64.6 4.3 59 971-1029 1-60 (69)
149 TIGR02063 RNase_R ribonuclease 97.7 0.00012 2.6E-09 96.3 9.8 75 756-830 622-708 (709)
150 KOG1067 Predicted RNA-binding 97.6 4.8E-05 1E-09 90.3 5.2 82 1372-1454 662-743 (760)
151 COG1097 RRP4 RNA-binding prote 97.5 0.0021 4.6E-08 70.7 14.7 87 1376-1474 62-152 (239)
152 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.4 0.00054 1.2E-08 65.1 8.5 62 1378-1440 1-73 (88)
153 COG1095 RPB7 DNA-directed RNA 97.4 0.00037 8.1E-09 73.4 7.9 72 585-657 81-168 (183)
154 PRK11642 exoribonuclease R; Pr 97.4 0.00045 9.8E-09 91.0 9.6 73 759-831 641-725 (813)
155 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.3 0.0013 2.8E-08 61.8 9.3 74 1376-1451 4-77 (86)
156 TIGR00358 3_prime_RNase VacB a 97.3 0.00079 1.7E-08 87.5 10.7 71 584-654 571-653 (654)
157 PHA02858 EIF2a-like PKR inhibi 97.3 0.00068 1.5E-08 61.6 6.6 70 1376-1447 14-85 (86)
158 PRK08563 DNA-directed RNA poly 97.3 0.001 2.2E-08 72.9 9.4 75 760-835 80-170 (187)
159 PHA02858 EIF2a-like PKR inhibi 97.2 0.00078 1.7E-08 61.3 6.4 69 760-830 15-85 (86)
160 PF10447 EXOSC1: Exosome compo 97.2 0.00099 2.1E-08 61.9 6.6 60 1377-1436 3-82 (82)
161 PF13509 S1_2: S1 domain; PDB: 97.1 0.0019 4.2E-08 56.9 7.4 61 761-831 1-61 (61)
162 PF13509 S1_2: S1 domain; PDB: 97.1 0.0017 3.7E-08 57.2 6.8 61 669-742 1-61 (61)
163 PRK12328 nusA transcription el 97.0 0.0012 2.7E-08 77.8 7.1 108 452-567 86-206 (374)
164 COG1107 Archaea-specific RecJ- 97.0 0.00098 2.1E-08 80.3 6.2 104 1372-1482 116-228 (715)
165 PRK12328 nusA transcription el 96.9 0.0014 3E-08 77.4 6.7 108 542-656 90-206 (374)
166 PRK05054 exoribonuclease II; P 96.9 0.003 6.5E-08 81.8 9.7 69 1379-1447 562-643 (644)
167 TIGR00757 RNaseEG ribonuclease 96.9 0.0026 5.6E-08 77.6 8.5 72 1377-1448 24-109 (414)
168 cd05700 S1_Rrp5_repeat_hs9 S1_ 96.8 0.0073 1.6E-07 51.0 8.2 64 875-938 1-65 (65)
169 PTZ00162 DNA-directed RNA poly 96.8 0.0055 1.2E-07 66.0 9.2 77 1377-1454 80-170 (176)
170 PRK12329 nusA transcription el 96.7 0.0029 6.4E-08 75.7 7.2 115 447-567 93-225 (449)
171 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.7 0.0096 2.1E-07 56.6 9.0 64 585-649 1-75 (88)
172 PF10447 EXOSC1: Exosome compo 96.6 0.0054 1.2E-07 57.1 6.3 61 1259-1330 4-82 (82)
173 KOG2916 Translation initiation 96.5 0.0015 3.3E-08 71.5 2.5 77 1376-1452 14-92 (304)
174 COG1107 Archaea-specific RecJ- 96.4 0.021 4.4E-07 69.4 11.7 155 755-938 116-282 (715)
175 COG0557 VacB Exoribonuclease R 96.4 0.0069 1.5E-07 79.6 8.7 75 1375-1449 619-705 (706)
176 COG1096 Predicted RNA-binding 96.4 0.03 6.4E-07 59.4 11.2 73 1257-1348 62-144 (188)
177 TIGR02062 RNase_B exoribonucle 96.3 0.0096 2.1E-07 77.1 8.9 68 1379-1446 558-638 (639)
178 PTZ00162 DNA-directed RNA poly 96.1 0.018 4E-07 62.0 8.4 71 497-568 80-166 (176)
179 KOG2916 Translation initiation 95.9 0.0066 1.4E-07 66.6 4.0 76 760-835 15-92 (304)
180 TIGR00757 RNaseEG ribonuclease 95.9 0.018 4E-07 70.3 8.2 73 759-831 23-109 (414)
181 COG1097 RRP4 RNA-binding prote 95.8 0.045 9.7E-07 60.5 9.9 74 760-834 63-140 (239)
182 KOG1856 Transcription elongati 95.8 0.0076 1.6E-07 78.0 4.4 81 1373-1453 980-1063(1299)
183 PRK05054 exoribonuclease II; P 95.7 0.028 6E-07 73.0 9.3 71 760-830 558-643 (644)
184 KOG1856 Transcription elongati 95.7 0.01 2.3E-07 76.7 4.8 76 582-657 982-1060(1299)
185 cd05790 S1_Rrp40 S1_Rrp40: Rrp 95.2 0.097 2.1E-06 49.4 8.3 70 497-567 5-75 (86)
186 PRK10811 rne ribonuclease E; R 94.7 0.07 1.5E-06 69.2 8.1 72 1377-1448 37-119 (1068)
187 TIGR02062 RNase_B exoribonucle 94.5 0.096 2.1E-06 68.0 8.8 68 762-829 558-638 (639)
188 PRK12329 nusA transcription el 94.3 0.13 2.8E-06 62.1 8.5 72 232-305 152-230 (449)
189 PRK11712 ribonuclease G; Provi 93.8 0.13 2.9E-06 64.0 7.6 71 1377-1447 37-121 (489)
190 COG0557 VacB Exoribonuclease R 93.2 0.22 4.7E-06 65.8 8.6 75 756-830 617-703 (706)
191 PF10246 MRP-S35: Mitochondria 92.3 0.55 1.2E-05 45.0 7.5 62 487-556 13-74 (104)
192 KOG3409 Exosomal 3'-5' exoribo 91.5 0.71 1.5E-05 48.2 7.9 76 1376-1452 66-151 (193)
193 PF08292 RNA_pol_Rbc25: RNA po 89.8 1.3 2.7E-05 44.9 7.9 59 498-556 3-74 (122)
194 KOG3409 Exosomal 3'-5' exoribo 88.1 2.1 4.5E-05 44.9 8.1 72 1162-1234 67-146 (193)
195 PRK10811 rne ribonuclease E; R 88.0 2.7 5.9E-05 55.3 11.0 86 1259-1350 38-124 (1068)
196 PRK11712 ribonuclease G; Provi 87.7 1.1 2.4E-05 56.1 7.1 59 584-642 37-109 (489)
197 COG1530 CafA Ribonucleases G a 87.5 0.78 1.7E-05 57.7 5.8 74 1376-1450 35-115 (487)
198 PF10246 MRP-S35: Mitochondria 86.5 2.8 6E-05 40.4 7.3 52 320-379 22-73 (104)
199 KOG3298 DNA-directed RNA polym 85.8 3.2 6.9E-05 43.2 7.9 64 1378-1441 81-154 (170)
200 KOG3298 DNA-directed RNA polym 82.7 7.4 0.00016 40.7 9.0 64 585-649 81-155 (170)
201 PRK06386 replication factor A; 79.5 1.5E+02 0.0033 35.8 20.6 114 1370-1486 107-237 (358)
202 PRK14699 replication factor A; 78.7 2E+02 0.0042 36.6 26.4 255 1209-1491 123-419 (484)
203 PF08292 RNA_pol_Rbc25: RNA po 77.6 7.8 0.00017 39.3 7.3 61 321-381 3-75 (122)
204 cd05701 S1_Rrp5_repeat_hs10 S1 73.4 3 6.6E-05 36.4 2.6 59 1165-1225 2-61 (69)
205 COG1530 CafA Ribonucleases G a 70.9 12 0.00027 47.2 8.4 80 1259-1348 37-116 (487)
206 KOG3013 Exosomal 3'-5' exoribo 66.2 8 0.00017 43.2 4.6 75 1376-1451 83-167 (301)
207 PRK12442 translation initiatio 63.2 34 0.00074 32.3 7.4 66 764-833 8-74 (87)
208 TIGR00008 infA translation ini 61.2 36 0.00078 30.8 7.0 60 764-827 6-66 (68)
209 cd05700 S1_Rrp5_repeat_hs9 S1_ 60.8 36 0.00079 29.6 6.5 62 322-391 1-65 (65)
210 KOG4078 Putative mitochondrial 54.0 29 0.00064 35.1 5.7 52 321-380 82-133 (173)
211 KOG1004 Exosomal 3'-5' exoribo 53.4 42 0.00091 36.8 7.2 62 1161-1225 63-124 (230)
212 PRK10676 DNA-binding transcrip 53.4 1.3E+02 0.0028 34.9 12.0 114 136-286 129-254 (263)
213 COG4148 ModC ABC-type molybdat 53.0 2E+02 0.0043 33.6 12.6 119 1162-1331 230-349 (352)
214 COG4044 Uncharacterized protei 52.4 19 0.00042 39.0 4.5 84 1369-1452 66-161 (247)
215 KOG4078 Putative mitochondrial 51.7 35 0.00076 34.6 5.8 53 497-556 81-133 (173)
216 COG4148 ModC ABC-type molybdat 47.8 1.9E+02 0.0041 33.8 11.5 115 1259-1437 231-349 (352)
217 PRK12442 translation initiatio 47.1 99 0.0022 29.4 7.7 65 1381-1450 8-74 (87)
218 KOG3297 DNA-directed RNA polym 46.1 36 0.00077 36.5 5.2 59 498-556 81-156 (202)
219 TIGR00008 infA translation ini 45.5 91 0.002 28.3 6.9 60 1381-1444 6-66 (68)
220 PF00313 CSD: 'Cold-shock' DNA 44.5 1.7E+02 0.0038 25.9 8.9 49 590-642 2-53 (66)
221 PF03459 TOBE: TOBE domain; I 42.4 38 0.00083 29.8 4.3 49 234-285 5-58 (64)
222 PF00313 CSD: 'Cold-shock' DNA 42.2 2.5E+02 0.0053 24.9 10.4 50 1382-1435 1-53 (66)
223 PRK06763 F0F1 ATP synthase sub 41.7 4.3E+02 0.0093 29.1 12.4 46 1164-1219 39-84 (213)
224 PF01938 TRAM: TRAM domain; I 41.7 1.4E+02 0.003 26.1 7.6 55 458-517 3-59 (61)
225 KOG1004 Exosomal 3'-5' exoribo 38.4 1.2E+02 0.0025 33.6 7.6 61 320-382 64-124 (230)
226 PRK10676 DNA-binding transcrip 38.2 1.7E+02 0.0036 34.1 9.8 116 763-926 128-254 (263)
227 PF01330 RuvA_N: RuvA N termin 36.4 1.6E+02 0.0034 25.9 7.1 47 501-556 4-51 (61)
228 PRK10943 cold shock-like prote 34.2 1.3E+02 0.0028 27.3 6.3 51 588-642 3-56 (69)
229 PF07076 DUF1344: Protein of u 33.4 1E+02 0.0023 27.2 5.2 45 1066-1121 4-48 (61)
230 KOG3013 Exosomal 3'-5' exoribo 32.4 91 0.002 35.3 5.9 74 1162-1236 84-165 (301)
231 PRK15464 cold shock-like prote 32.4 1.3E+02 0.0029 27.4 6.1 50 589-642 5-57 (70)
232 PF01938 TRAM: TRAM domain; I 31.3 2.6E+02 0.0056 24.4 7.7 56 275-341 3-60 (61)
233 PRK15463 cold shock-like prote 31.0 1.4E+02 0.0031 27.2 6.1 50 589-642 5-57 (70)
234 PRK09507 cspE cold shock prote 30.1 1.8E+02 0.0038 26.5 6.5 51 588-642 3-56 (69)
235 PRK15464 cold shock-like prote 29.0 2.3E+02 0.005 25.9 7.0 51 502-556 5-58 (70)
236 PF03459 TOBE: TOBE domain; I 28.6 1.2E+02 0.0026 26.5 5.2 49 876-924 5-57 (64)
237 PRK10943 cold shock-like prote 27.9 1.6E+02 0.0035 26.7 5.8 51 501-555 3-56 (69)
238 PRK09937 stationary phase/star 27.8 1.8E+02 0.0038 26.9 6.1 49 590-642 3-54 (74)
239 PRK06386 replication factor A; 27.2 1.2E+03 0.026 28.4 15.0 46 234-282 15-69 (358)
240 cd04458 CSP_CDS Cold-Shock Pro 26.6 3.4E+02 0.0073 23.9 7.7 50 1383-1436 2-54 (65)
241 PF12073 DUF3553: Protein of u 26.3 88 0.0019 26.7 3.4 26 131-156 1-35 (52)
242 COG0361 InfA Translation initi 26.0 2.9E+02 0.0062 25.7 7.0 56 876-936 7-69 (75)
243 PRK09507 cspE cold shock prote 25.4 2.4E+02 0.0052 25.6 6.5 51 501-555 3-56 (69)
244 PF07076 DUF1344: Protein of u 25.3 3.3E+02 0.0072 24.3 6.8 56 672-740 4-59 (61)
245 PRK14998 cold shock-like prote 24.4 2.2E+02 0.0047 26.3 6.1 49 590-642 3-54 (73)
246 PRK15463 cold shock-like prote 24.1 2.2E+02 0.0047 26.0 6.0 50 502-555 5-57 (70)
247 cd04322 LysRS_N LysRS_N: N-ter 24.0 2.4E+02 0.0053 27.7 6.9 64 1381-1447 3-74 (108)
248 PRK09890 cold shock protein Cs 23.9 2.7E+02 0.006 25.3 6.6 50 589-642 5-57 (70)
249 COG4044 Uncharacterized protei 22.9 1.1E+02 0.0023 33.6 4.3 79 747-826 62-152 (247)
250 PRK07218 replication factor A; 22.9 1.6E+03 0.034 28.2 19.2 113 1370-1488 162-299 (423)
251 TIGR02381 cspD cold shock doma 22.9 1.8E+02 0.004 26.2 5.3 49 590-642 3-54 (68)
252 PRK06763 F0F1 ATP synthase sub 22.7 1.1E+03 0.023 26.2 13.0 45 876-923 40-84 (213)
253 PRK10354 RNA chaperone/anti-te 22.0 2.9E+02 0.0064 25.1 6.4 49 590-642 6-57 (70)
254 PF15057 DUF4537: Domain of un 21.9 3.1E+02 0.0068 28.0 7.3 95 497-620 10-111 (124)
255 PF11604 CusF_Ec: Copper bindi 21.8 4.9E+02 0.011 23.7 7.8 45 639-683 2-59 (70)
256 TIGR00638 Mop molybdenum-pteri 21.6 2.3E+02 0.005 25.0 5.7 50 876-925 7-60 (69)
257 PRK10354 RNA chaperone/anti-te 21.4 2.4E+02 0.0053 25.6 5.8 50 502-555 5-57 (70)
258 COG2106 Uncharacterized conser 21.2 2.4E+02 0.0051 32.7 6.8 55 1370-1437 97-151 (272)
259 TIGR03833 conserved hypothetic 20.3 1E+02 0.0022 27.2 2.8 31 1062-1092 23-59 (62)
260 PF09962 DUF2196: Uncharacteri 20.2 1.1E+02 0.0025 27.1 3.1 32 1061-1092 23-60 (62)
261 COG0361 InfA Translation initi 20.0 6.2E+02 0.013 23.6 7.9 65 1379-1448 6-72 (75)
No 1
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=100.00 E-value=1.5e-132 Score=1224.30 Aligned_cols=1207 Identities=32% Similarity=0.466 Sum_probs=962.4
Q ss_pred cCCCCCCCCCcCCCCCcCCCCcchhhhhhhh--hcchhhcccccc-----ccccccccccccccccccccccCCccCCCc
Q 000449 43 LALPPDDDVPVFPRGGGHSLTQRERDEIHAE--VDAEFEAVERGL-----HKKNKKKKKKTERKANETVDDLGSLFGDGI 115 (1497)
Q Consensus 43 ~~~~~~~~e~~FPRGg~~~lt~~e~~~~~~~--~d~lf~~~~~~~-----~kk~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (1497)
..+...+++++|||||+|.|||+|++++..| .|.+|+....+. .+++++.++..++-+. .++...
T Consensus 27 ~~l~~~t~~~~fprgg~s~lt~~e~~kv~~E~~~e~l~~~~~vke~~~~~~~~~k~vk~~~s~~s~--------~~~~~~ 98 (1710)
T KOG1070|consen 27 SSLKRKTAAPDFPRGGASKLTPLEIEKVEEEAFIEGLTGFGVVKEVFDDGRPKKKTVKKSASKVSK--------KFTENF 98 (1710)
T ss_pred ccccccccccccccccccccChHHHHHHHHHHHhhhhhcccceecccCCCCccccccccchhhHHH--------hhhccc
Confidence 3446678899999999999999999999555 444554321110 1111111111111000 000011
Q ss_pred CCCCCeeecccccCCcCCCCEEEEEEEEEeCceEEEEcCCCcEEEEeccccCChhhcccccccccCCCCCccCCCCEEEE
Q 000449 116 SGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSC 195 (1497)
Q Consensus 116 ~~~~~~~~e~l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~~~~~~~~~L~~~f~vGq~v~~ 195 (1497)
...-+.++++++++++.|||++||+|++|+..|+.+++|++++|||+.+++|+.+
T Consensus 99 ~~~k~~~~~~~~~k~isPG~~llgvIs~i~~~Dl~isv~~~l~g~v~~t~lS~~~------------------------- 153 (1710)
T KOG1070|consen 99 NEEKPEIINAFQLKNISPGMLLLGVISKINGNDLKISVKGGLNGYVLNTHLSDEM------------------------- 153 (1710)
T ss_pred cccchhhhhhccccccCCcceeeeeeeeccccceeEEccCcccccccccccCHhH-------------------------
Confidence 1112556899999999999999999999999999999999999999999999762
Q ss_pred EEEEEecCCcccceeEEEEecchhhHhcCCCcccccCCcEEEEEEEEEEeCeEEEEeCCCCeEEEeeCCCCCCCCCCcCC
Q 000449 196 IVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVK 275 (1497)
Q Consensus 196 ~V~~~~~~~~~~~~~~i~LSl~p~~vn~~l~~~~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~ 275 (1497)
+.+||+|.+.|.|+||||+++|+|++..+||+...++++ .+..++
T Consensus 154 ----------------------------------~~~~~~l~~~v~S~ed~g~~l~~g~~~~~~~~e~~q~pn-~~~~lK 198 (1710)
T KOG1070|consen 154 ----------------------------------LAAGEVLDTAVVSIEDHGAILDVGLDEITGFIEKSQFPN-LGAKLK 198 (1710)
T ss_pred ----------------------------------hhhhhhhccccccccccccchhcCCccccchhhhccCch-hhhhcc
Confidence 235788999999999999999999999999999888753 334799
Q ss_pred CCcEEEEEEEEEcCCCcEEEEccCccccccccccccccccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccc
Q 000449 276 PGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQ 355 (1497)
Q Consensus 276 ~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~ 355 (1497)
+||.+.|.|++++. +.+++|..+.......++..+.++++.|.||++|.+.|++|.++|+.++|+++|+|+++..||.
T Consensus 199 vGq~l~~~V~k~~s--~~v~ks~~~~~~~t~~~t~~~~~~~~~LvpGt~vqa~V~sv~~~Gi~~dil~~ftG~l~~~hl~ 276 (1710)
T KOG1070|consen 199 VGQWLRVSVTKSTS--ERVVKSTKFVEVLTLNPTSCNGLALNDLVPGTMVQAEVQSVEDHGITLDILNGFTGFLDKKHLP 276 (1710)
T ss_pred cCceEEEEEEeccC--ceEEecccceeeecccchhccccchhhcCCcceEEEEecceecCcEEEEecccccceeehhhCC
Confidence 99999999999876 3888888888888888888889999999999999999999999999999999999999999998
Q ss_pred cCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecchhhhccCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCc
Q 000449 356 NTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVS 435 (1497)
Q Consensus 356 ~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p~~~~~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~ 435 (1497)
++. .|..|+...|.|+. +..+.+ .++.++.+....+.+. |+..
T Consensus 277 ~~~-------~~~~~~~~l~~vi~--~s~Rv~-------------------~~~f~~ka~ki~~l~~-~v~a-------- 319 (1710)
T KOG1070|consen 277 PFL-------RYFENQEKLGKVIH--KSDRVF-------------------VVDFFDKASKILVLKA-GVDA-------- 319 (1710)
T ss_pred chh-------hccccHHHhhcccc--hhhhee-------------------eechhhccceEEEecC-ccce--------
Confidence 764 48888888888643 222211 1222222222223332 3333
Q ss_pred cceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEcchhhcccccccccccCCCcEEEEEEEEEecCeeE
Q 000449 436 TPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAI 515 (1497)
Q Consensus 436 v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~ 515 (1497)
.+|-+.+. +-. ...+++|..++|||+++..++.+...+++.+.++.++.+..+++||.++.+++ .+..+
T Consensus 320 ---i~p~~~~~---~~~-~e~~k~G~~~K~~vi~~~~~~~~~~~tl~~s~ie~k~~~~s~V~~r~l~~~~~-svdt~--- 388 (1710)
T KOG1070|consen 320 ---IAPSRIEK---VLS-FEIFKIGNKVKCRVIDVLQMDSLALFTLKESAIEGKFSLVSDVSPRGLLKKPV-SVDTE--- 388 (1710)
T ss_pred ---EccCCccc---ccc-hhhcccCceEEEEEEEEeeccceEEeecchhhccCceEEEeccCCceEEEecc-cCChh---
Confidence 33322221 111 12489999999999999999999999999999999999999999999999998 76665
Q ss_pred EEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEEeCCeEEEEeecchhhhhhhHHhhhhhccCCcEEEEEEEE
Q 000449 516 VQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITK 595 (1497)
Q Consensus 516 V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~ 595 (1497)
..|++|+.|+..+...+|+.+|..|..|.|||+.+..+++.+|+| .+..+++|.+..|.++.+ ..+|++.+
T Consensus 389 ------~~~l~~L~hv~~f~~a~p~~~~~~~~di~~~vl~~~ak~~~vt~~-v~~~sK~pvis~y~~~~~--~t~~~l~~ 459 (1710)
T KOG1070|consen 389 ------EVGLSPLPHVLGFEYADPSKKISDGKDIGFRVLTCKAKCGSVTLK-VLCVSKLPVISMYADAVK--LTHGMLSK 459 (1710)
T ss_pred ------hhhccccchhhceeecCCCcccccccceeeEEeeccceeeeeeee-eeEeecCcceEEEeeccc--cCcchhhc
Confidence 568999999999999999999999999999999998889999999 888888888887766655 55666666
Q ss_pred EeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCCCCcccccccCCCCEEEE
Q 000449 596 IEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSG 675 (1497)
Q Consensus 596 i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~~~~~~~~~~~~vG~iv~g 675 (1497)
+. .|++|+-+++.++..+|..+|.+|+.+.|.+. ...+.++ +....++++|++|.|
T Consensus 460 v~------------q~~v~~~e~~te~~~rv~~v~~v~~v~~v~~~-----~svl~lk-------~~~~nDI~iG~~V~~ 515 (1710)
T KOG1070|consen 460 VP------------QGMVPIYEVGTEVKSRVWQVFYVGKVVIVSVR-----ESVLGLK-------FLRVNDIEIGQLVPG 515 (1710)
T ss_pred cc------------cCCCCceecCCcccCccceecccCcEEEEEEe-----hHhhccc-------ccccccccccceeee
Confidence 55 56666655555555555555555555555443 1122222 233456999999999
Q ss_pred EEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeeeccccccccccccCCc
Q 000449 676 VVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSD 755 (1497)
Q Consensus 676 ~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~ 755 (1497)
+|.++++.|+.|.+. .+++.|+||..||+|++.+.+....++..|.++ |+|.++.+.+++.+++|++|++-..++|.+
T Consensus 516 ~I~~vt~~Gv~v~v~-~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~-RVl~~~~~~~~v~l~~K~slv~~~~plp~d 593 (1710)
T KOG1070|consen 516 VIRKVTPQGVEVLVT-FGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKL-RVLSVNRDRNRVALTLKKSLVNTQLPLPSD 593 (1710)
T ss_pred EEEEecCCcEEEEEe-cCceeeecChHhhhhcccccccceeeeccccEE-EEEEEEccCCeeEEEechhhhcccCCCccc
Confidence 999999999999985 367999999999999999888887788888888 899999999999999999999998889999
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 756 ASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
|+++++|+++.|+++++.++||||+|++++.||+|.+++++.++.+++++|.+||+|.++|.++|++++||.++++++.|
T Consensus 594 ~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~ 673 (1710)
T KOG1070|consen 594 FEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC 673 (1710)
T ss_pred hhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCCCcEEEEEEEEEeeceeEEEecCCCceEEEEeeeecCC----
Q 000449 836 SSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG---- 911 (1497)
Q Consensus 836 ~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~vG~~V~g~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~---- 911 (1497)
+.++..+..+||.+- .+..+.+.+.+...++|.+.+. ++.|.+...++.+
T Consensus 674 ~~a~~~~~~e~~~~g-------------------------~v~s~~~~~~tkd~viVei~~~-~~~~v~~~~~L~dg~v~ 727 (1710)
T KOG1070|consen 674 ARACVKRSVENFVKG-------------------------GVKSLKSIDKTKDSVIVEIVDQ-GITGVGVFGELVDGSVV 727 (1710)
T ss_pred HHHHHHHHHHHhhcc-------------------------ccccceeehhccccEEEEccCc-ceEEEEEEEEEccCceE
Confidence 555555555555443 3333333333333344444432 3444444443331
Q ss_pred ---------------ccccCCCEEEEEEEEEecCCCEEEEEeehhhhhhhhhcchhhHHhhhhhccccccccCCCcEEEE
Q 000449 912 ---------------ATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVHQTVNA 976 (1497)
Q Consensus 912 ---------------~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~a 976 (1497)
-.+.+||.+.++|+.++..++.+.+++++.|.+.. .++..|....|
T Consensus 728 ~~~~~~~kl~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~~-------------------~~l~k~~~~~~ 788 (1710)
T KOG1070|consen 728 VNKVLENKLRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTDLPNNA-------------------TKLLKGSYALA 788 (1710)
T ss_pred EccchhhhhhhcchhheeeecceeEEEEEEeehhhhhhhccccccccchH-------------------HHHhcCchhHH
Confidence 13689999999999999999999999999888753 35667788889
Q ss_pred EEEEEecceEEEEecCCCceEEEEeecccC-cCCCCccCcCCCCEEEEEEEeecCC-----------CcccceEEEeecc
Q 000449 977 IVEIVKENYLVLSLPEYNHSIGYASVSDYN-TQKFPQKQFLNGQSVIATVMALPSS-----------STAGRLLLLLKAI 1044 (1497)
Q Consensus 977 ~V~~v~~~~~~vsl~~~~~~~g~~~~~~~n-~~~~~~~~f~~Gq~V~~~V~~~~~~-----------~~~~~~~l~~~~~ 1044 (1497)
+|+++...+.|+++-+ .++++...++.+ ....+......||+|.++...+... ...++..+...+.
T Consensus 789 ~v~~is~~~~~~a~~~--~~i~~v~~s~~v~s~~~d~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~~~~~~ 866 (1710)
T KOG1070|consen 789 LVRSISKEGKFVAFVS--NLIALVKVSHLVDSELDDLTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKFIKVSS 866 (1710)
T ss_pred HHHhhhhheeheeecc--cccceeeccccccccccccceeeeecccceEEEecChhHHHHHHhhcchhhccceeEEEecc
Confidence 9999999999999964 488899999876 4445666777779999999887521 1111111111111
Q ss_pred cccccccccccccCCCCCCcceEEEEEEEEecCeEEEEeCCCceeeEEeeeecCCccccccccccCcCCCCEEEEEEEee
Q 000449 1045 SETETSSSKRAKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAK 1124 (1497)
Q Consensus 1045 ~~~~~~~~~~~~~~~~~~~G~~v~~~V~~vk~~~l~V~L~~~~~GrVhvsev~d~~~~~~~~Pl~~fk~G~~V~~rVl~~ 1124 (1497)
....-+..++.++.+++.+|.++.|.|++|+|+||+|.|+++.+||||+||++|++.++ .+|+++|++||.|.|||+|.
T Consensus 867 ~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~ei-tDp~~k~~vG~~I~vrviG~ 945 (1710)
T KOG1070|consen 867 NDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEI-TDPLDKFKVGDGIFVRVIGG 945 (1710)
T ss_pred ccCCCccccccccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhcccccc-CChhhhcccCCeEEEEEEcC
Confidence 11112223346678899999999999999999999999999999999999999998864 44999999999999999999
Q ss_pred e-cC-----CCCCCceEEEEeecccccccccccccc-ccccccCCCCCEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccC
Q 000449 1125 S-NK-----PDMKKSFLWELSIKPSMLTVSEIGSKL-LFEECDVSIGQRVTGYVYKVDNEWALLTISRHLKAQLFILDSA 1197 (1497)
Q Consensus 1125 ~-~~-----~~~~~~~v~eLSlr~s~l~~~~~~~~~-~~~~~~~~~G~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s 1197 (1497)
| .+ ...++.+++|||+|||.++... ... +.+ +|+.||.|+|||++++.+|+|++++|.++||||+++++
T Consensus 946 ~D~k~lpith~i~k~~v~ElSvkps~les~~--~~t~s~~--q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s 1021 (1710)
T KOG1070|consen 946 HDVKDLPITHLISKEQVLELSVKPSELESDE--FNTTSTK--QFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTS 1021 (1710)
T ss_pred CccccCccccccchhhhhhhccChhhhcccc--ccccchh--hhhcCCeEEEEEEccccceeEEEccccccceeeeeecc
Confidence 6 11 1234568999999999998443 111 222 56999999999999999999999999999999999999
Q ss_pred CCCchhhhccccCCCCCEEEEEEEEEeccCcEEEEEeccccCCCCCcccccccccccccccCCCEEEEEEEEEecCcCeE
Q 000449 1198 YEPSELQEFQRRFHIGKAVTGHVLSINKEKKLLRLVLRPFQDGISDKTVDISNDNMQTFIHEGDIVGGRISKILSGVGGL 1277 (1497)
Q Consensus 1198 ~~~~~~~~~~~~f~vG~~v~~~V~~~~~~~~~l~LS~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~g~V~~v~~~~~gl 1277 (1497)
.+...+++|+..|++|++++++|++.+.. . .+...... .+..... +|+++.|||.+++++ ++
T Consensus 1022 ~~~~~le~~e~~F~~g~al~~~V~~~~~~-~--tv~~iG~~--------~~~k~~s-----~G~~l~Grv~kv~~~--~~ 1083 (1710)
T KOG1070|consen 1022 LDLHVLELPESLFPLGKALDEYVVRNDKS-K--TVRAIGFS--------KSDKNPS-----PGDILFGRVSKVLPG--YL 1083 (1710)
T ss_pred chhhhhhCchhhcccccceeeEEecccce-e--EEEecccc--------cCCCCCC-----cchhhcceeeeeccc--ee
Confidence 99999999999999999999999999833 2 22222210 0111222 899999999999999 89
Q ss_pred EEEECCceEEEEecc-cccccccCCCCCCCCCCCCCCCCCcCCCCEEEEEEEEeecccCCccEEEEEeeccccCCCCCCC
Q 000449 1278 VVQIGPHLYGRVHFT-ELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCKVLEISRTVRGTFHVELSLRSSLDGMSSTNS 1356 (1497)
Q Consensus 1278 ~V~l~~~~~G~v~~t-dl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~Vl~~d~~~~g~~~i~lS~R~s~~~~~~~~~ 1356 (1497)
+++++++..|+++.+ +++|+|... |...|..++.+.|++|.++.. ++.+.||+|.|++++.+
T Consensus 1084 ~l~~~~~~~G~~~~i~~~~d~~~~~-----------P~~~f~~~~~v~~~~L~vs~~---n~~leLslr~sr~~~t~--- 1146 (1710)
T KOG1070|consen 1084 ILQLPFKVFGRVSFIEDMSDSYSMT-----------PVEHFTKIQIVYVCVLSVSAL---NKGLELSLRESRTKITP--- 1146 (1710)
T ss_pred EEecCCccccceEEeeehhccccCC-----------hHHhcccccEEEEEEEEEecc---cccceeecccccccCcc---
Confidence 999999999977766 999999998 889999999999999999976 66699999999843322
Q ss_pred CCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEE
Q 000449 1357 SDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSV 1436 (1497)
Q Consensus 1357 ~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~v 1436 (1497)
....++++++++|+++|++++|||.++.+.|+|+.|+++++|+++||++++.|.+.|.++|++||+|.++|+++
T Consensus 1147 ------~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~v 1220 (1710)
T KOG1070|consen 1147 ------VDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSV 1220 (1710)
T ss_pred ------ccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEe
Confidence 33468899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCeEEEEEEeCCCCcccccccCCCCCCCCCCEEEEEEEEEeeceeEEEECCe-eeccC
Q 000449 1437 EPLSKRVEVTLKTSDSRTASQSEINNLSNLHVGDIVIGQIKRVESYGLFITIENT-NLVRN 1496 (1497)
Q Consensus 1437 d~~~~~i~lslk~~~~~~~~~~~~~~~~d~~~G~iv~G~V~~v~~~GvFV~l~~s-~~~~~ 1496 (1497)
+...+||+|+|++++...... ...++.++++||...|+|+++.+||+||+|++| |++|+
T Consensus 1221 e~~s~riel~Lk~s~~~d~~~-~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~ 1280 (1710)
T KOG1070|consen 1221 EEDSKRIELSLKNSDIKDTVK-LLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGL 1280 (1710)
T ss_pred eccCceEEEEEeccccCCchh-hhhhhhhhhccccccceEEEecCCceEEEecCcceeccc
Confidence 999999999999998863222 367889999999999999999999999999999 89886
No 2
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=100.00 E-value=2.2e-89 Score=843.29 Aligned_cols=1130 Identities=22% Similarity=0.258 Sum_probs=892.4
Q ss_pred eeecccccCCcCCCCEEEEEEEEEeCceEEEEcC-CCcEEEEeccccCChhhcccccccccCCCCCccCCCCEEEEEEEE
Q 000449 121 RYANKITLKNISAGMKLWGVVAEVNEKDLVICLP-GGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQ 199 (1497)
Q Consensus 121 ~~~e~l~~k~l~~G~~vlG~V~~i~~~~l~vslp-~~l~G~v~~~~is~~~~~~~~~~~~~~~L~~~f~vGq~v~~~V~~ 199 (1497)
+...+||-..+.+|+.+-+.|.++.+++-+++.+ ..++|++-..++ ..+...|++|||++|.|++
T Consensus 144 v~~t~lS~~~~~~~~~l~~~v~S~ed~g~~l~~g~~~~~~~~e~~q~--------------pn~~~~lKvGq~l~~~V~k 209 (1710)
T KOG1070|consen 144 VLNTHLSDEMLAAGEVLDTAVVSIEDHGAILDVGLDEITGFIEKSQF--------------PNLGAKLKVGQWLRVSVTK 209 (1710)
T ss_pred ccccccCHhHhhhhhhhccccccccccccchhcCCccccchhhhccC--------------chhhhhcccCceEEEEEEe
Confidence 3467899999999999999999999999999885 122333322222 2567889999999999998
Q ss_pred EecCC-cccceeEEEEecchhhHhcCCCcccccCCcEEEEEEEEEEeCeEEEEeCCCCeEEEeeCCCCCCCCCCcCCCCc
Q 000449 200 LDDDK-KEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGL 278 (1497)
Q Consensus 200 ~~~~~-~~~~~~~i~LSl~p~~vn~~l~~~~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~ 278 (1497)
..... ....++++++++.|...| +|..++|.|||.++|.|.||||||+++|| +.+++|||++.++++.. .+.+||
T Consensus 210 ~~s~~v~ks~~~~~~~t~~~t~~~-~~~~~~LvpGt~vqa~V~sv~~~Gi~~di-l~~ftG~l~~~hl~~~~--~~~~~~ 285 (1710)
T KOG1070|consen 210 STSERVVKSTKFVEVLTLNPTSCN-GLALNDLVPGTMVQAEVQSVEDHGITLDI-LNGFTGFLDKKHLPPFL--RYFENQ 285 (1710)
T ss_pred ccCceEEecccceeeecccchhcc-ccchhhcCCcceEEEEecceecCcEEEEe-cccccceeehhhCCchh--hccccH
Confidence 65411 111367999999999999 89999999999999999999999999999 79999999999997655 588999
Q ss_pred EEEEEEEEEcCCCcEEEEccCccccccccccccccccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCC
Q 000449 279 LLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTF 358 (1497)
Q Consensus 279 ~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~ 358 (1497)
.++|.|+... .|++.+.+.. -..+... -..+++.+.||.++.-....+.+.|..+++.+--.+..+..|+....
T Consensus 286 ~~l~~vi~~s--~Rv~~~~f~~--ka~ki~~--l~~~v~ai~p~~~~~~~~~e~~k~G~~~K~~vi~~~~~~~~~~~tl~ 359 (1710)
T KOG1070|consen 286 EKLGKVIHKS--DRVFVVDFFD--KASKILV--LKAGVDAIAPSRIEKVLSFEIFKIGNKVKCRVIDVLQMDSLALFTLK 359 (1710)
T ss_pred HHhhcccchh--hheeeechhh--ccceEEE--ecCccceEccCCcccccchhhcccCceEEEEEEEEeeccceEEeecc
Confidence 9999987643 6776665511 1111111 13467889999999999999999999999887777777888887665
Q ss_pred CCCCCcccCCCCCEEEEEEEEEeC---CCceEEEecchhhhccCC--C----CCCCCCCCeEEceEEEEEeCCceEEEEe
Q 000449 359 PTTNWKNDYNQHKKVNARILFVDP---TSRAVGLTLNPYLLHNRA--P----PSHVKVGDIYDQSKVVRVDRGLGLLLDI 429 (1497)
Q Consensus 359 ~~~~~~~~~~vG~~v~arVl~~~~---~~~~i~LSl~p~~~~~~~--~----~~~~~~G~iv~~~~V~~v~~~~G~~v~l 429 (1497)
+ .+++..|..+.-|++|++..-| .+-.+.+|-+||+..+.. + ....++|.++-+|..+...--++.++..
T Consensus 360 ~-s~ie~k~~~~s~V~~r~l~~~~~svdt~~~~l~~L~hv~~f~~a~p~~~~~~~~di~~~vl~~~ak~~~vt~~v~~~s 438 (1710)
T KOG1070|consen 360 E-SAIEGKFSLVSDVSPRGLLKKPVSVDTEEVGLSPLPHVLGFEYADPSKKISDGKDIGFRVLTCKAKCGSVTLKVLCVS 438 (1710)
T ss_pred h-hhccCceEEEeccCCceEEEecccCChhhhhccccchhhceeecCCCcccccccceeeEEeeccceeeeeeeeeeEee
Confidence 4 4788899999999999998766 233789999999987432 2 2456666666666666655444666666
Q ss_pred CCCCCccceeeeeccchhHHHhhc----ccccCCCCEEEEEEEEEecCCCeEEEEcchhhcccccccccccCCCcEEEEE
Q 000449 430 PSTPVSTPAYVTISDVAEEEVRKL----EKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGK 505 (1497)
Q Consensus 430 ~~~~~~v~gfv~~s~~~~~~~~~~----~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~ 505 (1497)
.. +.+.+|++...+....+... ...|++|+++.|||..|.+.+..++||+.++.+..++.+.+||++|++|.|+
T Consensus 439 K~--pvis~y~~~~~~t~~~l~~v~q~~v~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nDI~iG~~V~~~ 516 (1710)
T KOG1070|consen 439 KL--PVISMYADAVKLTHGMLSKVPQGMVPIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVNDIEIGQLVPGV 516 (1710)
T ss_pred cC--cceEEEeeccccCcchhhccccCCCCceecCCcccCccceecccCcEEEEEEehHhhcccccccccccccceeeeE
Confidence 54 23589999888776655554 2359999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCeeEEEeCCC-eEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeEEEEeecchhhhhhhHHhhhhh
Q 000449 506 VIAVDSFGAIVQFPGG-VKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYAE 582 (1497)
Q Consensus 506 V~~v~~~G~~V~i~~g-v~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~~~ 582 (1497)
|.++++.|+.|.+..+ +.|++|..||+|.+...|...|++|..+++|||.+ +.+++.||+|++|++..+|....|++
T Consensus 517 I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~ 596 (1710)
T KOG1070|consen 517 IRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQ 596 (1710)
T ss_pred EEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhh
Confidence 9999999999998765 99999999999999999999999999999999999 68999999999999999999999999
Q ss_pred ccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCCCCc-
Q 000449 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRV- 661 (1497)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~~~~~- 661 (1497)
+.+|+++.|+|..+.++||||+|++|++||+|.++|+..++.+++++|.+||++.+.|+++|++++||.+||+.+.+..
T Consensus 597 ~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~~~a 676 (1710)
T KOG1070|consen 597 AIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSCARA 676 (1710)
T ss_pred cCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhhHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999987522
Q ss_pred ---ccccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccc-cccccccc---------cCCCCeEe-EE
Q 000449 662 ---SEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLE-HATVMKSV---------IKPGYEFD-QL 727 (1497)
Q Consensus 662 ---~~~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~-~~~~~~~~---------~k~G~~l~-~v 727 (1497)
...+.+..|.+..+.+.+++.+.++|++. ..++.|++...||.|... .+..+..+ +.+|+... ++
T Consensus 677 ~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~-~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~~t~~~~lv~gq~~~~~i 755 (1710)
T KOG1070|consen 677 CVKRSVENFVKGGVKSLKSIDKTKDSVIVEIV-DQGITGVGVFGELVDGSVVVNKVLENKLRKNTSLLHLVVGQVTVGVI 755 (1710)
T ss_pred HHHHHHHHhhccccccceeehhccccEEEEcc-CcceEEEEEEEEEccCceEEccchhhhhhhcchhheeeecceeEEEE
Confidence 23457888989999999999999999993 247999999999998431 22212222 34677666 66
Q ss_pred EEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcC
Q 000449 728 LVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYY 807 (1497)
Q Consensus 728 l~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~ 807 (1497)
+.+|..+..+.++.++. +|....++..|....++|.+|+..|.|+.|..++.++++.+++.+....+... ..
T Consensus 756 ~~isl~k~lv~~s~~~~-------L~~~~~~l~k~~~~~~~v~~is~~~~~~a~~~~~i~~v~~s~~v~s~~~d~~~-~~ 827 (1710)
T KOG1070|consen 756 LSISLKKSLVLISLCTD-------LPNNATKLLKGSYALALVRSISKEGKFVAFVSNLIALVKVSHLVDSELDDLTK-AE 827 (1710)
T ss_pred EEeehhhhhhhcccccc-------ccchHHHHhcCchhHHHHHhhhhheeheeecccccceeeccccccccccccce-ee
Confidence 66666555555555555 44445667889999999999999999999999999999999987766555543 33
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCCCcEEEEEEEEEee
Q 000449 808 VGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESND 887 (1497)
Q Consensus 808 ~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~vG~~V~g~V~~i~~ 887 (1497)
.||.|.|++.++++......++++.....
T Consensus 828 y~Q~v~~~~~st~~~~~~~~~a~e~p~~K--------------------------------------------------- 856 (1710)
T KOG1070|consen 828 YGQSVTVKLLSTEPKVVKDLKAVEKPKKK--------------------------------------------------- 856 (1710)
T ss_pred eecccceEEEecChhHHHHHHhhcchhhc---------------------------------------------------
Confidence 45999999999887655555544433210
Q ss_pred ceeEEEecCCCceEEEEeeeecCCccccCCCEEEEEEEEEecCCCEEEEEeehhhhhhhhhcchhhHHhhhhhccccccc
Q 000449 888 FGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKD 967 (1497)
Q Consensus 888 ~G~~v~l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 967 (1497)
+.+ .....+.+..+.-++.+++ ...+
T Consensus 857 -----------------------------~~~-~~~~~~~~~~d~~Vd~a~k------------------------~~~~ 882 (1710)
T KOG1070|consen 857 -----------------------------KEK-KFIKVSSNDSDNEVDLAIK------------------------STED 882 (1710)
T ss_pred -----------------------------cce-eEEEeccccCCCccccccc------------------------cccc
Confidence 000 0000011111122222221 2467
Q ss_pred cCCCcEEEEEEEEEecceEEEEecCCCceEEEEeecccC----cCCCCccCcCCCCEEEEEEEeecCCCcccceEEEeec
Q 000449 968 LGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYN----TQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKA 1043 (1497)
Q Consensus 968 l~~G~~v~a~V~~v~~~~~~vsl~~~~~~~g~~~~~~~n----~~~~~~~~f~~Gq~V~~~V~~~~~~~~~~~~~l~~~~ 1043 (1497)
+.+|+.++|+|..|+++.+.+.|. .+..|-++.++.- +--.|..+|++|+.|.++|+...... .++....-
T Consensus 883 ~~igsiv~a~v~svKp~~L~v~l~--~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k---~lpith~i 957 (1710)
T KOG1070|consen 883 LSIGSIVRAYVKSVKPDQLNVLLA--ANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVK---DLPITHLI 957 (1710)
T ss_pred eeeeeEEEEEEeeecccceEEecc--ccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCccc---cCcccccc
Confidence 899999999999999999999985 5567888887662 12237889999999999999874221 12222110
Q ss_pred ----ccccccc----cccc--cccCCCCCCcceEEEEEEEEecCeEEEEeCCCceeeEEeeeecCCccccccccccCcCC
Q 000449 1044 ----ISETETS----SSKR--AKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKI 1113 (1497)
Q Consensus 1044 ----~~~~~~~----~~~~--~~~~~~~~~G~~v~~~V~~vk~~~l~V~L~~~~~GrVhvsev~d~~~~~~~~Pl~~fk~ 1113 (1497)
..+..+. .+.. .+....++.|+.|.|.|..+....+.|.+...+.|||.+-.+.-+.. ..++|=+.|..
T Consensus 958 ~k~~v~ElSvkps~les~~~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~-~le~~e~~F~~ 1036 (1710)
T KOG1070|consen 958 SKEQVLELSVKPSELESDEFNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLH-VLELPESLFPL 1036 (1710)
T ss_pred chhhhhhhccChhhhccccccccchhhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhh-hhhCchhhccc
Confidence 0110000 0111 22235789999999999999999999999999999999888764433 24788899999
Q ss_pred CCEEEEEEEeee-cCCCCCCceEEEEeeccccccccccccccccccccCCCCCEEEEEEEEEeCCEEEEEEcCCeEEEEE
Q 000449 1114 GQTVTARIIAKS-NKPDMKKSFLWELSIKPSMLTVSEIGSKLLFEECDVSIGQRVTGYVYKVDNEWALLTISRHLKAQLF 1192 (1497)
Q Consensus 1114 G~~V~~rVl~~~-~~~~~~~~~v~eLSlr~s~l~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~~l~V~ls~~~~g~i~ 1192 (1497)
|+.++|.|++.+ |+ ++.-++.-. +.+ ...+|++.-|.|..+..+++.+++.+..-|++.
T Consensus 1037 g~al~~~V~~~~~~~------tv~~iG~~~------------~~k--~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~ 1096 (1710)
T KOG1070|consen 1037 GKALDEYVVRNDKSK------TVRAIGFSK------------SDK--NPSPGDILFGRVSKVLPGYLILQLPFKVFGRVS 1096 (1710)
T ss_pred ccceeeEEeccccee------EEEeccccc------------CCC--CCCcchhhcceeeeeccceeEEecCCccccceE
Confidence 999999998876 11 111111111 111 236899999999999999999999999999877
Q ss_pred ee-ccCCCCchhhhccccCCCCCEEEEEEEEEeccCcEEEEEeccccCCCC-----CcccccccccccccccCCCEEEEE
Q 000449 1193 IL-DSAYEPSELQEFQRRFHIGKAVTGHVLSINKEKKLLRLVLRPFQDGIS-----DKTVDISNDNMQTFIHEGDIVGGR 1266 (1497)
Q Consensus 1193 ~~-~~s~~~~~~~~~~~~f~vG~~v~~~V~~~~~~~~~l~LS~~~~~~~~~-----~~~~~~~~~~~~~~l~~G~~v~g~ 1266 (1497)
.. +++++++ .+|...|-.++.+.+.++.++...+-++||+|.+..... +....+.++++ .|+++.|+
T Consensus 1097 ~i~~~~d~~~--~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk-----~g~iv~G~ 1169 (1710)
T KOG1070|consen 1097 FIEDMSDSYS--MTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLK-----IGDIVRGF 1169 (1710)
T ss_pred Eeeehhcccc--CChHHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcc-----cCceeEEE
Confidence 76 8888765 468889999999999999999888779999996544221 12222335555 99999999
Q ss_pred EEEEecCcCeEEEEECCceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEEEEEeecccCCccEEEEEeec
Q 000449 1267 ISKILSGVGGLVVQIGPHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCKVLEISRTVRGTFHVELSLRS 1346 (1497)
Q Consensus 1267 V~~v~~~~~gl~V~l~~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~Vl~~d~~~~g~~~i~lS~R~ 1346 (1497)
|..+.+. |+++.|++++.+++++++++|.|... ....|++|+.|.++|+.++.. .+++.|||++
T Consensus 1170 V~nv~~~--glfi~ls~~v~a~v~is~~~ds~~k~-----------w~k~~~~gklv~~rv~~ve~~---s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1170 VKNVETK--GLFIALSRKVEAFVPISGLSDSFEKE-----------WEKHLPVGKLVTGRVLSVEED---SKRIELSLKN 1233 (1710)
T ss_pred EEEecCC--cEEEEEccceEEEEEccccccchhhh-----------hhccCCccceeeeEEEEeecc---CceEEEEEec
Confidence 9999999 99999999999999999999999876 677899999999999999976 6799999999
Q ss_pred cccCCCCCCCCCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEeceeEEEEeCCCe--EEEEEccccCCCcccCCCCccC
Q 000449 1347 SLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKL--DAKVLLSNLSDGYVESPEKEFP 1424 (1497)
Q Consensus 1347 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~--~g~v~is~lsd~~~~~~~~~~~ 1424 (1497)
+. .. + .........+|++||.+.|+|.++.++|.||++.+++ .|++|+++++|+..++....|.
T Consensus 1234 s~-----~~--------d-~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~ 1299 (1710)
T KOG1070|consen 1234 SD-----IK--------D-TVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYY 1299 (1710)
T ss_pred cc-----cC--------C-chhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhccccee
Confidence 86 21 0 0114455789999999999999999999999999876 9999999999999999999999
Q ss_pred CCCEEEEEEEEEcCCCCeEEEEEEeCCCCc
Q 000449 1425 IGKLVAGRVLSVEPLSKRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1425 ~g~~V~~~V~~vd~~~~~i~lslk~~~~~~ 1454 (1497)
.|+.|++.++..+.+.++|.|.++.+....
T Consensus 1300 ~~~~V~a~~lk~~~ek~rIsl~~k~s~~~~ 1329 (1710)
T KOG1070|consen 1300 AGDRVKACVLKEDSEKKRISLGLKSSYLSS 1329 (1710)
T ss_pred ccceeeeEeeeccchhhhhhhhhhhhccCC
Confidence 999999999999999999999999886643
No 3
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-67 Score=625.20 Aligned_cols=491 Identities=23% Similarity=0.286 Sum_probs=443.9
Q ss_pred ccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecch
Q 000449 314 ISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1497)
Q Consensus 314 ~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p 393 (1497)
.+...+.||++|.|+|++|.+++++|+++++.+|+||+.+++.... ...|++|+.+.+.|+.+.++...+.||.+.
T Consensus 14 ~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~----~~~~~~gd~v~v~v~~~e~~~g~~~lS~~k 89 (541)
T COG0539 14 KSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPV----EDVVQVGDEVEVLVLRVEDGEGELVLSRRK 89 (541)
T ss_pred cchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccc----cceecCCCEEEEEEEEEecCCceEEeeHHH
Confidence 4678899999999999999999999999999999999999987753 237999999999999999988999999987
Q ss_pred hhhc--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEe
Q 000449 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1497)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~ 471 (1497)
.... |.....++..|.+++ ++|....++ |+.|++. +++||+|.|+++..+++++. -.+|.++.+.|++++
T Consensus 90 ~~~~~~w~~l~~~~e~~~~V~-~~v~~~vKG-G~~Vdi~----gvr~FlP~S~v~~r~v~d~~--~~~Gk~~~~kiie~d 161 (541)
T COG0539 90 AERERAWEKLEEAFENGEIVE-GKITGKVKG-GLTVDIE----GVRAFLPGSLVDVRPVRDLD--PLIGKELEFKILELD 161 (541)
T ss_pred HHHHHhHHHHHHHHhcCCeEE-EEEEEEecC-cEEEEEC----CEEEeccHHHhccccccccc--ccCCceEEEEEEEEc
Confidence 6554 666667899999998 577777788 9999996 36999999999988887764 479999999999999
Q ss_pred cCCCeEEEEcchhhc----ccccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCC
Q 000449 472 HLEGLATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGA 547 (1497)
Q Consensus 472 ~~~~~~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~ 547 (1497)
..++.+++|++.... ++++..++++++|++|+|+|++++++|+||+|+ |++|++|.+||||.++.+|++.|++||
T Consensus 162 ~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd 240 (541)
T COG0539 162 KKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGD 240 (541)
T ss_pred cccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec-CeeeEEehhhccccccCCHHHhcccCC
Confidence 999999999887765 456788999999999999999999999999998 699999999999999999999999999
Q ss_pred EEEEEEEEE--eCCeEEEEeecchhhhhhhHHhhh-hhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCC
Q 000449 548 ELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGC 624 (1497)
Q Consensus 548 ~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~ 624 (1497)
+|+|+|+++ +++||.||+|+++.+ +|..+ +.+.+|+.+.|+|+++.+|||||++++|++||+|+|||+|.+..
T Consensus 241 ~VkvkVi~~D~e~~RVsLSlK~l~~d----Pw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~ 316 (541)
T COG0539 241 EVKVKVISLDEERGRVSLSLKQLEED----PWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKN 316 (541)
T ss_pred EEEEEEEEEccCCCeEEEEehhcccC----cHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccC
Confidence 999999999 689999999999886 45554 45679999999999999999999999999999999999999888
Q ss_pred CCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCC
Q 000449 625 EPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTE 702 (1497)
Q Consensus 625 ~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~ 702 (1497)
.|++++++||+|.|+|++||++++||+||||+. .+||.. ...+++|+.++|+|.+++++|+|+.+ +++++|+++.+
T Consensus 317 ~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~l--e~gidG~vh~~ 394 (541)
T COG0539 317 VPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVEL--EGGIDGLVHLS 394 (541)
T ss_pred CHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEcc--CCCccceEEHH
Confidence 899999999999999999999999999999996 467765 44699999999999999999999999 78899999888
Q ss_pred ccccccccccccccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEe
Q 000449 703 HLADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRF 781 (1497)
Q Consensus 703 hLsd~~~~~~~~~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~ 781 (1497)
+++|.....+. ..|+.|++++ .+|.+|.+++++.|+.|++..+||+.. ...++.|+.++|+|+++.++|+||+|
T Consensus 395 d~sw~~~~~~~--~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~---~~~~~~~~~v~~~v~~i~~~G~~v~l 469 (541)
T COG0539 395 DLSWDRPGEEA--EKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEF---SEKYKKGSVVKGKVKSVKDKGAFVEL 469 (541)
T ss_pred hcCccccCcHH--HhhccCcEEEEEEEEEecccceeeeehhhhccCchhhh---HhhccCCCeEEEEEEEEccCceEEEe
Confidence 88774433222 2899999999 999999999999999999999999753 34589999999999999999999999
Q ss_pred CCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 782 LGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 782 ~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.++++||+|.++++.. .|++||+|.|+|+++|+.++++.||+|....
T Consensus 470 ~~~v~G~i~~~~~~~~-------~~~~gd~v~a~v~~id~k~~ki~lSik~~~~ 516 (541)
T COG0539 470 GGGVEGLIRLSELSRD-------VLKVGDEVEAVVVSIDKKNRKILLSIKALER 516 (541)
T ss_pred cCceeeeeecchhhhh-------hccCCCEEEEEEEEEcCCCCEEEEEechhhh
Confidence 9999999999999864 8999999999999999999999999998864
No 4
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-62 Score=582.01 Aligned_cols=495 Identities=24% Similarity=0.327 Sum_probs=439.5
Q ss_pred CCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEc
Q 000449 402 PSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGIL 481 (1497)
Q Consensus 402 ~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~ 481 (1497)
...+.+|+++.| +|..+++. +++|+++.+ .+|++|+++++..+... .|++|+.+.+.|+.....++.+++|.
T Consensus 16 ~~~~~~G~vV~G-~Vv~i~~~-~v~Vdig~K---seg~ip~~E~~~~~~~~---~~~~gd~v~v~v~~~e~~~g~~~lS~ 87 (541)
T COG0539 16 DEEFEPGDVVKG-TVVSIEKD-GVLVDIGGK---SEGVIPISEFSNEPVED---VVQVGDEVEVLVLRVEDGEGELVLSR 87 (541)
T ss_pred hhccCCCCEEEE-EEEEEeCC-eEEEEecCc---cccEeEHHHhccccccc---eecCCCEEEEEEEEEecCCceEEeeH
Confidence 457899999985 78889998 899999964 38999999998755433 48999999999999999899999998
Q ss_pred chhhcc-cccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eC
Q 000449 482 KASAFE-GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KS 558 (1497)
Q Consensus 482 k~~~~~-~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~ 558 (1497)
++.... .|......+..|.+|+|+|+...+.|++|+++ |+.||+|.+|++..+..+. .-.+|.+++++|+.+ ++
T Consensus 88 ~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~-gvr~FlP~S~v~~r~v~d~--~~~~Gk~~~~kiie~d~~~ 164 (541)
T COG0539 88 RKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIE-GVRAFLPGSLVDVRPVRDL--DPLIGKELEFKILELDKKR 164 (541)
T ss_pred HHHHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEEC-CEEEeccHHHhcccccccc--cccCCceEEEEEEEEcccc
Confidence 876554 46666778899999999999999999999998 6999999999987544443 235999999999999 68
Q ss_pred CeEEEEeecchhhhhhhH-HhhhhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEE
Q 000449 559 KRITVTHKKTLVKSKLAI-LSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVK 637 (1497)
Q Consensus 559 ~~i~lS~K~~l~~~~~~~-~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~ 637 (1497)
+++.+|+|..+....... ...++++++|+++.|+|+++++|||||++ +|++||+|++||+|.++.+|++.|++||+|+
T Consensus 165 n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi-gGvdGLlHiseiS~~rv~~P~~vvkvGd~Vk 243 (541)
T COG0539 165 NNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHPSEVVKVGDEVK 243 (541)
T ss_pred CcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEe-cCeeeEEehhhccccccCCHHHhcccCCEEE
Confidence 899999999887544322 22356788999999999999999999999 5699999999999999999999999999999
Q ss_pred EEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccc
Q 000449 638 CRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMK 715 (1497)
Q Consensus 638 v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~ 715 (1497)
|+|+++|++++|++||+|+. .+||.. ...+++|+.+.|+|+++++||+||++ ..|++||+|.+++|+..... +.
T Consensus 244 vkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei--~~GvEGlvhvSEisw~~~~~--P~ 319 (541)
T COG0539 244 VKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEI--EEGVEGLVHVSEISWTKKNV--PS 319 (541)
T ss_pred EEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEe--cCCccceeechhhcccccCC--HH
Confidence 99999999999999999986 468876 56899999999999999999999999 88999999888887643222 67
Q ss_pred cccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCC
Q 000449 716 SVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKA 794 (1497)
Q Consensus 716 ~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sel 794 (1497)
+.+++||+++ ++|.+|++++||+||+|++..+||+... ..+++|+.+.|.|.++|++|+||.+.+|++||+|.+++
T Consensus 320 evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~---~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~ 396 (541)
T COG0539 320 EVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFA---DKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDL 396 (541)
T ss_pred HhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhh---hhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhc
Confidence 7899999999 9999999999999999999999998654 34899999999999999999999999999999999999
Q ss_pred CcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCC
Q 000449 795 VDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFII 874 (1497)
Q Consensus 795 s~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~v 874 (1497)
+|.....+...|+.|+.+.|+|+.+|++++|+.|++|++.. +||+. +...|+.
T Consensus 397 sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~------------~p~~~---------------~~~~~~~ 449 (541)
T COG0539 397 SWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEE------------SPWEE---------------FSEKYKK 449 (541)
T ss_pred CccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhcc------------Cchhh---------------hHhhccC
Confidence 99888888779999999999999999999999999999976 34522 3566999
Q ss_pred CcEEEEEEEEEeeceeEEEecCCCceEEEEeeeecCCccccCCCEEEEEEEEEecCCCEEEEEeehhhhh
Q 000449 875 GSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFID 944 (1497)
Q Consensus 875 G~~V~g~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~l~~ 944 (1497)
|+.|+|+|.++.++|+++.+.+ ++.||++.++++...+++||+|+|+|+.+|+.++++.||+|+...+
T Consensus 450 ~~~v~~~v~~i~~~G~~v~l~~--~v~G~i~~~~~~~~~~~~gd~v~a~v~~id~k~~ki~lSik~~~~~ 517 (541)
T COG0539 450 GSVVKGKVKSVKDKGAFVELGG--GVEGLIRLSELSRDVLKVGDEVEAVVVSIDKKNRKILLSIKALERK 517 (541)
T ss_pred CCeEEEEEEEEccCceEEEecC--ceeeeeecchhhhhhccCCCEEEEEEEEEcCCCCEEEEEechhhhh
Confidence 9999999999999999999997 6899999999998899999999999999999999999999987654
No 5
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.3e-59 Score=597.35 Aligned_cols=494 Identities=20% Similarity=0.246 Sum_probs=425.4
Q ss_pred cccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecc
Q 000449 313 GISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLN 392 (1497)
Q Consensus 313 ~~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~ 392 (1497)
..++..+.+|++|.|+|.+|++++++|+++++.+|+||..++.. .+++|++|+|+|+.+++. + +.||+.
T Consensus 313 ~~~~~~~~~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~---------~~kvGd~i~~~V~~~~~~-~-~~LS~~ 381 (863)
T PRK12269 313 RYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA---------PPKAGDGVRVYVERVTPY-G-PELSKT 381 (863)
T ss_pred hhccccCCCCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhcc---------CCCCCCEEEEEEEEEcCC-c-eEEEeh
Confidence 44578899999999999999999999999999999999999832 378999999999998875 3 789987
Q ss_pred hhhh--ccCCCCCCCCCCCeEEceEEEEEe--CCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEE
Q 000449 393 PYLL--HNRAPPSHVKVGDIYDQSKVVRVD--RGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRIL 468 (1497)
Q Consensus 393 p~~~--~~~~~~~~~~~G~iv~~~~V~~v~--~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi 468 (1497)
.... .|+...+++..|++++ ++|.+++ ++ |++|+++. +++||||.|+++....++++ ..+|++++|.|+
T Consensus 382 ~~~~~~~~~~l~~a~~~g~~V~-G~Vv~v~~~kg-G~~Vdig~---~~~gfiP~se~~~~~~~~~~--~~vG~~ie~~V~ 454 (863)
T PRK12269 382 KADRLGLKVKLRDAERDGTPVE-GRIVRLTEKKS-GFEVDLGA---GMMAFLPISQSDCQKVDAPE--SLIGLTSKFYIE 454 (863)
T ss_pred HhhhhHHHHHHHHHHhCCCeEE-EEEEEEEeecC-EEEEEECC---CcEEEEEHHHhccccccchH--HhCCCeEEEEEE
Confidence 5532 2555668899999998 5777763 46 99999963 25999999999765555443 369999999999
Q ss_pred EEec-----CCCeEEEEcchhhccc----ccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCC
Q 000449 469 GFRH-----LEGLATGILKASAFEG----LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKP 539 (1497)
Q Consensus 469 ~~~~-----~~~~~~lS~k~~~~~~----~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~ 539 (1497)
.++. .++.+++|++....+. ....++++++|++|+|+|.++.++|+||+++ |++||||.+|++|.+..+|
T Consensus 455 ~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~ 533 (863)
T PRK12269 455 RISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARP 533 (863)
T ss_pred EEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCH
Confidence 9875 3468999988754332 2334578999999999999999999999996 8999999999999988899
Q ss_pred CccccCCCEEEEEEEEE--eCCeEEEEeecchhhhhhhHHhhh-hhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecc
Q 000449 540 GKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRS 616 (1497)
Q Consensus 540 ~~~~kvG~~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~s 616 (1497)
.+.|++|++++|+|+.+ +++++.||+|+.+.+ +|..+ +.+.+|+++.|+|+++.+||+||++.+|++||+|+|
T Consensus 534 ~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~----p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiS 609 (863)
T PRK12269 534 REFVKKGQTIELKVIRLDQAEKRINLSLKHFQPD----PWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHIS 609 (863)
T ss_pred HHhccCCCEEEEEEEEEecCCCeEEEEEeccccc----hhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHH
Confidence 98899999999999999 478999999997654 45554 457899999999999999999999988999999999
Q ss_pred cccC-CCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecC
Q 000449 617 ELGL-DPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKG 693 (1497)
Q Consensus 617 el~~-~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~ 693 (1497)
|++| .+..+|.+.|++||+|+|+|+++|++++|+.||+|+. .+||.. .+.+++|++++|+|++++++|+||++ .+
T Consensus 610 Els~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l--~~ 687 (863)
T PRK12269 610 EFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEM--EE 687 (863)
T ss_pred HhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEe--CC
Confidence 9999 5678999999999999999999999999999999985 467866 46799999999999999999999999 78
Q ss_pred cEEEEEcCCccccccccccccccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEE
Q 000449 694 YSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNI 772 (1497)
Q Consensus 694 ~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i 772 (1497)
|++|+||.++||+.... ......+++||.++ +++.+|+++++|.||+|+++.+||+.+ .+++++|+.+.|+|+++
T Consensus 688 gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~---~~~~~vG~iV~GkV~~v 763 (863)
T PRK12269 688 GIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVF---ANAYGVGSTVEGEVSSV 763 (863)
T ss_pred CcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHH---HhhCCCCCEEEEEEEEE
Confidence 99999998888763311 12345799999999 999999999999999999999999753 34588999999999999
Q ss_pred ecceEEEEeCCCeEEEEeCCCCCcccccCcc---cCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 773 IETGCFVRFLGRLTGFAPRSKAVDGQRADLS---KTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 773 ~~~G~FV~~~~gl~Glvp~sels~~~~~~~~---~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
+++|+||++.++++||+|.++++|++..++. ..|++||.|.|+|+++|+++++|.||+|+...
T Consensus 764 ~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~~~~ 829 (863)
T PRK12269 764 TDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQR 829 (863)
T ss_pred ecCeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEechhh
Confidence 9999999999999999999999998765443 45999999999999999999999999997754
No 6
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.5e-58 Score=582.21 Aligned_cols=496 Identities=20% Similarity=0.255 Sum_probs=437.9
Q ss_pred cccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecchhhh
Q 000449 317 DLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLL 396 (1497)
Q Consensus 317 ~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p~~~ 396 (1497)
..+.+|++|+|+|.++.++|++|+++++.+|++|..|++... ....|++|++++|+|+.+++..+++.||+++...
T Consensus 26 ~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~----~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~ 101 (565)
T PRK06299 26 SETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ----GELEVKVGDEVEVYVERIEDGFGETVLSREKAKR 101 (565)
T ss_pred ccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc----ccccCCCCCEEEEEEEEEECCCCcEEEechHHHH
Confidence 457899999999999999999999988899999999998542 2247999999999999999988999999987754
Q ss_pred c--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCC
Q 000449 397 H--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLE 474 (1497)
Q Consensus 397 ~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~ 474 (1497)
. |....+++..|++++ ++|..+.++ |++|+++ +++||+|.|++++....++. +.+|++++|+|++++...
T Consensus 102 ~~~~~~l~~~~~~g~~v~-g~V~~~~~~-G~~V~~~----g~~gfip~s~~~~~~~~~~~--~~vG~~i~~~V~~~d~~~ 173 (565)
T PRK06299 102 LEAWDKLEKAFENGEIVE-GVINGKVKG-GFTVDLN----GVEAFLPGSQVDVRPVRDTD--PLEGKELEFKVIKLDKKR 173 (565)
T ss_pred HHHHHHHHHHhhCCCEEE-EEEEEEECC-EEEEEEC----CEEEEEEHHHccCcCCCChH--HhCCCEEEEEEEEEECCC
Confidence 3 555567889999998 578888887 9999997 36999999999987665554 579999999999999999
Q ss_pred CeEEEEcchhhcc----cccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEE
Q 000449 475 GLATGILKASAFE----GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELV 550 (1497)
Q Consensus 475 ~~~~lS~k~~~~~----~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~ 550 (1497)
+.+.+|+++...+ ++...++++++|++++|+|+++.++|+||+++ |++|+||.++++|.+..+|.+.|++|++|+
T Consensus 174 ~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~ 252 (565)
T PRK06299 174 NNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVK 252 (565)
T ss_pred CEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEE
Confidence 9999999987643 23445678999999999999999999999998 999999999999998889999999999999
Q ss_pred EEEEEE--eCCeEEEEeecchhhhhhhHHhhh-hhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCC-CCCCC
Q 000449 551 FRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLD-PGCEP 626 (1497)
Q Consensus 551 ~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~-~~~~~ 626 (1497)
|+|+++ +++++.||+|++..+ +|..+ +.+++|+++.|+|+++.++|+||++.+++.||+|.++++|. ...+|
T Consensus 253 v~V~~~d~~~~~i~lS~k~~~~~----p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~ 328 (565)
T PRK06299 253 VKVLKFDKEKKRVSLGLKQLGED----PWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHP 328 (565)
T ss_pred EEEEEEeCCCCeEEEEEEecccC----hhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCH
Confidence 999999 478999999987764 45554 35789999999999999999999999899999999999985 45677
Q ss_pred CCCccCCCEEEEEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCcc
Q 000449 627 SSMYHVGQVVKCRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHL 704 (1497)
Q Consensus 627 ~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hL 704 (1497)
.+.|++||.|+|+|+++|++++++.||+++. .+||.. ...+++|+++.|+|..++++|+||++ +++++|++|.++|
T Consensus 329 ~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l--~~~v~g~i~~s~l 406 (565)
T PRK06299 329 SKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGL--EGGIDGLVHLSDI 406 (565)
T ss_pred HHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEEC--CCCCEEEEEHHHc
Confidence 7889999999999999999999999999975 356653 34688999999999999999999999 6799999988888
Q ss_pred ccccccccccccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCC
Q 000449 705 ADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLG 783 (1497)
Q Consensus 705 sd~~~~~~~~~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~ 783 (1497)
++... ...+.+.+++||.++ +++.+|.++++|.||+|++..+||... .+++++|+++.|+|+++.++|+||++.+
T Consensus 407 ~~~~~-~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~---~~~~~~G~vV~G~V~~v~~~G~fV~l~~ 482 (565)
T PRK06299 407 SWDKK-GEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEF---AKKHKKGSIVTGTVTEVKDKGAFVELED 482 (565)
T ss_pred Ccccc-ccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHH---HhhcCCCCEEEEEEEEEecCceEEecCC
Confidence 75321 133457899999999 899999999999999999999998643 4568999999999999999999999999
Q ss_pred CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 784 RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 784 gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
++.||+|.+++++.+..++.+.|++||.|.|+|+++|++++|+.||+|....
T Consensus 483 gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~~~ 534 (565)
T PRK06299 483 GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDE 534 (565)
T ss_pred CcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeehhh
Confidence 9999999999999999999999999999999999999999999999998754
No 7
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=4.9e-58 Score=577.27 Aligned_cols=490 Identities=22% Similarity=0.298 Sum_probs=429.6
Q ss_pred cccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecchhhh
Q 000449 317 DLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLL 396 (1497)
Q Consensus 317 ~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p~~~ 396 (1497)
..+.||++|.|+|.++.++|++|+|+++.+|+||..+++... +.|++||.++++|+.+++..+++.||.++...
T Consensus 14 ~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~~------~~~~vGd~i~~~V~~~~~~~g~i~lS~~~~~~ 87 (516)
T TIGR00717 14 EETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAP------LEIQVGDEVEVYLDRVEDRFGETVLSREKAQR 87 (516)
T ss_pred ccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCCc------cCCCCCCEEEEEEEEEeCCCCcEEEEHHHhhh
Confidence 458999999999999999999999999999999999998542 47999999999999999888999999987653
Q ss_pred c--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCC
Q 000449 397 H--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLE 474 (1497)
Q Consensus 397 ~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~ 474 (1497)
. |.....++..|++++ ++|.++.++ |++|+++ +++||+|.|++++....+. .+.+|++++|+|++++...
T Consensus 88 ~~~~~~l~~a~~~g~~v~-g~V~~~~~~-g~~V~i~----g~~~flP~s~~~~~~~~~~--~~~vG~~i~~~v~~~~~~~ 159 (516)
T TIGR00717 88 HELWIKLEKAYEEGSIVE-GKIVGKVKG-GFIVDLN----GVEAFLPGSQVDVKPIKDL--DSLIGKTLKFKIIKLDQKR 159 (516)
T ss_pred hHHHHHHHHHhhCCCeEE-EEEEEEECC-EEEEEEC----CEEEEEeHHHhcCcccCch--hhhCCCEEEEEEEEEECCC
Confidence 2 444456789999998 588889988 9999997 3699999999875433333 3679999999999999999
Q ss_pred CeEEEEcchhhccc----ccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEE
Q 000449 475 GLATGILKASAFEG----LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELV 550 (1497)
Q Consensus 475 ~~~~lS~k~~~~~~----~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~ 550 (1497)
+.+++|+++...+. +...++++++|++++|+|.++.++|+||+++ +++||+|.+|++|.+..+|...|++|++++
T Consensus 160 ~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~ 238 (516)
T TIGR00717 160 NNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVK 238 (516)
T ss_pred CcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHhccCCCEEE
Confidence 99999988764332 3445678999999999999999999999996 799999999999988888888899999999
Q ss_pred EEEEEE--eCCeEEEEeecchhhhhhhHHhhh-hhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCC-CCCCC
Q 000449 551 FRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLD-PGCEP 626 (1497)
Q Consensus 551 ~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~-~~~~~ 626 (1497)
|+|+++ +++++.||+|+...+ +|..+ +.+++|+++.|+|+++.++|+||++.+++.||+|.++++|. ...+|
T Consensus 239 v~Vl~~d~~~~~i~lS~k~~~~~----p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~ 314 (516)
T TIGR00717 239 VKVIKFDKEKGRISLSLKQLGED----PWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHP 314 (516)
T ss_pred EEEEEEECCCCcEEEEEEecchh----HHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCH
Confidence 999999 578999999987654 45554 35789999999999999999999998899999999999985 45667
Q ss_pred CCCccCCCEEEEEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCcc
Q 000449 627 SSMYHVGQVVKCRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHL 704 (1497)
Q Consensus 627 ~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hL 704 (1497)
.+.|++||.++|+|+++|++++++.||++.. .++|.. .+.+++|++++|+|++++++|+||++ +++++|++|.++|
T Consensus 315 ~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l--~~~v~glv~~s~l 392 (516)
T TIGR00717 315 SKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVEL--EGGIDGLIHLSDI 392 (516)
T ss_pred HHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEEC--CCCCEEEEEHHHC
Confidence 7789999999999999999999999999975 356644 34688999999999999999999999 7799999998888
Q ss_pred ccccccccccccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCC
Q 000449 705 ADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLG 783 (1497)
Q Consensus 705 sd~~~~~~~~~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~ 783 (1497)
++... .......+++||.+. +++.+|.++++|.||+|+++.+||... .+++++|+.+.|+|++++++|+||++.+
T Consensus 393 s~~~~-~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~---~~~~~~G~~v~g~V~~v~~~G~fV~l~~ 468 (516)
T TIGR00717 393 SWDKD-GREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKF---AAKYKVGSVVKGKVTEIKDFGAFVELPG 468 (516)
T ss_pred cCccc-CCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhh---hhccCcceEEEEEEEEEecceEEEEcCC
Confidence 86432 112346899999999 899999999999999999999998643 3568999999999999999999999999
Q ss_pred CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 784 RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 784 gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
+++||+|.++++|.+..++.+.|++||.++|+|+++|.+++|+.||+|
T Consensus 469 ~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 469 GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred CeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 999999999999999999999999999999999999999999999986
No 8
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=3.9e-57 Score=576.91 Aligned_cols=489 Identities=18% Similarity=0.270 Sum_probs=415.9
Q ss_pred CCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEc
Q 000449 402 PSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGIL 481 (1497)
Q Consensus 402 ~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~ 481 (1497)
...+..|++++| +|.+++++ ++||++|.+ .+|+||.+++.. .+++|++++|.|+..+.. + +.||.
T Consensus 316 ~~~~~~G~iV~G-~Vv~i~~~-~v~VdiG~K---~eGiI~~~E~~~--------~~kvGd~i~~~V~~~~~~-~-~~LS~ 380 (863)
T PRK12269 316 FEAPEPGSVRMG-TVVQVNAG-TVFVDIGGK---SEGRVPVEEFEA--------PPKAGDGVRVYVERVTPY-G-PELSK 380 (863)
T ss_pred cccCCCCCEEEE-EEEEEECC-EEEEEeCCC---ceEEeEHHHhcc--------CCCCCCEEEEEEEEEcCC-c-eEEEe
Confidence 456889999995 78889988 899999865 389999888742 368999999999999864 4 77887
Q ss_pred chhhc-ccccccccccCCCcEEEEEEEEEe--cCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEEe-
Q 000449 482 KASAF-EGLVFTHSDVKPGMVVKGKVIAVD--SFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVK- 557 (1497)
Q Consensus 482 k~~~~-~~~~~~~~~l~~G~iv~g~V~~v~--~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~- 557 (1497)
+.... ..|....+.++.|++|+|+|++++ +.|++|+++.+++||||.+|++.....++. ..+|++++|+|+.++
T Consensus 381 ~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~--~~vG~~ie~~V~~~~~ 458 (863)
T PRK12269 381 TKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE--SLIGLTSKFYIERISQ 458 (863)
T ss_pred hHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchH--HhCCCeEEEEEEEEec
Confidence 76543 345555677899999999999985 469999998789999999999653332222 349999999999882
Q ss_pred ------CCeEEEEeecchhhhhhhHH-hhhhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCc
Q 000449 558 ------SKRITVTHKKTLVKSKLAIL-SSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMY 630 (1497)
Q Consensus 558 ------~~~i~lS~K~~l~~~~~~~~-~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~ 630 (1497)
++++.||+|+.+........ ..++++++|+++.|+|.++.++|+||++ +|++||+|.|+++|.++.+|.+.|
T Consensus 459 ~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v~~~~~~~ 537 (863)
T PRK12269 459 SKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFV 537 (863)
T ss_pred ccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEchhccccccCCHHHhc
Confidence 25899999998765432222 2245567899999999999999999999 799999999999999999999999
Q ss_pred cCCCEEEEEEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCcccccc
Q 000449 631 HVGQVVKCRIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHL 708 (1497)
Q Consensus 631 ~vGq~v~v~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~ 708 (1497)
++||+++|+|+++|++++|+.||+|+. .+||.. .+.+++|++++|+|++++++|+||++ .++++|++|.+++|+..
T Consensus 538 kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL--~~gveGLvhiSEls~~~ 615 (863)
T PRK12269 538 KKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIEL--AEGIEGLAHISEFSWVK 615 (863)
T ss_pred cCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEe--cCCceeeeEHHHhcCcc
Confidence 999999999999999999999999985 356655 45799999999999999999999999 77999999777776521
Q ss_pred ccccccccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEE
Q 000449 709 EHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTG 787 (1497)
Q Consensus 709 ~~~~~~~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~G 787 (1497)
....+.+.+++||+++ +++.+|.+++++.||+|++..+||+.+ .+++++|++++|+|+++++||+||++.+|++|
T Consensus 616 -~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~---~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~G 691 (863)
T PRK12269 616 -KTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEI---EARYPVGARFTRRIVKVTNAGAFIEMEEGIDG 691 (863)
T ss_pred -ccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHH---HHhCCCCCEEEEEEEEEecceEEEEeCCCcEE
Confidence 1223456799999999 999999999999999999999999865 35689999999999999999999999999999
Q ss_pred EEeCCCCCcccc-cCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCccc
Q 000449 788 FAPRSKAVDGQR-ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSEL 866 (1497)
Q Consensus 788 lvp~sels~~~~-~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~ 866 (1497)
|+|.++++|.+. .++...|++||.|.|+|+++|++++||.||+|+... +||+.
T Consensus 692 lIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~------------dpw~~-------------- 745 (863)
T PRK12269 692 FLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSD------------NPWQV-------------- 745 (863)
T ss_pred EEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEeccccc------------ChHHH--------------
Confidence 999999999665 445568999999999999999999999999998754 45633
Q ss_pred ccccccCCCcEEEEEEEEEeeceeEEEecCCCceEEEEeeeecCCc----------cccCCCEEEEEEEEEecCCCEEEE
Q 000449 867 KWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGA----------TVESGSVIQAAILDVAKAERLVDL 936 (1497)
Q Consensus 867 ~~~~~~~vG~~V~g~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~~----------~~~~G~~v~~~Vl~vd~~~~~v~l 936 (1497)
+...|++|+.|+|+|.+++++|+||++++ ++.|++|.+++++. .|++||+|+++|+++|.++++|.|
T Consensus 746 -~~~~~~vG~iV~GkV~~v~~~GvFVeL~~--gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~L 822 (863)
T PRK12269 746 -FANAYGVGSTVEGEVSSVTDFGIFVRVPG--GVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAF 822 (863)
T ss_pred -HHhhCCCCCEEEEEEEEEecCeEEEEcCC--CeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEE
Confidence 24568999999999999999999999986 79999999999742 389999999999999999999999
Q ss_pred Eeehhhh
Q 000449 937 SLKTVFI 943 (1497)
Q Consensus 937 Slk~~l~ 943 (1497)
|+|+...
T Consensus 823 Slk~~~~ 829 (863)
T PRK12269 823 SVRDYQR 829 (863)
T ss_pred EEechhh
Confidence 9997654
No 9
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=9.7e-57 Score=570.03 Aligned_cols=495 Identities=22% Similarity=0.302 Sum_probs=428.8
Q ss_pred CCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEcc
Q 000449 403 SHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILK 482 (1497)
Q Consensus 403 ~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k 482 (1497)
..+..|++++ ++|.+++++ |++|+++.+ .+||+|.+++++.. .+..|++|++++|+|+.++..++.+++|++
T Consensus 26 ~~~~~G~~v~-G~V~~v~~~-~~~Vdig~k---~~g~lp~~e~~~~~---~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k 97 (565)
T PRK06299 26 SETREGSIVK-GTVVAIDKD-YVLVDVGLK---SEGRIPLEEFKNEQ---GELEVKVGDEVEVYVERIEDGFGETVLSRE 97 (565)
T ss_pred ccCCCCCEEE-EEEEEEECC-EEEEEeCCC---eEEEEEHHHhcCcc---ccccCCCCCEEEEEEEEEECCCCcEEEech
Confidence 3467899998 588889998 999999743 48999999997532 123589999999999999999999999998
Q ss_pred hhhccc-ccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCC
Q 000449 483 ASAFEG-LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSK 559 (1497)
Q Consensus 483 ~~~~~~-~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~ 559 (1497)
+..... |....+.++.|++|+|+|.++.++|++|+++ |++||||.+|++|....++. +.+|++++|+|+.+ +++
T Consensus 98 ~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~-g~~gfip~s~~~~~~~~~~~--~~vG~~i~~~V~~~d~~~~ 174 (565)
T PRK06299 98 KAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLN-GVEAFLPGSQVDVRPVRDTD--PLEGKELEFKVIKLDKKRN 174 (565)
T ss_pred HHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEEC-CEEEEEEHHHccCcCCCChH--HhCCCEEEEEEEEEECCCC
Confidence 775433 4455567889999999999999999999998 89999999999986544443 56999999999999 578
Q ss_pred eEEEEeecchhhhhhhHH-hhhhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEE
Q 000449 560 RITVTHKKTLVKSKLAIL-SSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKC 638 (1497)
Q Consensus 560 ~i~lS~K~~l~~~~~~~~-~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v 638 (1497)
++.||+|+++.......| ..+.++++|+++.|+|+++.++|+||++. |+.||+|.++++|.++.+|.+.|++||+|+|
T Consensus 175 ~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v 253 (565)
T PRK06299 175 NIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKV 253 (565)
T ss_pred EEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEE
Confidence 999999998865433333 33567889999999999999999999995 9999999999999999999999999999999
Q ss_pred EEEEEecCCCEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCcccccccccccccc
Q 000449 639 RIMSSIPASRRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKS 716 (1497)
Q Consensus 639 ~Vl~vd~~~~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~ 716 (1497)
+|+++|++++++.||++.. .+||.. ...+++|++++|+|++++++|+||++ .+++.|++|.+++++... ...+..
T Consensus 254 ~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l--~~~v~Glv~~sel~~~~~-~~~~~~ 330 (565)
T PRK06299 254 KVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVEL--EEGIEGLVHVSEMSWTKK-NKHPSK 330 (565)
T ss_pred EEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEe--CCCCEEEEEHHHcCcccc-ccCHHH
Confidence 9999999999999999975 457765 35789999999999999999999999 779999999888875321 122345
Q ss_pred ccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC
Q 000449 717 VIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAV 795 (1497)
Q Consensus 717 ~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels 795 (1497)
.+++||.++ +++.+|.+++++.||+|+++.+||... ..++++|+.+.|+|++++++|+||+++++++||+|.++++
T Consensus 331 ~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~---~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~ 407 (565)
T PRK06299 331 VVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEF---AEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDIS 407 (565)
T ss_pred hcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhH---HHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcC
Confidence 689999999 899999999999999999999998753 3557899999999999999999999988999999999999
Q ss_pred cccc-cCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCC
Q 000449 796 DGQR-ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFII 874 (1497)
Q Consensus 796 ~~~~-~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~v 874 (1497)
|.+. .++.+.|++||.|.|+|+++|++++||.||+|+... +||. .+...+++
T Consensus 408 ~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~------------~p~~---------------~~~~~~~~ 460 (565)
T PRK06299 408 WDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEE------------DPFE---------------EFAKKHKK 460 (565)
T ss_pred ccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhc------------Cchh---------------HHHhhcCC
Confidence 9776 788899999999999999999999999999998754 3442 22456899
Q ss_pred CcEEEEEEEEEeeceeEEEecCCCceEEEEeeeecCC-------ccccCCCEEEEEEEEEecCCCEEEEEeehhhhh
Q 000449 875 GSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG-------ATVESGSVIQAAILDVAKAERLVDLSLKTVFID 944 (1497)
Q Consensus 875 G~~V~g~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~-------~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~l~~ 944 (1497)
|+.|.|+|.++.++|++|.+.+ ++.|++|.+++++ ..+++||.|+|+|+.+|.+++++.||+++....
T Consensus 461 G~vV~G~V~~v~~~G~fV~l~~--gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~~~~ 535 (565)
T PRK06299 461 GSIVTGTVTEVKDKGAFVELED--GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535 (565)
T ss_pred CCEEEEEEEEEecCceEEecCC--CcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeehhhh
Confidence 9999999999999999999985 7999999999963 468999999999999999999999999987654
No 10
>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=2e-55 Score=553.62 Aligned_cols=496 Identities=20% Similarity=0.251 Sum_probs=424.2
Q ss_pred cccCCcCCCCEEEEEEEEEeCceEEEEcCCCcEEEEeccccCChhhcccccccccCCCCCccCCCCEEEEEEEEEecCCc
Q 000449 126 ITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKK 205 (1497)
Q Consensus 126 l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~~~~~~~~~L~~~f~vGq~v~~~V~~~~~~~~ 205 (1497)
|....+.+|+++.|+|.+|++.+++|+++++..|++|.+|+++. .+.|++||.+.|.|.+..+..+
T Consensus 11 ~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~--------------~~~~~vGd~i~~~V~~~~~~~g 76 (516)
T TIGR00717 11 LKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA--------------PLEIQVGDEVEVYLDRVEDRFG 76 (516)
T ss_pred cccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCC--------------ccCCCCCCEEEEEEEEEeCCCC
Confidence 44457899999999999999999999999999999999999864 3579999999999998865432
Q ss_pred ccceeEEEEecchhhHhcCCC--cccccCCcEEEEEEEEEEeCeEEEEeCCCCeEEEeeCCCCCCC--CCCcCCCCcEEE
Q 000449 206 EIGKRKIWLSLRLSLLYKGLS--LETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAEN--SGIDVKPGLLLQ 281 (1497)
Q Consensus 206 ~~~~~~i~LSl~p~~vn~~l~--~~~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~--~~~~l~~G~~~~ 281 (1497)
++.||..+....+.|. ..++.+|+++.|.|.++.++||+||+| ++.||||.+++... ......+|+.+.
T Consensus 77 -----~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~--g~~~flP~s~~~~~~~~~~~~~vG~~i~ 149 (516)
T TIGR00717 77 -----ETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLN--GVEAFLPGSQVDVKPIKDLDSLIGKTLK 149 (516)
T ss_pred -----cEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEEEEEC--CEEEEEeHHHhcCcccCchhhhCCCEEE
Confidence 7999999887777776 467789999999999999999999998 89999999987521 223568999999
Q ss_pred EEEEEEcCCCcEEEEccCccccccccccccccccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCC
Q 000449 282 GVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTT 361 (1497)
Q Consensus 282 ~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~ 361 (1497)
|.|++++..++.+.||+.+ +............+.++.+|+.+.|+|.++.++|++|++++ ++|++|..++++... .
T Consensus 150 ~~v~~~~~~~~~iv~Srk~--~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~~~-~ 225 (516)
T TIGR00717 150 FKIIKLDQKRNNIVVSRRA--YLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRV-K 225 (516)
T ss_pred EEEEEEECCCCcEEEEHHH--HHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCC-C
Confidence 9999999988899999843 22111111123356789999999999999999999999965 899999999998654 4
Q ss_pred CCcccCCCCCEEEEEEEEEeCCCceEEEecchhhhc-cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceee
Q 000449 362 NWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLH-NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYV 440 (1497)
Q Consensus 362 ~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p~~~~-~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv 440 (1497)
++.+.|++|+.+.|+|+++|+..+++.||++....+ |......+++|++++ ++|.++.+. |+||+++. ++.||+
T Consensus 226 ~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~-g~V~~v~~~-G~fV~l~~---~v~g~v 300 (516)
T TIGR00717 226 HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKIT-GRVTNLTDY-GVFVEIEE---GIEGLV 300 (516)
T ss_pred CHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEE-EEEEEeeCC-cEEEEeCC---CCEEEE
Confidence 567789999999999999999999999999876443 333345689999998 689999886 99999974 368999
Q ss_pred eeccchhH-HHhhcccccCCCCEEEEEEEEEecCCCeEEEEcchhhcccccccccccCCCcEEEEEEEEEecCeeEEEeC
Q 000449 441 TISDVAEE-EVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFP 519 (1497)
Q Consensus 441 ~~s~~~~~-~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~ 519 (1497)
|+++++|. ...++.+.|++|+.++|+|+++++.++.+.+|+++...++|....+++++|++++|+|++++++|+||+++
T Consensus 301 ~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~ 380 (516)
T TIGR00717 301 HVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE 380 (516)
T ss_pred EHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECC
Confidence 99999874 23334445899999999999999999999999998776666666678999999999999999999999999
Q ss_pred CCeEEEEecCCcccccc-cCCCccccCCCEEEEEEEEE--eCCeEEEEeecchhhhhhhHHhhh-hhccCCcEEEEEEEE
Q 000449 520 GGVKALCPLPHMSEFEI-VKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITK 595 (1497)
Q Consensus 520 ~gv~g~vp~~~ls~~~~-~~~~~~~kvG~~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~ 595 (1497)
.+++|+||.+|++|... .++...|++|+.|+|+|+++ ++++|.||+|++..+ +|..+ +++.+|+++.|+|++
T Consensus 381 ~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~----p~~~~~~~~~~G~~v~g~V~~ 456 (516)
T TIGR00717 381 GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTEN----PWEKFAAKYKVGSVVKGKVTE 456 (516)
T ss_pred CCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCC----chhhhhhccCcceEEEEEEEE
Confidence 89999999999998643 35667899999999999999 578999999987654 34444 346799999999999
Q ss_pred EeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 000449 596 IEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1497)
Q Consensus 596 i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k 655 (1497)
+.++|+||++.+++.||+|.+++++.++.++.+.|++||.++|+|+++|++++++.||+|
T Consensus 457 v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 457 IKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred EecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 999999999999999999999999998889999999999999999999999999999985
No 11
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=6.9e-50 Score=493.48 Aligned_cols=412 Identities=20% Similarity=0.288 Sum_probs=358.6
Q ss_pred CCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEcch
Q 000449 404 HVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKA 483 (1497)
Q Consensus 404 ~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~ 483 (1497)
.+..|++++ ++|.+++++ |++|+++.+ .+||||.+++.+.. .+..+++|++++|+|++++. +.+.+|.+.
T Consensus 31 ~~~~G~~v~-G~V~~v~~~-~v~Vdig~k---~eg~ip~~e~~~~~---~~~~~~~G~~i~~~Vi~~~~--~~~~lS~~~ 100 (491)
T PRK13806 31 ELRVGDKIT-GTVIAITED-SVFVDTGSK---VDGVVDRAELLDAD---GELTVAVGDEVELYVVSVNG--QEIRLSKAL 100 (491)
T ss_pred cCCCCCEEE-EEEEEEECC-EEEEEECCC---cEEEEEHHHhcCcc---ccccccCCCEEEEEEEEEcC--CEEEEEhHH
Confidence 488999998 578889998 999999854 38999999886421 12348999999999999884 468888665
Q ss_pred hhcccccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeE
Q 000449 484 SAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRI 561 (1497)
Q Consensus 484 ~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i 561 (1497)
.....|....+.+..|++|+|+|+++.++|++|+++ |+.||+|.+|+++....++.. + +|++++|+|+.+ +++++
T Consensus 101 ~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~-~-vG~~i~~~V~~id~~~~~v 177 (491)
T PRK13806 101 SGQGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPES-Y-VGQTFQFLITRVEENGRNI 177 (491)
T ss_pred hhhhhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHH-c-CCCeEEEEEEEEECCCCeE
Confidence 444456666788999999999999999999999997 899999999999876666654 3 999999999999 46799
Q ss_pred EEEeecchhhhhhhHHhh-hhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEE
Q 000449 562 TVTHKKTLVKSKLAILSS-YAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRI 640 (1497)
Q Consensus 562 ~lS~K~~l~~~~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~V 640 (1497)
.||+|+.+.......|.. +..+++|+++.|+|+++.++|+||++++|+.||+|.++++|.+..+|.+.|++||.++|+|
T Consensus 178 ~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkV 257 (491)
T PRK13806 178 VVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKV 257 (491)
T ss_pred EEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEE
Confidence 999998876544455555 4457899999999999999999999988999999999999999999999999999999999
Q ss_pred EEEecCC----CEEEEEEeeC-CCCccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCcccccccccccc
Q 000449 641 MSSIPAS----RRINLSFMMK-PTRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVM 714 (1497)
Q Consensus 641 l~vd~~~----~ri~lS~k~~-~~~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~ 714 (1497)
+++|+++ +|+.||+|+. .+||.. .+.+++|++++|+|++++++|+||++ .++++||+|.++|++... ...+
T Consensus 258 l~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l--~~gv~Glvh~sels~~~~-~~~~ 334 (491)
T PRK13806 258 LGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEI--LPGIEGLVHVSEMSWTRR-VNKP 334 (491)
T ss_pred EEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEe--CCCcEEEEEHHHcCcccc-cCCH
Confidence 9999987 4899999985 457765 45899999999999999999999999 779999998888875221 1234
Q ss_pred ccccCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCC
Q 000449 715 KSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSK 793 (1497)
Q Consensus 715 ~~~~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~se 793 (1497)
.+.+++||.++ +++.+|.+++++.||+|++..+||..+ .+++++|++++|+|+++++||+||++.+|++||||.++
T Consensus 335 ~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~---~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se 411 (491)
T PRK13806 335 EDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADV---AERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASV 411 (491)
T ss_pred HHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHh---hhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHH
Confidence 56899999999 999999999999999999999999864 35789999999999999999999999999999999999
Q ss_pred CCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 794 AVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 794 ls~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
++|.+..++.+.|++||.|.|+|+.+|++++||.||++...
T Consensus 412 ~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~~ 452 (491)
T PRK13806 412 ISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAA 452 (491)
T ss_pred cCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehhh
Confidence 99999999999999999999999999999999999999663
No 12
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=1e-48 Score=483.09 Aligned_cols=402 Identities=20% Similarity=0.254 Sum_probs=348.6
Q ss_pred cccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEEeCCeEEEEeecchhhhh
Q 000449 494 SDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSK 573 (1497)
Q Consensus 494 ~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~lS~K~~l~~~~ 573 (1497)
..+.+|++|+|+|+++++.|++|+++.+.+|+||.+|+++.. ....|++|++++|+|+.++.+.+.||++...
T Consensus 30 ~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~---~~~~~~~G~~i~~~Vi~~~~~~~~lS~~~~~---- 102 (491)
T PRK13806 30 TELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD---GELTVAVGDEVELYVVSVNGQEIRLSKALSG---- 102 (491)
T ss_pred ccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc---ccccccCCCEEEEEEEEEcCCEEEEEhHHhh----
Confidence 348999999999999999999999998999999999987421 2345899999999999996668999976432
Q ss_pred hhHHhhhh-hccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEE
Q 000449 574 LAILSSYA-EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINL 652 (1497)
Q Consensus 574 ~~~~~~~~-~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~l 652 (1497)
...|..+. .+..|+++.|+|.++.++|++|++ +|++||+|.|++++.+..++.. .+|++++|+|+++|++++++.|
T Consensus 103 ~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i-~g~~~flP~s~~~~~~~~~~~~--~vG~~i~~~V~~id~~~~~v~l 179 (491)
T PRK13806 103 QGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEV-LGRRAFCPVSQIDLRYVEDPES--YVGQTFQFLITRVEENGRNIVV 179 (491)
T ss_pred hhhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEE-CCEEEEEEHHHhccccCCChHH--cCCCeEEEEEEEEECCCCeEEE
Confidence 13455543 346899999999999999999998 5999999999999987778775 3999999999999999999999
Q ss_pred EEeeCCC-----Cccc-ccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEe-
Q 000449 653 SFMMKPT-----RVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD- 725 (1497)
Q Consensus 653 S~k~~~~-----~~~~-~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~- 725 (1497)
|.++... .|.. ...+++|++++|+|++++++|+||++ .++++|+||.+++++.... .+.+.+++||.++
T Consensus 180 Srk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l--~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~v 255 (491)
T PRK13806 180 SRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVEL--APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRV 255 (491)
T ss_pred EeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEc--CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEE
Confidence 9987532 1222 34689999999999999999999999 6799999999999875422 2456799999999
Q ss_pred EEEEeeccC----CceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCc-cccc
Q 000449 726 QLLVLDNES----SNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD-GQRA 800 (1497)
Q Consensus 726 ~vl~~d~~~----~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~-~~~~ 800 (1497)
+++.+|.++ +++.||+|++..+||..+ .+++++|+++.|+|++++++|+||++.+|++||+|.|+++| .+..
T Consensus 256 kVl~id~~~~~~~~ri~lS~K~~~~~p~~~~---~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~ 332 (491)
T PRK13806 256 KVLGIERAKKGKGLRISLSIKQAGGDPWDTV---GDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVN 332 (491)
T ss_pred EEEEEecccCCcceEEEEEehhhhcccchhh---hccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccC
Confidence 899999876 469999999999999754 45789999999999999999999999989999999999998 5668
Q ss_pred CcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCCCcEEEE
Q 000449 801 DLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEG 880 (1497)
Q Consensus 801 ~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~vG~~V~g 880 (1497)
+|.+.|++||.|.|+|+++|++++|+.||+|+... +||+. +...|++|+.|+|
T Consensus 333 ~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~------------~p~~~---------------~~~~~~vG~~v~G 385 (491)
T PRK13806 333 KPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEG------------DPWAD---------------VAERFAPGTTVTG 385 (491)
T ss_pred CHHHcCCCCCEEEEEEEEEEccCCEEEEEEeeccc------------ChhHH---------------hhhhCCCCCEEEE
Confidence 88999999999999999999999999999998765 45633 2567999999999
Q ss_pred EEEEEeeceeEEEecCCCceEEEEeeeecCC-------ccccCCCEEEEEEEEEecCCCEEEEEeehh
Q 000449 881 KVHESNDFGVVVSFEEHSDVYGFITHHQLAG-------ATVESGSVIQAAILDVAKAERLVDLSLKTV 941 (1497)
Q Consensus 881 ~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~-------~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~ 941 (1497)
+|.++++||+||.+.+ ++.||+|.++++. ..+++||+|+++|+.+|+++++|.||++..
T Consensus 386 ~V~~i~~~G~FV~l~~--gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~ 451 (491)
T PRK13806 386 TVEKRAQFGLFVNLAP--GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGA 451 (491)
T ss_pred EEEEEecCceEEEcCC--CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence 9999999999999986 8999999999973 468999999999999999999999999965
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=9.9e-44 Score=430.55 Aligned_cols=328 Identities=22% Similarity=0.268 Sum_probs=293.8
Q ss_pred ccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeEEEEeecchh
Q 000449 493 HSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLV 570 (1497)
Q Consensus 493 ~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~lS~K~~l~ 570 (1497)
+..+++|++|+|+|++++++|++|+|+.+++|+||..|+++.+..+|++.|++|++|+|+|+.+ +.+++.||+|++..
T Consensus 30 ~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~ 109 (486)
T PRK07899 30 IKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQY 109 (486)
T ss_pred HhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhhcc
Confidence 4569999999999999999999999998999999999999988888999999999999999999 46799999998764
Q ss_pred hhhhhHHhhhhhcc-CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCE
Q 000449 571 KSKLAILSSYAEAT-DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRR 649 (1497)
Q Consensus 571 ~~~~~~~~~~~~~~-~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~r 649 (1497)
. ..|..++++. .|+++.|+|+++.++|+||++ |++||+|.|++++.++.++.. .+||+|+|+|+++|+++++
T Consensus 110 ~---~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~~~~~ 182 (486)
T PRK07899 110 E---RAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI--GLRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDKNRNN 182 (486)
T ss_pred c---chHHHHHHHhcCCCEEEEEEEEEECCeEEEEE--CCEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEECCCCE
Confidence 4 4788888875 799999999999999999999 699999999999987777765 4999999999999999999
Q ss_pred EEEEEeeCC-----CCcc-cccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCe
Q 000449 650 INLSFMMKP-----TRVS-EDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYE 723 (1497)
Q Consensus 650 i~lS~k~~~-----~~~~-~~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~ 723 (1497)
+.||+|... .++. ....+++|++++|+|++++++|+||++ ++++||||.++||+... ..+.+.+++||+
T Consensus 183 ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl---ggv~Glv~~Sels~~~v--~~~~~~~kvGd~ 257 (486)
T PRK07899 183 VVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL---GGVDGLVHVSELSWKHI--DHPSEVVEVGQE 257 (486)
T ss_pred EEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHCCCccc--CCHHHhcCCCCE
Confidence 999998532 1222 235789999999999999999999999 57999999999987432 224567899999
Q ss_pred Ee-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCc
Q 000449 724 FD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADL 802 (1497)
Q Consensus 724 l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~ 802 (1497)
|+ +|+.+|.++++|.||+|+++.+||+.+ ...+++|+++.|+|++++++|+||++.+++.||+|.+++++.+..++
T Consensus 258 V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~---~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~ 334 (486)
T PRK07899 258 VTVEVLDVDMDRERVSLSLKATQEDPWQQF---ARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVP 334 (486)
T ss_pred EEEEEEEEECCCCEEEEEEeeccccchhhh---HHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCc
Confidence 99 899999999999999999999999753 34578899999999999999999999999999999999999988889
Q ss_pred ccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 803 SKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 803 ~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+.|++||+|.|+|+++|.+++|+.||+|+...
T Consensus 335 ~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~ 367 (486)
T PRK07899 335 EQVVQVGDEVFVKVIDIDLERRRISLSLKQANE 367 (486)
T ss_pred cceeCCCCEEEEEEEEEECCCCEEEEEEEEccc
Confidence 999999999999999999999999999998865
No 14
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=7.1e-42 Score=415.33 Aligned_cols=334 Identities=24% Similarity=0.304 Sum_probs=296.3
Q ss_pred cccccccccCCCcEEEEEEEEEecCeeEEEe-CCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeEEEE
Q 000449 488 GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQF-PGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVT 564 (1497)
Q Consensus 488 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i-~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~lS 564 (1497)
+.....+++++|++|+|+|++++++|++|++ +++++|+||..|+++.+..+|...|++|++|+|+|+.+ +++++.||
T Consensus 7 ~~~~~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS 86 (390)
T PRK06676 7 ESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86 (390)
T ss_pred HHhhhhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEE
Confidence 3445778999999999999999999999999 77999999999999988888998999999999999999 46689999
Q ss_pred eecchhhhhhhHHhhhhhc-cCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEE
Q 000449 565 HKKTLVKSKLAILSSYAEA-TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSS 643 (1497)
Q Consensus 565 ~K~~l~~~~~~~~~~~~~~-~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~v 643 (1497)
+|++... +.|..+.++ ++|++++|+|+++.++|+||++ +|++||+|.+++++.+..++.+. +||+++|+|+++
T Consensus 87 ~k~~~~~---~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~ 160 (390)
T PRK06676 87 KRRLEAE---KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDF--KGKTLEVKIIEL 160 (390)
T ss_pred HHHhhhh---hhHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEE
Confidence 9986533 567776544 7899999999999999999999 68999999999999877777653 999999999999
Q ss_pred ecCCCEEEEEEeeCCC-----Ccc-cccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccc
Q 000449 644 IPASRRINLSFMMKPT-----RVS-EDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSV 717 (1497)
Q Consensus 644 d~~~~ri~lS~k~~~~-----~~~-~~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~ 717 (1497)
|++++++.||+|.... +|. ....+++|++++|+|.+++++|+||++ ++++|+||.+++++... ..+.+.
T Consensus 161 d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l---~~v~g~v~~sels~~~~--~~~~~~ 235 (390)
T PRK06676 161 DPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERV--EKPSEV 235 (390)
T ss_pred ECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe---CCeEEEEEHHHcCcccc--CCHHHh
Confidence 9999999999997422 122 235689999999999999999999999 57999999999987432 234567
Q ss_pred cCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCc
Q 000449 718 IKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD 796 (1497)
Q Consensus 718 ~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~ 796 (1497)
+++||.++ +++.+|.+++++.+|+|+.+.+||..+ ++++++|+.+.|+|++++++|+||++.+++.||+|.+++++
T Consensus 236 ~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~---~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~ 312 (390)
T PRK06676 236 VSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGV---EEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISH 312 (390)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccc---hhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCc
Confidence 89999999 899999999999999999999998754 46799999999999999999999999999999999999999
Q ss_pred ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 797 GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 797 ~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+..++.+.|++||.|.|+|+++|++++|+.||+|....
T Consensus 313 ~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~ 351 (390)
T PRK06676 313 KHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351 (390)
T ss_pred cccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEeccc
Confidence 888888899999999999999999999999999998876
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=9.3e-41 Score=404.71 Aligned_cols=328 Identities=23% Similarity=0.264 Sum_probs=290.5
Q ss_pred cccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecchh
Q 000449 315 SIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPY 394 (1497)
Q Consensus 315 s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p~ 394 (1497)
++..+.+|++|.|+|.+|.++|++|+++++++|+||..|+++... .++.+.|++|+.|+|+|+.+++..+++.||+++.
T Consensus 29 ~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~-~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~ 107 (486)
T PRK07899 29 TIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHD-VDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRA 107 (486)
T ss_pred HHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhccccc-CChhhcCCCCCEEEEEEEEEECCCCeEEEEehhh
Confidence 467799999999999999999999999989999999999998653 4567789999999999999999999999999976
Q ss_pred hhc--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEec
Q 000449 395 LLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRH 472 (1497)
Q Consensus 395 ~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~ 472 (1497)
... |....+.+..|++++ ++|.++.++ |++|++| ++||+|.|++++..+.++.. .+|++++|+|++++.
T Consensus 108 ~~~~~w~~ie~~~e~g~~V~-G~V~~v~k~-G~~VdlG-----i~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~ 178 (486)
T PRK07899 108 QYERAWGTIEKIKEKDGVVT-GTVIEVVKG-GLILDIG-----LRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDK 178 (486)
T ss_pred cccchHHHHHHHhcCCCEEE-EEEEEEECC-eEEEEEC-----CEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEEC
Confidence 432 444445678899998 588889987 9999995 48999999999877666653 599999999999999
Q ss_pred CCCeEEEEcchhhc----ccccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCE
Q 000449 473 LEGLATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAE 548 (1497)
Q Consensus 473 ~~~~~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~ 548 (1497)
..+.++||++.... ..+...+.++++|++++|+|++++++|+||+|+ +++||||.+|++|.+..+|.+.|++|++
T Consensus 179 ~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~ 257 (486)
T PRK07899 179 NRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQE 257 (486)
T ss_pred CCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCE
Confidence 99999999886432 234455678999999999999999999999996 7999999999999888899889999999
Q ss_pred EEEEEEEE--eCCeEEEEeecchhhhhhhHHhhhhh-ccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCC
Q 000449 549 LVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYAE-ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCE 625 (1497)
Q Consensus 549 V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~~~~-~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~ 625 (1497)
|+|+|+.+ ++++|.||+|++..+ +|..+.+ +.+|+++.|+|+++.++|+||++.+|+.||+|.+++++.+..+
T Consensus 258 V~vkVl~iD~e~~rI~LSlK~~~~d----Pw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~ 333 (486)
T PRK07899 258 VTVEVLDVDMDRERVSLSLKATQED----PWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEV 333 (486)
T ss_pred EEEEEEEEECCCCEEEEEEeecccc----chhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccC
Confidence 99999999 578999999988765 4565543 5689999999999999999999998999999999999988888
Q ss_pred CCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 000449 626 PSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1497)
Q Consensus 626 ~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~ 657 (1497)
+.+.|++||+|+|+|+++|++++|+.||+|+.
T Consensus 334 ~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~ 365 (486)
T PRK07899 334 PEQVVQVGDEVFVKVIDIDLERRRISLSLKQA 365 (486)
T ss_pred ccceeCCCCEEEEEEEEEECCCCEEEEEEEEc
Confidence 99999999999999999999999999999975
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=5.1e-38 Score=381.64 Aligned_cols=335 Identities=22% Similarity=0.320 Sum_probs=291.5
Q ss_pred cccccCCCceEEEEEEEEeCCeEEEEe-CCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecch
Q 000449 315 SIDLLVPGMMVSTRVQSILENGVMLSF-LTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1497)
Q Consensus 315 s~~~l~pG~~V~g~V~~v~~~Gl~v~~-~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p 393 (1497)
++..+.+|++|.|+|.+++++|++|++ ++..+|++|..|+++... .++...|++|+.|+|+|+.++...+++.||+++
T Consensus 11 ~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~-~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~ 89 (390)
T PRK06676 11 SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHI-EDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR 89 (390)
T ss_pred hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccc-cCcccccCCCCEEEEEEEEEECCCCCEEEEHHH
Confidence 567899999999999999999999999 778999999999987643 356678999999999999999988899999998
Q ss_pred hhhc--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEe
Q 000449 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1497)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~ 471 (1497)
.... |.....++..|++++ ++|.++.++ |++|+++ +++||+|.+++++....++.. + +|++++|+|++++
T Consensus 90 ~~~~~~~~~~~~~~~~G~~v~-g~V~~v~~~-G~~V~~~----G~~gflp~~el~~~~~~~~~~-~-vG~~v~~~Vl~~d 161 (390)
T PRK06676 90 LEAEKAWDKLEEKFEEGEVVE-VKVTEVVKG-GLVVDVE----GVRGFIPASLISTRFVEDFSD-F-KGKTLEVKIIELD 161 (390)
T ss_pred hhhhhhHHHHHHhccCCCEEE-EEEEEEECC-eEEEEEC----CEEEEEEHHHcCCccCCChHH-c-CCCEEEEEEEEEE
Confidence 6432 444446789999998 588889887 9999995 249999999999876666543 4 9999999999999
Q ss_pred cCCCeEEEEcchhhcc----cccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCC
Q 000449 472 HLEGLATGILKASAFE----GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGA 547 (1497)
Q Consensus 472 ~~~~~~~lS~k~~~~~----~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~ 547 (1497)
..++.+.+|++..... .+...+.++++|++++|+|+++.++|+||+++ +++|+||.+|++|.+..+|.+.|++|+
T Consensus 162 ~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~~~~~~~~~~~~vGd 240 (390)
T PRK06676 162 PEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQ 240 (390)
T ss_pred CCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCccccCCHHHhcCCCC
Confidence 9999999999876432 33445678999999999999999999999996 799999999999987788888899999
Q ss_pred EEEEEEEEE--eCCeEEEEeecchhhhhhhHHhh-hhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCC
Q 000449 548 ELVFRVLGV--KSKRITVTHKKTLVKSKLAILSS-YAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGC 624 (1497)
Q Consensus 548 ~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~ 624 (1497)
.|+|+|+.+ ++++|.||+|+.+.+ +|.. ++++++|+++.|+|+++.++|+||++.+|+.||+|.|++++.+..
T Consensus 241 ~i~~~Vl~vd~~~~~i~lS~k~~~~~----~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~ 316 (390)
T PRK06676 241 EVEVKVLSIDWETERISLSLKDTLPG----PWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIA 316 (390)
T ss_pred EEEEEEEEEeCCCCEEEEEEeecccC----ccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccC
Confidence 999999999 468999999988765 2333 446789999999999999999999999899999999999998888
Q ss_pred CCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc
Q 000449 625 EPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE 663 (1497)
Q Consensus 625 ~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~~-~~~~~ 663 (1497)
++.+.|++||+|+|+|+++|++++++.||+++.. +||..
T Consensus 317 ~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~ 356 (390)
T PRK06676 317 TPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEE 356 (390)
T ss_pred ChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhh
Confidence 8889999999999999999999999999999854 45543
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=4.2e-38 Score=401.57 Aligned_cols=334 Identities=23% Similarity=0.271 Sum_probs=296.0
Q ss_pred cccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeEEEEe
Q 000449 488 GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTH 565 (1497)
Q Consensus 488 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~lS~ 565 (1497)
.+....+.+++|++|+|+|.+++++|++|+++++.+|++|..|++|.+..+|.+.|++|++++|+|+.+ +.+++.||+
T Consensus 292 ~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~ 371 (647)
T PRK00087 292 YMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSK 371 (647)
T ss_pred HHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEe
Confidence 344567789999999999999999999999998999999999999988889999999999999999999 478999999
Q ss_pred ecchhhhhhhHHhhhhh-ccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEe
Q 000449 566 KKTLVKSKLAILSSYAE-ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSI 644 (1497)
Q Consensus 566 K~~l~~~~~~~~~~~~~-~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd 644 (1497)
|+.... ..|..+.+ +++|+++.|+|+++.++|+||+++ +++||+|.+++++....+++. .+|++++|+|+++|
T Consensus 372 k~~~~~---~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d~~~--~vG~~v~v~Vl~vd 445 (647)
T PRK00087 372 KEADRE---KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLSE--YKGQELEVKIIEFN 445 (647)
T ss_pred ehhcch---hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCCHHH--hCCCEEEEEEEEEE
Confidence 987643 35666654 478999999999999999999995 699999999999887777765 29999999999999
Q ss_pred cCCCE-EEEEEeeCCC-----Cc-ccccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccc
Q 000449 645 PASRR-INLSFMMKPT-----RV-SEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSV 717 (1497)
Q Consensus 645 ~~~~r-i~lS~k~~~~-----~~-~~~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~ 717 (1497)
+++++ +.+|+|.... ++ ...+.+++|++++|+|.++.++|+||++ ++++|++|.+++++.... .+.+.
T Consensus 446 ~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l---~gv~Gll~~sels~~~~~--~~~~~ 520 (647)
T PRK00087 446 RKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVE--KPSDV 520 (647)
T ss_pred cCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE---CCEEEEEEHHHcCccccC--CHHHh
Confidence 99999 9999987531 11 2234688999999999999999999999 689999999999875432 24567
Q ss_pred cCCCCeEe-EEEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCc
Q 000449 718 IKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD 796 (1497)
Q Consensus 718 ~k~G~~l~-~vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~ 796 (1497)
+++||.++ +++.+|++++++.+|+|+.+.+||..+ .+++++|+.+.|.|++++++|+||++.+++.||+|.+++++
T Consensus 521 ~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~---~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~ 597 (647)
T PRK00087 521 LKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENV---EEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISW 597 (647)
T ss_pred cCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhh---hhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCc
Confidence 99999999 899999999999999999999999864 35678999999999999999999999999999999999999
Q ss_pred ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 797 GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 797 ~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+..++.+.|++||.|.|+|+++|++++|+.||+|....
T Consensus 598 ~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~ 636 (647)
T PRK00087 598 KRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEE 636 (647)
T ss_pred cccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence 999999999999999999999999999999999998764
No 18
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=3.1e-36 Score=384.37 Aligned_cols=330 Identities=24% Similarity=0.303 Sum_probs=290.9
Q ss_pred ccccccCCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEecch
Q 000449 314 ISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1497)
Q Consensus 314 ~s~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl~p 393 (1497)
.++..+.+|++|.|+|.++.++|++|++++..+|++|..++++... .++.+.|++|+.++|+|+.++...+++.||+++
T Consensus 295 ~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~-~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~ 373 (647)
T PRK00087 295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEI-SSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE 373 (647)
T ss_pred HHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccc-CChhhccCCCCEEEEEEEEEECCCCcEEEEeeh
Confidence 4678899999999999999999999999999999999999997643 467788999999999999999988999999987
Q ss_pred hhhc--cCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCccceeeeeccchhHHHhhcccccCCCCEEEEEEEEEe
Q 000449 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1497)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~v~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~ 471 (1497)
.... |....+++..|++++ ++|.++.++ |++++++. ++||+|.+++++....+++. | +|+.++|+|+.++
T Consensus 374 ~~~~~~~~~l~~~~~~G~iv~-g~V~~v~~~-G~~V~lgg----i~gfiP~sel~~~~~~d~~~-~-vG~~v~v~Vl~vd 445 (647)
T PRK00087 374 ADREKAWKELEEAFENGEPVK-GKVKEVVKG-GLLVDYGG----VRAFLPASHVELGYVEDLSE-Y-KGQELEVKIIEFN 445 (647)
T ss_pred hcchhHHHHHHHHhhCCCEEE-EEEEEEECC-eEEEEECC----EEEEEEHHHhCccccCCHHH-h-CCCEEEEEEEEEE
Confidence 6433 443445789999998 578888887 99999973 59999999998877666653 3 9999999999999
Q ss_pred cCCCe-EEEEcchhhc----ccccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCC
Q 000449 472 HLEGL-ATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVG 546 (1497)
Q Consensus 472 ~~~~~-~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG 546 (1497)
..++. +.+|++.... .++...++++++|++++|+|.++.++|+||++ ++++|++|.++++|.+..+|.+.|++|
T Consensus 446 ~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vG 524 (647)
T PRK00087 446 RKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVG 524 (647)
T ss_pred cCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCC
Confidence 99888 9999887642 23345567899999999999999999999999 699999999999998888888899999
Q ss_pred CEEEEEEEEE--eCCeEEEEeecchhhhhhhHHhh-hhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCC
Q 000449 547 AELVFRVLGV--KSKRITVTHKKTLVKSKLAILSS-YAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPG 623 (1497)
Q Consensus 547 ~~V~~rVl~v--~~~~i~lS~K~~l~~~~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~ 623 (1497)
+.|+|+|+++ +++++.||+|+.+.+ +|.. .+++++|+++.|+|+++.++|+||++.+++.||+|.+++++.+.
T Consensus 525 d~V~vkV~~id~~~~~I~lS~K~~~~~----p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~ 600 (647)
T PRK00087 525 DEIKVYILDIDKENKKLSLSLKKLLPD----PWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRI 600 (647)
T ss_pred CEEEEEEEEEECCCCEEEEEeeccccC----hhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcccc
Confidence 9999999999 478999999998765 3444 34568999999999999999999999999999999999999888
Q ss_pred CCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 000449 624 CEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1497)
Q Consensus 624 ~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~ 657 (1497)
.++.+.|++||+|+|+|+++|++++++.||+|..
T Consensus 601 ~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~ 634 (647)
T PRK00087 601 DKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634 (647)
T ss_pred CCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 8999999999999999999999999999999975
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.8e-32 Score=319.13 Aligned_cols=244 Identities=22% Similarity=0.306 Sum_probs=217.6
Q ss_pred HHhhhh-hccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 000449 576 ILSSYA-EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1497)
Q Consensus 576 ~~~~~~-~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~ 654 (1497)
.|..++ .++.|+++.|+|+++.++||||+|+++.+||+|.+|+++.++.++.+.|++||+++|+|+++|++++++.||+
T Consensus 21 ~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~ 100 (318)
T PRK07400 21 LLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSI 100 (318)
T ss_pred HHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEeh
Confidence 344443 3678999999999999999999998789999999999999989999999999999999999999999999999
Q ss_pred eeCC--CCccccc-ccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEe-EEEEe
Q 000449 655 MMKP--TRVSEDD-LVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVL 730 (1497)
Q Consensus 655 k~~~--~~~~~~~-~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~-~vl~~ 730 (1497)
|... .+|.... ....|++++|+|+++.++|++|++ +|++||||.+|||+... .+ ..+|++++ +|+.+
T Consensus 101 k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l---~Gv~gfip~s~ls~~~~-----~~-~~vG~~i~~kVl~i 171 (318)
T PRK07400 101 RRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRI---EGLRGFIPGSHISTRKP-----KE-ELVGEELPLKFLEV 171 (318)
T ss_pred hhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHcCccCC-----cc-ccCCCEEEEEEEEE
Confidence 9753 4455433 445799999999999999999999 69999999999997532 12 34999999 99999
Q ss_pred eccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCC
Q 000449 731 DNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQ 810 (1497)
Q Consensus 731 d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq 810 (1497)
|++++++.||+|+.+.+. .+.++++|+++.|+|+++++||+||++ +++.||+|.++++|.+..++.+.|++||
T Consensus 172 d~~~~~i~lS~K~~~~~~------~~~~~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd 244 (318)
T PRK07400 172 DEERNRLVLSHRRALVER------KMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVND 244 (318)
T ss_pred EcccCEEEEEhhHhhhhh------hhccCCCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcccccccChhhccCCCC
Confidence 999999999999887643 356799999999999999999999998 6899999999999999999999999999
Q ss_pred EEEEEEEEEeCCCCeEEEEeecccc
Q 000449 811 SVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 811 ~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.|.|+|+++|.+++|+.||+|+...
T Consensus 245 ~VkvkVl~iD~e~~rI~LS~K~l~~ 269 (318)
T PRK07400 245 EMKVMIIDLDAERGRISLSTKQLEP 269 (318)
T ss_pred EEEEEEEEEeCCCCEEEEEEecccc
Confidence 9999999999999999999999876
No 20
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=3.1e-30 Score=300.34 Aligned_cols=243 Identities=19% Similarity=0.303 Sum_probs=213.8
Q ss_pred ccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCCeEEEEeecchhhh
Q 000449 495 DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKS 572 (1497)
Q Consensus 495 ~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~lS~K~~l~~~ 572 (1497)
.+++|++|+|+|+++.++|++|+|+++.+||||.+|++|....+|.+.|++|++++|+|+.+ +++++.||+|++...
T Consensus 28 ~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~- 106 (318)
T PRK07400 28 HFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYM- 106 (318)
T ss_pred hcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhh-
Confidence 48999999999999999999999998899999999999987788888999999999999999 468999999987532
Q ss_pred hhhHHhhhhhcc-CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 000449 573 KLAILSSYAEAT-DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1497)
Q Consensus 573 ~~~~~~~~~~~~-~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~ 651 (1497)
..|..+.++. .|+++.|+|+++.++|+||++ +|++||+|.|+++|.. +.+. .+||.++|+|+++|+++++|.
T Consensus 107 --~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l-~Gv~gfip~s~ls~~~---~~~~-~vG~~i~~kVl~id~~~~~i~ 179 (318)
T PRK07400 107 --RAWERVRQLQKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRK---PKEE-LVGEELPLKFLEVDEERNRLV 179 (318)
T ss_pred --hHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCccC---Cccc-cCCCEEEEEEEEEEcccCEEE
Confidence 4688877775 589999999999999999999 6999999999999863 3333 499999999999999999999
Q ss_pred EEEeeCCCCcccccccCCCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEe-EEEEe
Q 000449 652 LSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVL 730 (1497)
Q Consensus 652 lS~k~~~~~~~~~~~~~vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~-~vl~~ 730 (1497)
||+|+... ......+++|+++.|+|++++++|+||++ +++.|++|.+.+++... ..+.+.|++||.++ +++.+
T Consensus 180 lS~K~~~~-~~~~~~~k~G~vv~G~V~~I~~~G~fV~i---~gv~Gllhisels~~~~--~~~~~~~~vGd~VkvkVl~i 253 (318)
T PRK07400 180 LSHRRALV-ERKMNRLEVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHI--ETPHSVFNVNDEMKVMIIDL 253 (318)
T ss_pred EEhhHhhh-hhhhccCCCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHcccccc--cChhhccCCCCEEEEEEEEE
Confidence 99986432 12356799999999999999999999999 58999998888887442 23467899999999 89999
Q ss_pred eccCCceeeeccccccccccc
Q 000449 731 DNESSNLLLSAKYSLINSAQQ 751 (1497)
Q Consensus 731 d~~~~~i~lS~K~~l~~~~~~ 751 (1497)
|.+++++.||+|+...+||+.
T Consensus 254 D~e~~rI~LS~K~l~~~P~~~ 274 (318)
T PRK07400 254 DAERGRISLSTKQLEPEPGDM 274 (318)
T ss_pred eCCCCEEEEEEeccccChhhh
Confidence 999999999999999999964
No 21
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.69 E-value=2.6e-15 Score=162.63 Aligned_cols=215 Identities=17% Similarity=0.149 Sum_probs=171.1
Q ss_pred cCCCCEEEEEEEEEecCcEEEEEEecC-cEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeeeccccc
Q 000449 667 VKLGSLVSGVVDVVTPNAVVVYVIAKG-YSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSL 745 (1497)
Q Consensus 667 ~~vG~iv~g~V~~i~~~Gv~V~l~~~~-~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS~K~~l 745 (1497)
..+|++.+..|.+.+++|+|++- ++ +-.-++|..... ...+.+||+++.+++.|.+.+ +++|.+..
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~--~~~~~~ilL~k~~~~---------~~e~evGdev~vFiY~D~~~r-l~aTt~~p- 69 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDA--GEDGTTILLPKSEPE---------EDELEVGDEVTVFIYVDSEDR-LIATTREP- 69 (287)
T ss_pred ccccceEEEEEEEeeceeEEEec--CCCceEEeccccCCc---------CCccccCcEEEEEEEECCCCc-eeheeecc-
Confidence 57899999999999999999986 32 336666555432 346789999999999998875 44444322
Q ss_pred cccccccCCcccCCCCCCEEEEEEEEEe-cceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCC
Q 000449 746 INSAQQLPSDASHIHPNSVVHGYVCNII-ETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETG 824 (1497)
Q Consensus 746 ~~~~~~~~~~~~~~~~G~~v~G~V~~i~-~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~ 824 (1497)
.+++|...+++|+.+. +.|+|++|+-..+.|+|.++++... +-.+++||.+.|++. +|. ++
T Consensus 70 ------------~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~wpq~Gd~l~v~l~-~Dk-k~ 131 (287)
T COG2996 70 ------------KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SLWPQKGDKLLVYLY-VDK-KG 131 (287)
T ss_pred ------------eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc----ccCCCCCCEEEEEEE-Ecc-CC
Confidence 2678999999999998 9999999988899999999987522 224789999999865 786 45
Q ss_pred eEEEEeeccccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccC---CCcEEEEEEEEEeeceeEEEecCCCceE
Q 000449 825 RITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFI---IGSVIEGKVHESNDFGVVVSFEEHSDVY 901 (1497)
Q Consensus 825 Ri~LSlK~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~---vG~~V~g~V~~i~~~G~~v~l~~~~~~~ 901 (1497)
||...++...... .+ +.... -+|.|+|+|++..+.|.|+.+++ ++.
T Consensus 132 Ri~g~~a~~~~l~-----------------~l------------~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~--~~~ 180 (287)
T COG2996 132 RIWGTLAIEKILE-----------------NL------------ATPAYNNLKNQEVDATVYRLLESGTFVITEN--GYL 180 (287)
T ss_pred cEEEEecchhHHH-----------------hc------------CCccchhhhcCeeeeEEEEEeccceEEEEcC--CeE
Confidence 9999987665410 00 12222 48999999999999999999965 899
Q ss_pred EEEeeeecCCccccCCCEEEEEEEEEecCCCEEEEEeehhhhhh
Q 000449 902 GFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDR 945 (1497)
Q Consensus 902 G~i~~~~l~~~~~~~G~~v~~~Vl~vd~~~~~v~lSlk~~l~~~ 945 (1497)
||||+++.. .+++.|+.++++|+.+.. +++|+||++|...+.
T Consensus 181 GfIh~sEr~-~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~ 222 (287)
T COG2996 181 GFIHKSERF-AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEM 222 (287)
T ss_pred EEEcchhhc-ccccCCceEEEEEEEEcc-CCeeecccccccHHh
Confidence 999999985 789999999999999987 999999999975543
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=2.7e-15 Score=143.45 Aligned_cols=79 Identities=18% Similarity=0.415 Sum_probs=75.5
Q ss_pred CCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCCc
Q 000449 1375 DLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1375 ~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~~ 1454 (1497)
.+++|+++.|+|+.|++|||||+|..+-+||||||++++.|++|..+++++||.|.|+|+++| ++++|+||+|.....|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~id-e~GKisLSIr~~~e~p 80 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID-ENGKISLSIRKLEEEP 80 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeec-cCCCcceehHHhhhCc
Confidence 468999999999999999999999999999999999999999999999999999999999999 5999999999987765
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.52 E-value=2.1e-14 Score=164.05 Aligned_cols=107 Identities=17% Similarity=0.247 Sum_probs=98.6
Q ss_pred CCCcEEEEEEEEEeceeEEEEeC--CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCCc
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLS--RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~--~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~~ 1454 (1497)
++|++|.|.|++|.+||+||+|. ++++|+||+|+||+.++.++.+.|++||.|.|+|+++|+++++|.||+|....+|
T Consensus 16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~p 95 (319)
T PTZ00248 16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPED 95 (319)
T ss_pred CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccch
Confidence 37999999999999999999996 5899999999999999999999999999999999999999999999999988876
Q ss_pred ccccccCCCCCCCCCCEEEEEEEEEee-ceeEEE
Q 000449 1455 ASQSEINNLSNLHVGDIVIGQIKRVES-YGLFIT 1487 (1497)
Q Consensus 1455 ~~~~~~~~~~d~~~G~iv~G~V~~v~~-~GvFV~ 1487 (1497)
|.. -.+.++.|++|.|.|+++.+ ||+|+.
T Consensus 96 w~~----~~e~~~~g~~v~~~V~~ia~~~g~~~e 125 (319)
T PTZ00248 96 IEA----CEEKFSKSKKVHSIMRHIAQKHGMSVE 125 (319)
T ss_pred HHH----HHHhCcCCCEEEEEEEEchhhcCCCHH
Confidence 443 35789999999999999965 999875
No 24
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.48 E-value=1.1e-13 Score=126.72 Aligned_cols=71 Identities=35% Similarity=0.632 Sum_probs=67.0
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCC---CCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESP---EKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~---~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
+++|++|.|+|++++++|+||+|+++++|+||++++||+++.++ .+.|++||.|+++|+++|+++++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 57899999999999999999999999999999999999997774 589999999999999999999999886
No 25
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.43 E-value=4.1e-13 Score=153.50 Aligned_cols=110 Identities=23% Similarity=0.258 Sum_probs=99.2
Q ss_pred cCCC-CCCEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 757 SHIH-PNSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 757 ~~~~-~G~~v~G~V~~i~~~G~FV~~~--~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
+.++ +|+++.|+|++|++||+||++. +|++||+|.|+++|.++.++.+.+++||.|.|+|+++|+++++|.||+|..
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v 91 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRV 91 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence 3466 7999999999999999999996 789999999999999999999999999999999999999999999999998
Q ss_pred ccCCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCCCcEEEEEEEEEee-ceeEEE
Q 000449 834 CCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESND-FGVVVS 893 (1497)
Q Consensus 834 ~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~vG~~V~g~V~~i~~-~G~~v~ 893 (1497)
.. +||+.. ...|+.|+.|+++|..+.+ +|+++.
T Consensus 92 ~~------------~pw~~~---------------~e~~~~g~~v~~~V~~ia~~~g~~~e 125 (319)
T PTZ00248 92 SP------------EDIEAC---------------EEKFSKSKKVHSIMRHIAQKHGMSVE 125 (319)
T ss_pred cc------------chHHHH---------------HHhCcCCCEEEEEEEEchhhcCCCHH
Confidence 76 466443 4668999999999999955 998765
No 26
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.41 E-value=2.1e-11 Score=132.60 Aligned_cols=229 Identities=17% Similarity=0.145 Sum_probs=173.7
Q ss_pred cCCcEEEEEEEEEeeeeEEEEEcCce-EEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCCCCcc
Q 000449 584 TDRLITHGWITKIEKHGCFVRFYNGV-QGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVS 662 (1497)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv-~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~~~~~~ 662 (1497)
.+|++....|.+..++|+|++=.++- .-++|.++.-.+ ...+|++|++-|. .|. ++|+.++.+.
T Consensus 4 ~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-------e~evGdev~vFiY-~D~-~~rl~aTt~~------ 68 (287)
T COG2996 4 KIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-------ELEVGDEVTVFIY-VDS-EDRLIATTRE------ 68 (287)
T ss_pred cccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC-------ccccCcEEEEEEE-ECC-CCceeheeec------
Confidence 57999999999999999999864332 678888866322 3579999999875 565 5677887753
Q ss_pred cccccCCCCEEEEEEEEEe-cCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeeec
Q 000449 663 EDDLVKLGSLVSGVVDVVT-PNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSA 741 (1497)
Q Consensus 663 ~~~~~~vG~iv~g~V~~i~-~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS~ 741 (1497)
+.+.+|+.-.++|+++. +.|+||+. +=.-+.++|.+++.... .-|.++||++-.-|++|+++ ||..++
T Consensus 69 --p~~tvg~~g~~~Vv~v~~~lGaFlD~--Gl~KDl~vp~~elp~~~------~~wpq~Gd~l~v~l~~Dkk~-Ri~g~~ 137 (287)
T COG2996 69 --PKATVGEYGWLKVVEVNKDLGAFLDW--GLPKDLLVPLDELPTLK------SLWPQKGDKLLVYLYVDKKG-RIWGTL 137 (287)
T ss_pred --ceEeecceeEEEEEEEcCCcceEEec--CCCcceeeehhhccccc------ccCCCCCCEEEEEEEEccCC-cEEEEe
Confidence 45778999999999998 88999998 33567899988886532 23789999999888999887 565554
Q ss_pred cccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeC
Q 000449 742 KYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNS 821 (1497)
Q Consensus 742 K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~ 821 (1497)
+. .+..++++....+--.|+.+.|+|.++...|.||-..++.-||+|.||.- ..++.||.+.++|+.+.+
T Consensus 138 a~--~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~--------~~prlG~~l~~rVi~~re 207 (287)
T COG2996 138 AI--EKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF--------AEPRLGERLTARVIGVRE 207 (287)
T ss_pred cc--hhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc--------ccccCCceEEEEEEEEcc
Confidence 32 22222333222222249999999999999999999999999999999874 367899999999999986
Q ss_pred CCCeEEEEeeccccCC--CCcchhhhhhhH
Q 000449 822 ETGRITLSLKQSCCSS--TDASFMQEHFLL 849 (1497)
Q Consensus 822 e~~Ri~LSlK~~~~~~--~~~~~~~~y~~~ 849 (1497)
.++|.||++...... .++..+-.|+..
T Consensus 208 -Dg~lnLSl~p~~~E~l~~daq~Il~yL~~ 236 (287)
T COG2996 208 -DGKLNLSLRPRAHEMLDEDAQMILTYLES 236 (287)
T ss_pred -CCeeecccccccHHhhhhhHHHHHHHHHH
Confidence 999999999875421 344444455533
No 27
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.41 E-value=1.7e-13 Score=131.31 Aligned_cols=77 Identities=30% Similarity=0.486 Sum_probs=73.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 758 HIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+++|++++|+|+.|++|||||+|.++-+||+|+|++.+.++.+..+.+++||.|.|+|+++|+ ++++.||+|....
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence 4679999999999999999999999999999999999999999999999999999999999997 9999999998865
No 28
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.40 E-value=7.1e-13 Score=120.96 Aligned_cols=71 Identities=28% Similarity=0.415 Sum_probs=67.3
Q ss_pred CCCCcEEEEEEEEEec-eeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTS-KGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~-~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|++|++|.|+|+++.+ +|+||+|+++.+|++|+|+++|+|+.++.+.|++||.|+|+|++++ ++++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~--~~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKK--DGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEec--CCEEEEEeC
Confidence 5789999999999986 8999999999999999999999999999999999999999999998 399999985
No 29
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=2e-12 Score=118.18 Aligned_cols=70 Identities=30% Similarity=0.565 Sum_probs=67.3
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCc--ccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGY--VESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~--~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|+++.|+|++++++|+||+|+++++|+||++++++++ .++|.+.|++||.|.|+|+++|+++++|.||++
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999999999999999999874 889999999999999999999999999999986
No 30
>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=99.34 E-value=5e-12 Score=116.01 Aligned_cols=73 Identities=25% Similarity=0.406 Sum_probs=70.0
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|++|++|.|+|++++++|+||+|+.+++|++|+++++|+|..++.+.|++||.|+++|+++|..++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 5789999999999999999999999999999999999999988999999999999999999988999999985
No 31
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.33 E-value=3.3e-12 Score=120.30 Aligned_cols=79 Identities=33% Similarity=0.520 Sum_probs=75.0
Q ss_pred ccCccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1369 HLEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1369 ~~~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
....+.++++|+++.|+|+++.++|+||+|+++++|++|+++++++++.++.+.|++||.|+++|+++|.++++|.|||
T Consensus 5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred chhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 4556788999999999999999999999999999999999999999999999999999999999999999999999986
No 32
>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=99.32 E-value=4.2e-12 Score=116.30 Aligned_cols=71 Identities=25% Similarity=0.386 Sum_probs=66.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCc---ccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADL---SKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~---~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
+++|+.+.|+|.+++++|+||++.++++||+|.++++|.+..+| .+.|++||.|.|+|+++|++++|+.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 46899999999999999999999999999999999999887665 578999999999999999999999886
No 33
>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=99.31 E-value=8.8e-12 Score=114.03 Aligned_cols=71 Identities=23% Similarity=0.287 Sum_probs=66.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 758 HIHPNSVVHGYVCNIIETGCFVRFL-GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~G~FV~~~-~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
+++.|++++|+|++|+++|+||+|+ ++++||+|+++++|. +.|++||.+.|+|+++|++++++.||+|+..
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 4788999999999999999999996 689999999999975 6899999999999999999999999999764
No 34
>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=99.31 E-value=3.9e-12 Score=123.28 Aligned_cols=90 Identities=40% Similarity=0.590 Sum_probs=73.7
Q ss_pred cCCCCEEEEEEEEEeCceEEEEcCCCcEEEEeccccCChhhccc----------ccccccCCCCCccCCCCEEEEEEEEE
Q 000449 131 ISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNE----------IEANEDNLLPTIFHVGQLVSCIVLQL 200 (1497)
Q Consensus 131 l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~----------~~~~~~~~L~~~f~vGq~v~~~V~~~ 200 (1497)
|++||.|+|+|.+|.+.++.|+||++++|+|+++++++.|.... ..+.+...+.++|++||.|+|.|++.
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 57999999999999999999999999999999999998752110 01122346789999999999999998
Q ss_pred ecCCcccceeEEEEecchhhHh
Q 000449 201 DDDKKEIGKRKIWLSLRLSLLY 222 (1497)
Q Consensus 201 ~~~~~~~~~~~i~LSl~p~~vn 222 (1497)
++..+ ++++|.||++|+++|
T Consensus 81 d~~~~--~~~~i~LSlr~~~vn 100 (100)
T cd05693 81 DKSKS--GKKRIELSLEPELVN 100 (100)
T ss_pred cCCcC--CCcEEEEEecHHHCC
Confidence 76532 156999999999998
No 35
>PRK08582 hypothetical protein; Provisional
Probab=99.28 E-value=1.6e-11 Score=126.09 Aligned_cols=79 Identities=25% Similarity=0.437 Sum_probs=74.6
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCCcc
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSRTA 1455 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~~~ 1455 (1497)
+++|++|.|+|++|+++|+||+|+++.+|+||++++++.|+.++.+.|++||.|+|+|+++|. .++|.||+++...+|+
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~~ 81 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRPK 81 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCch
Confidence 688999999999999999999999999999999999999999999999999999999999995 5999999999877663
No 36
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.27 E-value=2.7e-11 Score=110.83 Aligned_cols=72 Identities=18% Similarity=0.261 Sum_probs=67.1
Q ss_pred CCCCCcEEEEEEEEEeceeEEEEeC-CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1375 DLSPNMIVQGYVKNVTSKGCFIMLS-RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1375 ~l~~G~~v~G~V~~v~~~G~fV~l~-~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
||++|+++.|+|++|.++|+||+++ .+++||+|.+++++. +.|++||.+.|+|+++|++++++.||+++...
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 5889999999999999999999998 589999999999986 67999999999999999999999999998653
No 37
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.27 E-value=1.6e-11 Score=112.97 Aligned_cols=73 Identities=30% Similarity=0.517 Sum_probs=71.0
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
+++|+++.|+|.++.++|+||+|+.+++|+||++++++.+..++...|++||.|+++|+++|++++++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 6889999999999999999999999999999999999999999999999999999999999999999999985
No 38
>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=99.26 E-value=8.1e-12 Score=121.12 Aligned_cols=77 Identities=35% Similarity=0.513 Sum_probs=70.7
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcc-------------------cCCCCccCCCCEEEEEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYV-------------------ESPEKEFPIGKLVAGRVLSV 1436 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~-------------------~~~~~~~~~g~~V~~~V~~v 1436 (1497)
|++|++|.|.|++|+++|+||.|+.+++|++|+++++|+|. .++.+.|++||.|+|+|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 67899999999999999999999999999999999999873 34778899999999999999
Q ss_pred cCC---CCeEEEEEEeCCC
Q 000449 1437 EPL---SKRVEVTLKTSDS 1452 (1497)
Q Consensus 1437 d~~---~~~i~lslk~~~~ 1452 (1497)
|++ +++|.||||++..
T Consensus 81 d~~~~~~~~i~LSlr~~~v 99 (100)
T cd05693 81 DKSKSGKKRIELSLEPELV 99 (100)
T ss_pred cCCcCCCcEEEEEecHHHC
Confidence 976 7899999998764
No 39
>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=99.25 E-value=1.6e-11 Score=115.61 Aligned_cols=79 Identities=47% Similarity=0.685 Sum_probs=75.1
Q ss_pred cCCcccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 000449 752 LPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1497)
Q Consensus 752 ~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSl 830 (1497)
++..++++++|+++.|+|++++++|+||++.++++||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.|||
T Consensus 5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred chhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 5567888999999999999999999999999999999999999999999999999999999999999999999999986
No 40
>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=99.25 E-value=2.2e-11 Score=110.69 Aligned_cols=70 Identities=26% Similarity=0.558 Sum_probs=67.6
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|+++.|+|+++.++|+||+|+++++|++|+++++++++.++.+.|++||.++++|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 7899999999999999999998999999999999999999999999999999999999999999999985
No 41
>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=99.24 E-value=2.3e-11 Score=111.24 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=66.5
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc--ccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ--RADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~--~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
|+.+.|+|++++++|+||++.++++|++|.++++|.. ..++.+.|++||.|.|+|+++|++++|+.||++
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999999999999999999864 778999999999999999999999999999986
No 42
>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=99.24 E-value=2.4e-11 Score=110.17 Aligned_cols=69 Identities=38% Similarity=0.552 Sum_probs=66.7
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
|+++.|+|++|.++|+||+|+++++|+||++++++.+..++.+.|++||.++++|+++|++++++.|||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999899999999999999999999999999999999999999999999986
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.22 E-value=2.8e-11 Score=109.43 Aligned_cols=68 Identities=41% Similarity=0.798 Sum_probs=65.8
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
|++|.|+|+++.++|+||+|+++++|++|++++++++..++.+.|++||.|+++|+++|+++++|.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999999999999999999999999999999999999999999989999886
No 44
>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=99.22 E-value=5.6e-11 Score=109.35 Aligned_cols=73 Identities=37% Similarity=0.625 Sum_probs=70.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
+++|+++.|+|.++.++|+||++.++++||+|.+++++.+..++...|++||++.|+|+++|.+++++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 6789999999999999999999999999999999999998899999999999999999999999999999986
No 45
>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=99.22 E-value=5.3e-11 Score=109.08 Aligned_cols=70 Identities=24% Similarity=0.355 Sum_probs=64.9
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCC-CeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSR-KLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~-~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
+.|+++.|.|+++++||+||+|.. ..+|++|+|++++.++.++.+.|++||.|+++|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 579999999999999999999954 2799999999999999999999999999999999999765 999987
No 46
>PRK07252 hypothetical protein; Provisional
Probab=99.22 E-value=9.1e-11 Score=117.33 Aligned_cols=77 Identities=14% Similarity=0.360 Sum_probs=73.7
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
++|++|.|+|++|+++|+||+|..+++|++|+++|+++++.++.+.|++||.|+|+|+++|.+.+++.||++....+
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~ 78 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEE 78 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence 57999999999999999999999899999999999999999999999999999999999999899999999998764
No 47
>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=99.21 E-value=4.9e-11 Score=108.54 Aligned_cols=69 Identities=26% Similarity=0.344 Sum_probs=66.2
Q ss_pred CcEEE-EEEEEE-eceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1379 NMIVQ-GYVKNV-TSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1379 G~~v~-G~V~~v-~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
|++|. |.|+++ .++|+||+|.++++|++|+|++++.++.++.+.|++||.+.++|+++|+.+++|.|||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 7999999999899999999999999999999999999999999999999999999996
No 48
>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=99.20 E-value=4.7e-11 Score=108.59 Aligned_cols=70 Identities=30% Similarity=0.558 Sum_probs=67.2
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
|+++.|+|.+++++|+||+|++++.||+|.+++++++..++.+.|++||.+.|+|+++|++++|+.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 7899999999999999999999999999999999888889999999999999999999999999999985
No 49
>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=99.18 E-value=7.1e-11 Score=107.52 Aligned_cols=69 Identities=23% Similarity=0.334 Sum_probs=64.9
Q ss_pred CcEEE-EEEEEE-eeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 000449 586 RLITH-GWITKI-EKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1497)
Q Consensus 586 G~~~~-G~V~~i-~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~ 654 (1497)
|+++. |+|+++ .++|+||++.+|++||+|.|++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 67888 999999 6999999999999999999999988888888999999999999999999999999995
No 50
>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=99.17 E-value=1.2e-10 Score=107.64 Aligned_cols=74 Identities=22% Similarity=0.324 Sum_probs=69.2
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCC--CeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEe
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSR--KLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKT 1449 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~--~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~ 1449 (1497)
+++|+++.|.|.++.++|+||+|.. +.+|++|++++++.+..++.+.|++||.|+++|+++|.+.+++.||+|.
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 3679999999999999999999973 5999999999999999999999999999999999999888999999873
No 51
>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=99.16 E-value=1.4e-10 Score=106.36 Aligned_cols=72 Identities=24% Similarity=0.436 Sum_probs=69.2
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeC
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTS 1450 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~ 1450 (1497)
|++|.|+|+++.++|+||+|..+++|++|+++++++|+.++.+.|++||.++++|+++|..++++.||++..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999999999999999999999999999999999999999999998889999999864
No 52
>PRK08059 general stress protein 13; Validated
Probab=99.16 E-value=1.8e-10 Score=116.50 Aligned_cols=82 Identities=20% Similarity=0.424 Sum_probs=77.6
Q ss_pred cCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1373 IEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1373 ~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
++++++|++|.|.|.++.++|+||+|..+.+|++|++++++.|+.++.+.|++||.|+|+|+++|.+++++.||+++...
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 45689999999999999999999999999999999999999999999999999999999999999889999999999877
Q ss_pred Cc
Q 000449 1453 RT 1454 (1497)
Q Consensus 1453 ~~ 1454 (1497)
+|
T Consensus 82 ~~ 83 (123)
T PRK08059 82 AP 83 (123)
T ss_pred Cc
Confidence 65
No 53
>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=99.15 E-value=1.6e-10 Score=107.06 Aligned_cols=74 Identities=28% Similarity=0.434 Sum_probs=70.2
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCC-CeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeC
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSR-KLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTS 1450 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~-~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~ 1450 (1497)
++|++|.|+|++++++|+||+|.. +.+|++|++++++++..++.+.|++||.|+|+|+++|.+.+++.||+|++
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 469999999999999999999985 79999999999999999999999999999999999999899999999975
No 54
>PRK05807 hypothetical protein; Provisional
Probab=99.14 E-value=2.2e-10 Score=117.44 Aligned_cols=74 Identities=23% Similarity=0.399 Sum_probs=70.4
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
+++|++|.|+|+.|+++|+||+| .+.+|+||++++++.|+.++.+.|++||.|+|+|+++|. +++|.||++...
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 67899999999999999999999 578999999999999999999999999999999999996 799999999975
No 55
>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=99.14 E-value=1.4e-10 Score=105.14 Aligned_cols=69 Identities=28% Similarity=0.512 Sum_probs=65.5
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~ 654 (1497)
|+++.|+|+++.++|+||++.++++||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999899999999999988877888899999999999999999999999985
No 56
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.11 E-value=1.8e-10 Score=104.11 Aligned_cols=68 Identities=31% Similarity=0.503 Sum_probs=65.3
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
|+.+.|+|+++.++|+||++.++++||+|.+++++.+..++.+.|++||.+.|+|+++|++++|+.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 78899999999999999999999999999999999989999999999999999999999999999876
No 57
>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=99.10 E-value=2.3e-10 Score=104.48 Aligned_cols=71 Identities=25% Similarity=0.342 Sum_probs=66.6
Q ss_pred CCCCCEEEEEEEEEec-ceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 759 IHPNSVVHGYVCNIIE-TGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~-~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
+++|+++.|.|+++.+ +|+||+++++.+||+|.++++|++..++.+.|++||.|.|+|+++|. +|+.||++
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 3689999999999986 89999999999999999999999999999999999999999999984 89999985
No 58
>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=99.10 E-value=3.2e-10 Score=103.09 Aligned_cols=70 Identities=27% Similarity=0.334 Sum_probs=67.5
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|++|.|+|.++.++|+||+|+.+.+|++|++++++.+..++.+.|++||.++++|+++|+++++|.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 7899999999999999999999999999999999999999999999999999999999988899999985
No 59
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.09 E-value=2.9e-10 Score=103.04 Aligned_cols=68 Identities=26% Similarity=0.422 Sum_probs=63.9
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCC-CcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSD-GYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd-~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
|+++.|.|++++++|+||+|.++++|++|++++++ .+..++.+.|++||.|+|+|+++|.+.++|.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999999999999999996 578888899999999999999999999999875
No 60
>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=99.09 E-value=6.3e-10 Score=102.10 Aligned_cols=73 Identities=22% Similarity=0.339 Sum_probs=68.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
+++|+++.|+|++++++|+||++.++++|++|.+++++++..++.+.|++||.+.|+|+++|.+++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 3689999999999999999999999999999999999988778888999999999999999999999999974
No 61
>PRK08582 hypothetical protein; Provisional
Probab=99.08 E-value=5.2e-10 Score=115.01 Aligned_cols=76 Identities=30% Similarity=0.434 Sum_probs=71.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
+++|+++.|+|++|+++|+||++.++++||+|.+++++.++.++.+.|++||.|.|+|+++|. +++|.||+++...
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~ 78 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKD 78 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEeccc
Confidence 678999999999999999999999999999999999999999999999999999999999997 4999999998854
No 62
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.07 E-value=1.6e-10 Score=143.09 Aligned_cols=90 Identities=31% Similarity=0.569 Sum_probs=84.2
Q ss_pred CCCCCccCccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeE
Q 000449 1364 DTPGKHLEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRV 1443 (1497)
Q Consensus 1364 ~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i 1443 (1497)
++.+..+.++++|++|+++.|.|+|+++||+||+||-+.+|+||||++++.|+++|.+.+++||.|+++|+++|...++|
T Consensus 644 ~~~~~~v~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI 723 (780)
T COG2183 644 PTLDEGVESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRI 723 (780)
T ss_pred cchhhhhhhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCee
Confidence 33455677889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeCCCC
Q 000449 1444 EVTLKTSDSR 1453 (1497)
Q Consensus 1444 ~lslk~~~~~ 1453 (1497)
.|||+..+..
T Consensus 724 ~Lsmr~~~~~ 733 (780)
T COG2183 724 ALSMRLDEEE 733 (780)
T ss_pred eeEeeccCCc
Confidence 9999988764
No 63
>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=99.05 E-value=6.8e-10 Score=100.34 Aligned_cols=69 Identities=23% Similarity=0.404 Sum_probs=66.2
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
|+++.|.|.+++++|+||+|+.+.+|++|+++++++++.++.+.|++||.|+++|+++|. ++++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999999999999999999999999999999999999999999997 899999985
No 64
>PRK07252 hypothetical protein; Provisional
Probab=99.05 E-value=9e-10 Score=110.22 Aligned_cols=76 Identities=24% Similarity=0.319 Sum_probs=72.3
Q ss_pred CCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
++|+++.|+|.+++++|+||++.++++||+|.+++++.+..++...|++||.|.|+|+++|.+.+|+.||++....
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~ 77 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEE 77 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence 5799999999999999999999999999999999999988889889999999999999999999999999998864
No 65
>PHA02945 interferon resistance protein; Provisional
Probab=99.04 E-value=9.6e-10 Score=99.93 Aligned_cols=73 Identities=19% Similarity=0.218 Sum_probs=67.9
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeC--CCeEEEEEcccc--CCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLS--RKLDAKVLLSNL--SDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~--~~~~g~v~is~l--sd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
..+|+++.|+|+. .++|+||.|. ++.+|+||+|++ ++.|+++ .+++ .||.|.|+|+.+|+..+.|.||||...
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 3679999999999 9999999997 489999999955 9999999 9999 999999999999999999999999754
No 66
>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=99.03 E-value=1.3e-09 Score=101.58 Aligned_cols=73 Identities=25% Similarity=0.416 Sum_probs=67.6
Q ss_pred CcEEEEEEEEEeceeEEEEeC---CCeEEEEEccccCCCcc-cCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLS---RKLDAKVLLSNLSDGYV-ESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~---~~~~g~v~is~lsd~~~-~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
|+++.|.|+++.++|+||+|. ++.+|++|++++++.+. .++.+.|++||.|+++|+++| .+++.||+|..+.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~~ 77 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQD 77 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecccC
Confidence 789999999999999999998 46999999999999986 899999999999999999999 89999999986543
No 67
>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=99.02 E-value=6.4e-10 Score=100.81 Aligned_cols=68 Identities=29% Similarity=0.423 Sum_probs=63.3
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCc-ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD-GQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~-~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
|+.+.|+|.+++++|+||++.++++||+|.++++| ....++.+.|++||+|.|+|+++|.+++|+.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 68899999999999999999999999999999996 566788889999999999999999999999875
No 68
>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=99.02 E-value=1e-09 Score=98.41 Aligned_cols=66 Identities=23% Similarity=0.404 Sum_probs=59.7
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS 653 (1497)
|+++.|+|+++.++|+||++.++++||+|.++++..+.. .+.|++|+.++|+|+++|++++++.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998899999999999754333 677999999999999999999999886
No 69
>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=99.02 E-value=1.2e-09 Score=99.96 Aligned_cols=71 Identities=24% Similarity=0.361 Sum_probs=64.5
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCC-cccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDG-YVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~-~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
+.+|+++.|.|++++++|+||+|.++++|++|++++++. +..++.+.|++||.|+++|+++|.+++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 367999999999999999999999899999999999865 55577889999999999999999999998774
No 70
>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=99.01 E-value=1.5e-09 Score=100.41 Aligned_cols=73 Identities=25% Similarity=0.331 Sum_probs=68.5
Q ss_pred CCCCEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeec
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLG--RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQ 832 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~--gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~ 832 (1497)
+.|+++.|+|.++.++|+||++.+ +++||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.||+|+
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 479999999999999999999963 6999999999999999999999999999999999999999999999874
No 71
>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=99.01 E-value=1.4e-09 Score=99.76 Aligned_cols=70 Identities=26% Similarity=0.406 Sum_probs=64.5
Q ss_pred CCCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSl 830 (1497)
..|+++.|.|+++++||+||++.+ +.+||+|.++++|.+..++.+.|++||+|.|+|+++|.++ |+.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 479999999999999999999954 3799999999999998999999999999999999999876 999886
No 72
>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=99.01 E-value=1.3e-09 Score=101.00 Aligned_cols=74 Identities=32% Similarity=0.558 Sum_probs=69.5
Q ss_pred CCCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
++|+.+.|+|.+++++|+||++.+ +++||+|.+++++.+..++.+.|++||.|.|+|+++|++++++.|++|..
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 368999999999999999999985 89999999999998888888999999999999999999999999999875
No 73
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.99 E-value=1.7e-09 Score=96.87 Aligned_cols=66 Identities=26% Similarity=0.375 Sum_probs=61.3
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
|+++.|.|+++.++|+||+|..+++|++|.+++++.+.. .+.|++||.|.|+|+++|+++++|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998789999999999877665 778999999999999999999999886
No 74
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.98 E-value=1.8e-09 Score=97.25 Aligned_cols=67 Identities=30% Similarity=0.370 Sum_probs=61.1
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k 655 (1497)
|+++.|+|+++.++|++|+| +|++||+|.+++++.+..++.+ .+||.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 8999999999999876666655 4899999999999999999999974
No 75
>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=98.98 E-value=1.8e-09 Score=98.79 Aligned_cols=71 Identities=27% Similarity=0.407 Sum_probs=64.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcc-cccCcccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG-QRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~-~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
+++|+.+.|+|++++++|+||++.++++||+|.++++|. ...++...|++||+|.|+|.++|.+++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999999999999999999999999999999999874 44577788999999999999999999998764
No 76
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.97 E-value=1.4e-09 Score=98.00 Aligned_cols=68 Identities=28% Similarity=0.559 Sum_probs=65.0
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
|+++.|.|++++++|+||+|+.+.+|++|++++++.+..++.+.|++||.|+|+|+++|.+.+++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999999999999999999999999999999999999999999888999876
No 77
>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=98.97 E-value=2.3e-09 Score=98.23 Aligned_cols=72 Identities=25% Similarity=0.433 Sum_probs=68.6
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
|+++.|+|+++.++|+||++.++++|++|.+++++.+..++.+.|++||.+.|+|+++|.+++++.||++..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999999999999999999998888999999999999999999999999999999864
No 78
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.97 E-value=2.4e-09 Score=97.37 Aligned_cols=70 Identities=20% Similarity=0.218 Sum_probs=66.5
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k 655 (1497)
|+++.|+|.++.++|+||++.++.+||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 7899999999999999999988999999999999988889999999999999999999998999999974
No 79
>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=98.94 E-value=2.9e-09 Score=96.04 Aligned_cols=68 Identities=28% Similarity=0.393 Sum_probs=64.9
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
|+++.|.|.++.++|+||+|+.+.+|++|++++++.++.++.+.|++||.|+++|+++|+ ++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 789999999999999999999899999999999999999998999999999999999998 89999884
No 80
>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=98.93 E-value=3.2e-09 Score=100.75 Aligned_cols=76 Identities=20% Similarity=0.133 Sum_probs=68.7
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCC----CcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSD----GYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd----~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
+++|++|.|.|+++.++|+||+|+.+.+|++|++++++ .+..+..+.|++||.+.|+|++++++ +++.||++...
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~~ 82 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSLK 82 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCccc
Confidence 47899999999999999999999999999999999995 56677788899999999999999865 99999998754
Q ss_pred C
Q 000449 1452 S 1452 (1497)
Q Consensus 1452 ~ 1452 (1497)
.
T Consensus 83 ~ 83 (86)
T cd05789 83 Y 83 (86)
T ss_pred c
Confidence 3
No 81
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.91 E-value=9.8e-10 Score=119.41 Aligned_cols=78 Identities=24% Similarity=0.409 Sum_probs=73.4
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeC--CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLS--RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~--~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
..+|++|-|+|++|.+||+||.|. ++++|+||||+++..|+++.++++++||.|.|+|+++|+..+.|.||||....+
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 367999999999999999999996 589999999999999999999999999999999999999999999999987653
No 82
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.91 E-value=2.4e-09 Score=95.04 Aligned_cols=72 Identities=26% Similarity=0.412 Sum_probs=64.7
Q ss_pred CCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeeecc
Q 000449 670 GSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAK 742 (1497)
Q Consensus 670 G~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS~K 742 (1497)
|++|+|+|.++++++++|++. +.+++|+||..||||+..+++.+.+++++||++..+++++...+.+.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEeccccEEEEecC
Confidence 789999999999999999993 249999999999999888889999999999999877888888777888876
No 83
>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=98.90 E-value=5.1e-09 Score=94.57 Aligned_cols=69 Identities=23% Similarity=0.384 Sum_probs=65.0
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k 655 (1497)
|+++.|+|+++.++|+||++.++..||+|.+++++.+..++.+.|++||.++|+|+++|+ ++++.||++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 788999999999999999999899999999999988888888889999999999999999 899999985
No 84
>PRK08059 general stress protein 13; Validated
Probab=98.90 E-value=6.1e-09 Score=105.41 Aligned_cols=80 Identities=30% Similarity=0.417 Sum_probs=75.1
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 756 ASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
++++++|+.+.|.|.+++++|+||++.+++.||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.||++....
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 45688999999999999999999999999999999999999888888889999999999999999999999999998854
No 85
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.90 E-value=2.8e-09 Score=136.53 Aligned_cols=82 Identities=16% Similarity=0.313 Sum_probs=76.1
Q ss_pred CCCCCcEEE-EEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1375 DLSPNMIVQ-GYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1375 ~l~~G~~v~-G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
+.++|++|. |+|++|++||+||+|.++++||||||+|+|.|+.++.+.|++||.|+|+|+++|. .++|.||+|....+
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 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLPE 828 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEeccccC
Confidence 568999996 6999999999999999999999999999999999999999999999999999996 79999999998887
Q ss_pred cccc
Q 000449 1454 TASQ 1457 (1497)
Q Consensus 1454 ~~~~ 1457 (1497)
||..
T Consensus 829 Pw~~ 832 (891)
T PLN00207 829 ANSE 832 (891)
T ss_pred chhh
Confidence 7543
No 86
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.89 E-value=6e-09 Score=94.60 Aligned_cols=72 Identities=32% Similarity=0.487 Sum_probs=68.2
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
++|+++.|+|.+++++|+||+++.+..|++|.+++++.+..++.+.|++||.++++|++++..++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 369999999999999999999999999999999999999888888999999999999999988899999985
No 87
>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=98.89 E-value=5.6e-09 Score=94.17 Aligned_cols=68 Identities=29% Similarity=0.475 Sum_probs=64.5
Q ss_pred CCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1378 PNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1378 ~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
+|+++.|.|.++.++|+||+|+ +.+|++|.+++++.++.++.+.|++||.|+++|+++|.+++++.||
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 4899999999999999999998 7999999999999999999999999999999999999889999876
No 88
>PRK05807 hypothetical protein; Provisional
Probab=98.89 E-value=7.7e-09 Score=106.10 Aligned_cols=74 Identities=27% Similarity=0.466 Sum_probs=70.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
+++|+++.|+|+.++++|+||++ ++..||+|.+++++.++.++.+.|++||.|.|+|+++|. +++|.||+|...
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 67899999999999999999999 778999999999999999999999999999999999998 799999999875
No 89
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.87 E-value=8.2e-09 Score=92.99 Aligned_cols=67 Identities=27% Similarity=0.477 Sum_probs=61.4
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
|+.+.|+|.++.++|+||+| ++++||+|.+++++.+..++.. .+||.+.|+|+++|.+++++.||.|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78899999999999999999 8899999999999877777665 4899999999999999999999975
No 90
>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=98.85 E-value=1.3e-08 Score=95.77 Aligned_cols=70 Identities=30% Similarity=0.448 Sum_probs=62.8
Q ss_pred CCcEEEEEEEEEeceeEEEEeCC-CeEEEEEccccCCCccc-----------CCCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1378 PNMIVQGYVKNVTSKGCFIMLSR-KLDAKVLLSNLSDGYVE-----------SPEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1378 ~G~~v~G~V~~v~~~G~fV~l~~-~~~g~v~is~lsd~~~~-----------~~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
+|+++.|+|++++++|+||+|++ +++|++|++++++.+.. .+...|++||.|+++|+++|.+.+++.|
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 38999999999999999999998 79999999999976432 3557899999999999999988899999
Q ss_pred EE
Q 000449 1446 TL 1447 (1497)
Q Consensus 1446 sl 1447 (1497)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 86
No 91
>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=98.85 E-value=1.1e-08 Score=96.26 Aligned_cols=76 Identities=20% Similarity=0.154 Sum_probs=70.9
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
.++|++|.|+|+++.+.|++|+++...+|++|+++++..+.+++.+.|++||.+.|+|++++.+ +++.||++..+.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~~~ 79 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNEL 79 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCCCC
Confidence 4789999999999999999999999999999999999999999999999999999999999965 899999987543
No 92
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.85 E-value=1.1e-08 Score=96.95 Aligned_cols=75 Identities=16% Similarity=0.108 Sum_probs=66.2
Q ss_pred CCCCCcEEEEEEEEEece--eEEEEeCCCeEEEEEccccCC---CcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEe
Q 000449 1375 DLSPNMIVQGYVKNVTSK--GCFIMLSRKLDAKVLLSNLSD---GYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKT 1449 (1497)
Q Consensus 1375 ~l~~G~~v~G~V~~v~~~--G~fV~l~~~~~g~v~is~lsd---~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~ 1449 (1497)
.+++|++|.|+|+++.++ ||||+|+++.+||+|++++++ ..+.++.+.|++||.|.|+|+......+...||..-
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~ 83 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNI 83 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEE
Confidence 456899999999999997 999999999999999999998 567788889999999999999987667766776654
No 93
>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=98.84 E-value=7.4e-09 Score=93.29 Aligned_cols=68 Identities=31% Similarity=0.440 Sum_probs=64.0
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
|+.+.|+|++++++|+||++.++..||+|.+++++.+..++...|++||.+.|+|+++|++++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 67899999999999999999999999999999998888888889999999999999999999999875
No 94
>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=98.84 E-value=1.4e-08 Score=94.66 Aligned_cols=72 Identities=31% Similarity=0.505 Sum_probs=66.3
Q ss_pred CCEEEEEEEEEecceEEEEeC---CCeEEEEeCCCCCcccc-cCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 762 NSVVHGYVCNIIETGCFVRFL---GRLTGFAPRSKAVDGQR-ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~---~gl~Glvp~sels~~~~-~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
|+++.|.|++++++|+||++. ++..||+|.++++|.+. .++...|++||.|.|+|+++| ++++.+|+|....
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 678999999999999999998 47999999999999876 888889999999999999999 8999999998754
No 95
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.82 E-value=9.2e-09 Score=131.84 Aligned_cols=87 Identities=16% Similarity=0.184 Sum_probs=78.5
Q ss_pred cCCCCCCEEE-EEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 757 SHIHPNSVVH-GYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 757 ~~~~~G~~v~-G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+.++|+++. |+|++|++||+||++.++++||+|.|+++|+++.++.+.|++||.|.|+|+++|+ ++||.||+|....
T Consensus 749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~ 827 (891)
T PLN00207 749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLP 827 (891)
T ss_pred cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecccc
Confidence 4567999995 6999999999999999999999999999999999999999999999999999997 7999999998765
Q ss_pred CCCCcchhhhhhhHHHHHHHh
Q 000449 836 SSTDASFMQEHFLLEEKIAML 856 (1497)
Q Consensus 836 ~~~~~~~~~~y~~~~~~~~~~ 856 (1497)
+||+....+
T Consensus 828 ------------~Pw~~~~~~ 836 (891)
T PLN00207 828 ------------EANSEKSSQ 836 (891)
T ss_pred ------------Cchhhhhhh
Confidence 678766554
No 96
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.82 E-value=1.3e-08 Score=115.49 Aligned_cols=78 Identities=23% Similarity=0.425 Sum_probs=72.8
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCC--CeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSR--KLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~--~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
+++|++|.|.|++|.++|+||+|.. +++|++|+|++++.++.++.+.|++||.|.|+|+++|.++++|.||+|....+
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 4689999999999999999999974 79999999999999999999999999999999999999999999999976643
No 97
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.81 E-value=1.3e-08 Score=92.43 Aligned_cols=62 Identities=21% Similarity=0.360 Sum_probs=58.3
Q ss_pred CcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCc--ccCCCCccCCCCEEEEEEEEEcCCC
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGY--VESPEKEFPIGKLVAGRVLSVEPLS 1440 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~--~~~~~~~~~~g~~V~~~V~~vd~~~ 1440 (1497)
|++|.|+|+++.++|+||+|+.+++|++|+++++++| ..++.+.|++||.|+|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 7899999999999999999999999999999999997 7889899999999999999998543
No 98
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.80 E-value=1.8e-08 Score=90.90 Aligned_cols=68 Identities=29% Similarity=0.381 Sum_probs=63.5
Q ss_pred CcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 000449 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1497)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~ 654 (1497)
|+++.|+|+++.++|+||++.++..||+|.+++++.+..++.+.|++||.++|+|+++|+ ++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 678999999999999999998899999999999988877888899999999999999999 89999884
No 99
>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=98.77 E-value=2.4e-08 Score=90.03 Aligned_cols=68 Identities=25% Similarity=0.428 Sum_probs=63.4
Q ss_pred CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 000449 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1497)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS 653 (1497)
+|+++.|+|+++.++|+||++. ++.||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||
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 4899999999999999999995 7999999999998888888889999999999999999999999876
No 100
>PHA02945 interferon resistance protein; Provisional
Probab=98.77 E-value=3.2e-08 Score=90.15 Aligned_cols=72 Identities=17% Similarity=0.314 Sum_probs=66.1
Q ss_pred CCCCEEEEEEEEEecceEEEEeC--CCeEEEEeCCCC--CcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKA--VDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~--~gl~Glvp~sel--s~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
.+|+.+.|+|.. .++|+||.+. +|++||+|.|+. +...+.+ .+.+ +||+|.|+|+++|+.++.|-||||...
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V~ 85 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC 85 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence 579999999999 9999999995 699999999955 8888888 8888 999999999999999999999999764
No 101
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.75 E-value=6.1e-08 Score=105.90 Aligned_cols=111 Identities=23% Similarity=0.266 Sum_probs=88.2
Q ss_pred CCCcCCCCEEEEEEEEeec-ccCCccEEEEEeeccccCCCCCCCCCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEece
Q 000449 1314 LSGYDEGQFVKCKVLEISR-TVRGTFHVELSLRSSLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSK 1392 (1497)
Q Consensus 1314 ~~~~~~g~~v~~~Vl~~d~-~~~g~~~i~lS~R~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~ 1392 (1497)
...|..+..+.+.+++.-. +. .++++.| .|-. .....+++|++|.|+|+++.++
T Consensus 24 ~Gty~~~~~i~as~~G~~~id~-~~~~Isv--~P~~----------------------~~~~~~~~GdiV~GkV~~i~~~ 78 (189)
T PRK09521 24 EGTYEDNGEVYASVVGKVFIDD-INRKISV--IPFK----------------------KTPPLLKKGDIVYGRVVDVKEQ 78 (189)
T ss_pred CCEEeeCCEEEEEeeEEEEEcC-CCCEEEE--ecCc----------------------CCCCCCCCCCEEEEEEEEEcCC
Confidence 3466678889999888632 11 1345544 3321 1134567999999999999999
Q ss_pred eEEEEeC----------CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1393 GCFIMLS----------RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1393 G~fV~l~----------~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
|+||+|+ .+.+|++|++++++.+..++.+.|++||.|.|+|++++ +++.||++....
T Consensus 79 g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~~l 145 (189)
T PRK09521 79 RALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGKDL 145 (189)
T ss_pred eEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecCCc
Confidence 9999985 36899999999999999999999999999999999998 789999998654
No 102
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.74 E-value=3.8e-08 Score=89.32 Aligned_cols=72 Identities=36% Similarity=0.522 Sum_probs=67.0
Q ss_pred CCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
++|+.+.|.|.+++++|+||++.+++.|++|.+++++.+..++...|++||.+.|+|+++|.+++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 369999999999999999999998999999999999887777778899999999999999999999999975
No 103
>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=98.73 E-value=2e-08 Score=126.15 Aligned_cols=71 Identities=17% Similarity=0.220 Sum_probs=66.2
Q ss_pred CCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccC----CCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1375 DLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLS----DGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1375 ~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~ls----d~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
++++|++|.|+|++|++||+||+|.++.+||||+|+++ +.++.++.+.|++||.|+++|+++| .++||.|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID-~~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID-DRGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC-CCCCeeec
Confidence 47899999999999999999999999999999999996 4689999999999999999999999 57899886
No 104
>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=98.70 E-value=4.7e-08 Score=92.76 Aligned_cols=75 Identities=16% Similarity=0.146 Sum_probs=67.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCc----ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD----GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~----~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
.++|+++.|.|.+++++|+||++.++++|++|.+++++ ....++.+.|++||.+.|+|+++|++ +++.||++...
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~~ 82 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSLK 82 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCccc
Confidence 46899999999999999999999999999999999986 34466777899999999999999976 99999998764
No 105
>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=98.69 E-value=1.1e-07 Score=88.22 Aligned_cols=68 Identities=24% Similarity=0.407 Sum_probs=61.9
Q ss_pred CccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1371 EKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1371 ~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
..+.++++|+++.|.|++++++|+||+|.++.+|++|++++. +.|++||.++++|.++ .+++++.+|+
T Consensus 9 ~~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred cchhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 346779999999999999999999999999999999999864 4599999999999999 7899999986
No 106
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.69 E-value=4.8e-08 Score=126.19 Aligned_cols=76 Identities=24% Similarity=0.315 Sum_probs=72.1
Q ss_pred CCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeC
Q 000449 1374 EDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTS 1450 (1497)
Q Consensus 1374 ~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~ 1450 (1497)
.++++|++|.|+|++|.+||+||+|.++.+|++|+|++++.|+.++.+.|++||.|+++|+++|.. ++|.||+|..
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 457899999999999999999999999999999999999999999999999999999999999976 9999999863
No 107
>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=98.68 E-value=7.2e-08 Score=91.44 Aligned_cols=75 Identities=17% Similarity=0.150 Sum_probs=66.1
Q ss_pred CCCCCCEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCc---ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeec
Q 000449 758 HIHPNSVVHGYVCNIIET--GCFVRFLGRLTGFAPRSKAVD---GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQ 832 (1497)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~--G~FV~~~~gl~Glvp~sels~---~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~ 832 (1497)
.+++|+++.|.|++|.++ |+||++.++.+||+|.++++| .++.++.+.|++||.|.|+|++.....+.-.|+...
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~ 83 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNI 83 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEE
Confidence 467899999999999997 999999999999999999998 667888889999999999999987766666666543
No 108
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.67 E-value=5.6e-08 Score=86.32 Aligned_cols=65 Identities=34% Similarity=0.581 Sum_probs=61.3
Q ss_pred EEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEE
Q 000449 1382 VQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVT 1446 (1497)
Q Consensus 1382 v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ls 1446 (1497)
+.|+|.++.++|+||+++.+.+|++|.+++++.+..++.+.|++||.|+++|+++|.+++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999999999999999999998888999999999999999999888888875
No 109
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.62 E-value=3.6e-07 Score=103.06 Aligned_cols=109 Identities=19% Similarity=0.164 Sum_probs=87.1
Q ss_pred CcCCCCEEEEEEEEeecccCCccEEEEEeeccccCCCCCCCCCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEeceeEE
Q 000449 1316 GYDEGQFVKCKVLEISRTVRGTFHVELSLRSSLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSKGCF 1395 (1497)
Q Consensus 1316 ~~~~g~~v~~~Vl~~d~~~~g~~~i~lS~R~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G~f 1395 (1497)
.|..+..+++++.+.-... ++ .++.++.. . .--.++||+|.|+|++++++|+|
T Consensus 28 ty~~~g~i~As~~G~~~~~--~~--~i~V~p~~-----~------------------~y~P~vGDiViG~V~~i~~~~~~ 80 (235)
T PRK04163 28 TYKENGKIYSTVVGLVDIK--DD--KVRVIPLE-----G------------------KYIPKVGDLVIGKVTDVTFSGWE 80 (235)
T ss_pred eEEeCCEEEEEEeEEEEEE--CC--EEEEEECC-----C------------------cccCCCCCEEEEEEEEEeCceEE
Confidence 4556777888888864311 11 46666643 0 12347899999999999999999
Q ss_pred EEeCCCeEEEEEccccCCCcc----cCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1396 IMLSRKLDAKVLLSNLSDGYV----ESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1396 V~l~~~~~g~v~is~lsd~~~----~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
|+|+...+|++|++++++.++ .++.+.|++||+|+|+|+++++ .+.+.||++....
T Consensus 81 vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~LS~k~~~l 140 (235)
T PRK04163 81 VDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVVLTLKGKGL 140 (235)
T ss_pred EEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEEEEEcCCCC
Confidence 999999999999999999998 7888999999999999999984 4569999987544
No 110
>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=98.59 E-value=7.5e-08 Score=121.17 Aligned_cols=71 Identities=21% Similarity=0.324 Sum_probs=66.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCC----cccccCcccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 000449 758 HIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAV----DGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1497)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels----~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LS 829 (1497)
+.++|+++.|+|++|++||+||++.+|++||+|.|+++ |.++.++.+.|++||.|.|+|+++|. ++|+.|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 47899999999999999999999999999999999995 47889999999999999999999994 7899886
No 111
>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=98.59 E-value=2.3e-07 Score=86.03 Aligned_cols=71 Identities=24% Similarity=0.337 Sum_probs=62.9
Q ss_pred hHHhhhhhccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 000449 575 AILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1497)
Q Consensus 575 ~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~ 654 (1497)
+++..+++++.|+.+.|+|+++.++|+||++.++..||+|.+++. +.|++||.++++|+++ .+++++.+|+
T Consensus 6 ~~~~~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 6 DPACTMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred ccccchhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 344556678899999999999999999999998999999999863 4589999999999999 8899999885
No 112
>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=98.58 E-value=2.1e-07 Score=87.54 Aligned_cols=70 Identities=19% Similarity=0.335 Sum_probs=61.6
Q ss_pred CCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCccccc-----------CcccCcCCCCEEEEEEEEEeCCCCeEEE
Q 000449 761 PNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVNSETGRITL 828 (1497)
Q Consensus 761 ~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~~-----------~~~~~~~~Gq~V~v~V~~iD~e~~Ri~L 828 (1497)
+|+.+.|+|.+++++|+||++.+ +++||+|.++++++... .+...|++||.|.|+|.++|.+++++.+
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 38899999999999999999988 89999999999865321 3456899999999999999999999998
Q ss_pred Ee
Q 000449 829 SL 830 (1497)
Q Consensus 829 Sl 830 (1497)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 86
No 113
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.57 E-value=5.6e-08 Score=105.99 Aligned_cols=76 Identities=26% Similarity=0.390 Sum_probs=72.0
Q ss_pred CCCCEEEEEEEEEecceEEEEe--CCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRF--LGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~--~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+|+.+-|+|.+|.+||+||.+ ++|++||+|.||++...+.+..+++++||.+.|+|+++|++++.+-||||....
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 3699999999999999999999 479999999999999999999999999999999999999999999999998754
No 114
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.56 E-value=1.8e-07 Score=106.45 Aligned_cols=76 Identities=26% Similarity=0.359 Sum_probs=71.4
Q ss_pred CCCCEEEEEEEEEecceEEEEeCC--CeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLG--RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~--gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
++|+.+.|+|.++.++|+||++.+ +++||+|.|++++.+..++.+.|++||.|.|+|+++|.+++++.||+|....
T Consensus 7 ~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~ 84 (262)
T PRK03987 7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 579999999999999999999974 8999999999999989999999999999999999999999999999997754
No 115
>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=98.54 E-value=1.8e-07 Score=82.99 Aligned_cols=65 Identities=34% Similarity=0.543 Sum_probs=59.6
Q ss_pred EEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 000449 589 THGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1497)
Q Consensus 589 ~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS 653 (1497)
+.|+|+++.++|+||++.++..||+|.+++++....++.+.|++||.++|+|+++|++++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 36999999999999999889999999999998776778888999999999999999999998875
No 116
>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=98.54 E-value=2.5e-07 Score=84.11 Aligned_cols=63 Identities=14% Similarity=0.206 Sum_probs=58.2
Q ss_pred CCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc--ccCcccCcCCCCEEEEEEEEEeCCCC
Q 000449 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ--RADLSKTYYVGQSVRSNILDVNSETG 824 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~--~~~~~~~~~~Gq~V~v~V~~iD~e~~ 824 (1497)
|+++.|.|.++.++|+||++.++++|++|.+++++.+ ..++.+.|++||.|.|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 7899999999999999999999999999999999874 77888899999999999999997654
No 117
>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=98.52 E-value=3.9e-07 Score=85.60 Aligned_cols=74 Identities=16% Similarity=0.218 Sum_probs=68.7
Q ss_pred CCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
++|+++.|+|.++.+.|++|++..+.+|++|.++++.....++.+.|++||.+.|+|+++|.+ +++.||++...
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~~ 78 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNE 78 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCCC
Confidence 579999999999999999999999999999999999877778888999999999999999987 89999998654
No 118
>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=98.51 E-value=3.8e-07 Score=88.96 Aligned_cols=74 Identities=20% Similarity=0.445 Sum_probs=65.2
Q ss_pred cEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccC-----------CCCccCCCCEEEEEEEEEcCCC-----CeE
Q 000449 1380 MIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVES-----------PEKEFPIGKLVAGRVLSVEPLS-----KRV 1443 (1497)
Q Consensus 1380 ~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~-----------~~~~~~~g~~V~~~V~~vd~~~-----~~i 1443 (1497)
+++.|+|+++.++|+||+|. .++|++|++++++++... +...|++||.|+++|.++|.+. +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47999999999999999998 599999999999887643 4578999999999999999653 589
Q ss_pred EEEEEeCCCCc
Q 000449 1444 EVTLKTSDSRT 1454 (1497)
Q Consensus 1444 ~lslk~~~~~~ 1454 (1497)
.||++....+|
T Consensus 80 ~ls~k~~~~g~ 90 (99)
T cd04460 80 GLTMRQPGLGK 90 (99)
T ss_pred EEEEecCCCCc
Confidence 99999988776
No 119
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.49 E-value=1.4e-07 Score=117.45 Aligned_cols=81 Identities=23% Similarity=0.383 Sum_probs=77.6
Q ss_pred cccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 755 DASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 755 ~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
++.++++|+.+.|+|.|+++||+||+++-+.+||+|.|.+++.++.+|.+.+++||.|+|+|+++|..++||.|||+...
T Consensus 652 ~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 652 SITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred hHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999886
Q ss_pred c
Q 000449 835 C 835 (1497)
Q Consensus 835 ~ 835 (1497)
.
T Consensus 732 ~ 732 (780)
T COG2183 732 E 732 (780)
T ss_pred C
Confidence 5
No 120
>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=98.46 E-value=5.3e-07 Score=86.27 Aligned_cols=76 Identities=12% Similarity=0.119 Sum_probs=68.3
Q ss_pred CCCCcEEEEEEEEEeceeEEEEe--------CCCeEEEEEccccCCCccc--CCCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIML--------SRKLDAKVLLSNLSDGYVE--SPEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l--------~~~~~g~v~is~lsd~~~~--~~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
+++|++|.|+|++++...++|+| .....|.+|++++.+.+.. ++.+.|++||+|+|+|++++ +...+.|
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~-~~~~~~L 82 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG-DASSYYL 82 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcC-CCCCcEE
Confidence 47899999999999999999999 7889999999999998887 68899999999999999997 3477999
Q ss_pred EEEeCCC
Q 000449 1446 TLKTSDS 1452 (1497)
Q Consensus 1446 slk~~~~ 1452 (1497)
|++..+.
T Consensus 83 st~~~~l 89 (92)
T cd05791 83 STAENEL 89 (92)
T ss_pred EecCCCC
Confidence 9987553
No 121
>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=98.45 E-value=2.8e-07 Score=118.90 Aligned_cols=71 Identities=23% Similarity=0.330 Sum_probs=66.4
Q ss_pred CCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1374 EDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1374 ~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
..+++|++|.|+|++|.+||+||+|.++.+|++|+|++++.|+.++.+.|++||.|+|+|+++|. .++|.|
T Consensus 614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 35789999999999999999999999999999999999999999999999999999999999996 677764
No 122
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.43 E-value=5.8e-07 Score=116.26 Aligned_cols=76 Identities=25% Similarity=0.418 Sum_probs=72.1
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
.+.++|+++.|.|+++.+||+||++.++.+||+|.|+++|.++.++.+.|++||.|.|+|+++|++ +|+.||+|..
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 457899999999999999999999999999999999999999999999999999999999999987 9999999864
No 123
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.41 E-value=4.1e-07 Score=111.31 Aligned_cols=119 Identities=17% Similarity=0.261 Sum_probs=92.9
Q ss_pred ceeeeeccchhHHHhhcccccCCCCEEEEEEEEEecCCCeEEEEcchhhccc-----ccccccccC--CCcEEEEEEEEE
Q 000449 437 PAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEG-----LVFTHSDVK--PGMVVKGKVIAV 509 (1497)
Q Consensus 437 ~gfv~~s~~~~~~~~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~~-----~~~~~~~l~--~G~iv~g~V~~v 509 (1497)
.++++.++.. .....+++|+.+++.|...+ +++....+.++..... +...++.++ .|++|+|+|.++
T Consensus 72 ~~eI~L~eAk-----~~~~~~~vGD~ie~~I~~~~-fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri 145 (470)
T PRK09202 72 TKEISLEEAR-----KIDPDAEVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRV 145 (470)
T ss_pred cceeeHHHHh-----hhCccccCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEE
Confidence 4677765543 22335899999999999877 5555555555544332 335577786 999999999999
Q ss_pred ecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE--eCC--eEEEEeecc
Q 000449 510 DSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSK--RITVTHKKT 568 (1497)
Q Consensus 510 ~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~~--~i~lS~K~~ 568 (1497)
+++|++|+++ +++||+|.++++ |.+.|++|+.++|+|+.+ +++ +|.||++..
T Consensus 146 ~~~giiVDLg-gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 146 ERGNIIVDLG-RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred ecCCEEEEEC-CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 9999999996 899999999884 778999999999999999 344 899999854
No 124
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=4.2e-07 Score=111.51 Aligned_cols=76 Identities=22% Similarity=0.343 Sum_probs=72.6
Q ss_pred CCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeC
Q 000449 1374 EDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTS 1450 (1497)
Q Consensus 1374 ~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~ 1450 (1497)
.++++|++|.|+|+++.+||+||.|.++.+|++|||++++.++....+.+++||.|.+||+++| ..+|+.||++..
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD-~~Gri~ls~~~~ 690 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID-KQGRIRLSIKAV 690 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeec-ccCCccceehhc
Confidence 6789999999999999999999999999999999999999999999999999999999999999 679999999854
No 125
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.37 E-value=1.6e-06 Score=94.81 Aligned_cols=96 Identities=18% Similarity=0.308 Sum_probs=78.7
Q ss_pred EEEeeccCCceeeeccccccccccccCCcccCCCCCCEEEEEEEEEecceEEEEeC----------CCeEEEEeCCCCCc
Q 000449 727 LLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFL----------GRLTGFAPRSKAVD 796 (1497)
Q Consensus 727 vl~~d~~~~~i~lS~K~~l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~G~FV~~~----------~gl~Glvp~sels~ 796 (1497)
.+.+|.+++++.+ +||... ....++|+++.|+|+++.++|+||++. .+++|++|.+++++
T Consensus 40 ~~~id~~~~~Isv-------~P~~~~---~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~ 109 (189)
T PRK09521 40 KVFIDDINRKISV-------IPFKKT---PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSD 109 (189)
T ss_pred EEEEcCCCCEEEE-------ecCcCC---CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcCh
Confidence 4556666666665 244321 234679999999999999999999984 37999999999999
Q ss_pred ccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 797 GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 797 ~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
....++.+.|++||.|.|+|+++| +++.||++....
T Consensus 110 ~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~~l 145 (189)
T PRK09521 110 GYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGKDL 145 (189)
T ss_pred hhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecCCc
Confidence 888888899999999999999998 799999997643
No 126
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.37 E-value=5.7e-07 Score=110.08 Aligned_cols=122 Identities=20% Similarity=0.240 Sum_probs=89.7
Q ss_pred EEEecCCcccccccCCCccccCCCEEEEEEEEEeCCe-EEEEeecchhhhhh--hHHhhhhhcc--CCcEEEEEEEEEee
Q 000449 524 ALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKR-ITVTHKKTLVKSKL--AILSSYAEAT--DRLITHGWITKIEK 598 (1497)
Q Consensus 524 g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~~~~-i~lS~K~~l~~~~~--~~~~~~~~~~--~G~~~~G~V~~i~~ 598 (1497)
+.|+.++.- ..+| .+++|+.+++.|...+-++ ...+.|+.+..... ..-.-|+.++ .|+++.|+|.++.+
T Consensus 73 ~eI~L~eAk---~~~~--~~~vGD~ie~~I~~~~fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~ 147 (470)
T PRK09202 73 KEISLEEAR---KIDP--DAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVER 147 (470)
T ss_pred ceeeHHHHh---hhCc--cccCCCeEEEEEccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEec
Confidence 556554332 2244 4789999999987764333 34444444433211 0001244454 89999999999999
Q ss_pred eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCC--EEEEEEeeC
Q 000449 599 HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR--RINLSFMMK 657 (1497)
Q Consensus 599 ~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~--ri~lS~k~~ 657 (1497)
+|+||++ +|+.||||.+++. |.+.|++|+.++|+|+++|++++ .|.||.+..
T Consensus 148 ~giiVDL-ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 148 GNIIVDL-GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred CCEEEEE-CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 9999999 7999999999995 67889999999999999999887 999999764
No 127
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.27 E-value=2.9e-06 Score=76.36 Aligned_cols=62 Identities=31% Similarity=0.470 Sum_probs=53.2
Q ss_pred CCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE-e---CCeEEEEe
Q 000449 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-K---SKRITVTH 565 (1497)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v-~---~~~i~lS~ 565 (1497)
+.|++|+|+|.+++++|++|+++ +++|++|.++++ |.+.|++|+++++.|+.+ + ..+|.||+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 47999999999999999999997 599999999886 345789999999999999 2 24688874
No 128
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.24 E-value=2.9e-06 Score=109.65 Aligned_cols=70 Identities=24% Similarity=0.335 Sum_probs=64.6
Q ss_pred hccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEE
Q 000449 582 EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINL 652 (1497)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~l 652 (1497)
..++|+++.|+|+++.++|+||+++++.+||+|+|++++.++.++.+.|++||.|+|+|+++|+ ++++.|
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 3468999999999999999999999999999999999999999999999999999999999997 677643
No 129
>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=98.23 E-value=4.7e-06 Score=90.35 Aligned_cols=77 Identities=22% Similarity=0.384 Sum_probs=67.0
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCccc-C----------CCCccCCCCEEEEEEEEEc-----CCC
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVE-S----------PEKEFPIGKLVAGRVLSVE-----PLS 1440 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~-~----------~~~~~~~g~~V~~~V~~vd-----~~~ 1440 (1497)
.+|+++.|.|++++++|+||+|+ ..+|++|++++.+++.. + ....|+.||.|+++|++++ ++.
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~ 158 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEG 158 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCc
Confidence 45999999999999999999997 59999999999977642 2 3468999999999999998 567
Q ss_pred CeEEEEEEeCCCCc
Q 000449 1441 KRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1441 ~~i~lslk~~~~~~ 1454 (1497)
.+|.||+|+.-.+|
T Consensus 159 ~~I~lt~k~~~LG~ 172 (179)
T TIGR00448 159 SKIGLTMRQPLLGK 172 (179)
T ss_pred ceEEEEeccCcCCc
Confidence 89999999987764
No 130
>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=98.22 E-value=6.5e-06 Score=74.12 Aligned_cols=63 Identities=22% Similarity=0.323 Sum_probs=54.5
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCC--CeEEEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLS--KRVEVT 1446 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~--~~i~ls 1446 (1497)
+.|++|.|+|.++.++|+||+++. .+|+++.++++ +.+.|++||.|++.|++++.++ .+|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 469999999999999999999985 99999999987 3457899999999999998543 456666
No 131
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.20 E-value=1.8e-06 Score=106.10 Aligned_cols=77 Identities=23% Similarity=0.437 Sum_probs=72.5
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 756 ASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
..++.+|+++.|+|+.+.+||+||+|.++-+||+|+|++++.++...++.+++||.+.|+++.+|+ ++|+.||++..
T Consensus 614 ~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 614 TREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred HhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence 367899999999999999999999999999999999999999999999999999999999999994 78999998754
No 132
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.20 E-value=1.3e-05 Score=90.56 Aligned_cols=72 Identities=14% Similarity=0.151 Sum_probs=65.3
Q ss_pred cCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCC----CCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 000449 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPG----CEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1497)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~----~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~ 656 (1497)
++|+++.|+|+++.++|++|++.....|+||.+++++.++ .++.+.|++|+.|.|+|++++++. .+.||++.
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~-~~~LS~k~ 137 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTR-DVVLTLKG 137 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCC-cEEEEEcC
Confidence 5799999999999999999999888999999999998765 678888999999999999999754 59999975
No 133
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.18 E-value=4.6e-06 Score=87.47 Aligned_cols=77 Identities=23% Similarity=0.433 Sum_probs=66.2
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCccc----------C-CCCccCCCCEEEEEEEEEcCCC-----
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVE----------S-PEKEFPIGKLVAGRVLSVEPLS----- 1440 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~----------~-~~~~~~~g~~V~~~V~~vd~~~----- 1440 (1497)
..|++|.|.|.++.++|+||.|| ..+||+|++++.|+|+. + .+..|++|+.|++||+++....
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~ 158 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE 158 (183)
T ss_pred ccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence 34999999999999999999999 99999999999999643 1 3448999999999999987544
Q ss_pred CeEEEEEEeCCCCc
Q 000449 1441 KRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1441 ~~i~lslk~~~~~~ 1454 (1497)
.+|.+|||+.-.++
T Consensus 159 ~~I~lTmrq~~LGk 172 (183)
T COG1095 159 SKIGLTMRQPGLGK 172 (183)
T ss_pred ceEEEEeccccCCc
Confidence 68999999877654
No 134
>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=98.17 E-value=6.8e-06 Score=80.20 Aligned_cols=72 Identities=28% Similarity=0.434 Sum_probs=61.0
Q ss_pred CEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccC-----------cccCcCCCCEEEEEEEEEeCCC-----CeE
Q 000449 763 SVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRAD-----------LSKTYYVGQSVRSNILDVNSET-----GRI 826 (1497)
Q Consensus 763 ~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~-----------~~~~~~~Gq~V~v~V~~iD~e~-----~Ri 826 (1497)
+++.|.|.++.++|+||++. +++||+|.+++++.+... +...|++||.|.|+|.++|.+. .++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 36899999999999999997 599999999998765432 3467999999999999999764 589
Q ss_pred EEEeecccc
Q 000449 827 TLSLKQSCC 835 (1497)
Q Consensus 827 ~LSlK~~~~ 835 (1497)
.||+|....
T Consensus 80 ~ls~k~~~~ 88 (99)
T cd04460 80 GLTMRQPGL 88 (99)
T ss_pred EEEEecCCC
Confidence 999997754
No 135
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=98.09 E-value=2.3e-05 Score=82.26 Aligned_cols=113 Identities=23% Similarity=0.333 Sum_probs=86.2
Q ss_pred CCCcCCCCEEEEEEEEeecccCCccEEEEEeeccccCCCCCCCCCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEecee
Q 000449 1314 LSGYDEGQFVKCKVLEISRTVRGTFHVELSLRSSLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSKG 1393 (1497)
Q Consensus 1314 ~~~~~~g~~v~~~Vl~~d~~~~g~~~i~lS~R~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G 1393 (1497)
...|..|..|+|.+.++-.-. .+....|..+-. ..+.-+|.|++|.|+|+++....
T Consensus 24 ~gt~~~~g~i~Aa~~G~~~~d--~~n~~~~V~p~~----------------------~~~~~~K~GdiV~grV~~v~~~~ 79 (188)
T COG1096 24 EGTYEEGGEIRAAATGVVRRD--DKNRVISVKPGK----------------------KTPPLPKGGDIVYGRVTDVREQR 79 (188)
T ss_pred CCeEeECCEEEEeecccEEEc--ccceEEEeccCC----------------------CCCCCCCCCCEEEEEEeeccceE
Confidence 345666778888777652110 123334443332 23556799999999999999999
Q ss_pred EEEEeC----------CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCCC
Q 000449 1394 CFIMLS----------RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDSR 1453 (1497)
Q Consensus 1394 ~fV~l~----------~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~~ 1453 (1497)
+.|++. ....|-+|+|++++.|+++..+.|++||+|+|+|++.. ..+.||.+..+..
T Consensus 80 a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~~~Lst~~~dlG 146 (188)
T COG1096 80 ALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DPIQLSTKGNDLG 146 (188)
T ss_pred EEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CCeEEEecCCcce
Confidence 999964 24778999999999999999999999999999999974 7799999887653
No 136
>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=98.08 E-value=8.6e-06 Score=106.87 Aligned_cols=72 Identities=28% Similarity=0.405 Sum_probs=64.6
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCC-CeEEEEEccccCCCcc-----------cCCCCccCCCCEEEEEEEEEcCCCCeE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSR-KLDAKVLLSNLSDGYV-----------ESPEKEFPIGKLVAGRVLSVEPLSKRV 1443 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~-~~~g~v~is~lsd~~~-----------~~~~~~~~~g~~V~~~V~~vd~~~~~i 1443 (1497)
-++|+++.|.|++|++||+||+|.+ +++|+||+++++++|. .+..+.|++||.|+|+|+++|..+++|
T Consensus 625 ~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I 704 (709)
T TIGR02063 625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKI 704 (709)
T ss_pred ccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence 3679999999999999999999987 7999999999997754 234568999999999999999999999
Q ss_pred EEEE
Q 000449 1444 EVTL 1447 (1497)
Q Consensus 1444 ~lsl 1447 (1497)
.+++
T Consensus 705 ~~~l 708 (709)
T TIGR02063 705 DFEL 708 (709)
T ss_pred EEEE
Confidence 9986
No 137
>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=98.04 E-value=8.4e-06 Score=96.13 Aligned_cols=110 Identities=20% Similarity=0.301 Sum_probs=82.3
Q ss_pred hhcccccCCCCEEEEEEEEEecCCCeEEEEcchhh-----ccccccccccc--CCCcEEEEEEEEEecCe-eEEEeCCCe
Q 000449 451 RKLEKKYKEGSCVRVRILGFRHLEGLATGILKASA-----FEGLVFTHSDV--KPGMVVKGKVIAVDSFG-AIVQFPGGV 522 (1497)
Q Consensus 451 ~~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~-----~~~~~~~~~~l--~~G~iv~g~V~~v~~~G-~~V~i~~gv 522 (1497)
..+...+++|+.+++.|...+ +++.+..+.++.. ..++...++.+ +.|++|+|+|.++.+.| ++|+++ ++
T Consensus 78 ~~~d~~~~vGD~I~~~I~~~~-fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ 155 (341)
T TIGR01953 78 REIDPDVQIGDEVKKEIPPEN-FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG-KT 155 (341)
T ss_pred HhhccccccCCEEEEEecccC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC-Ce
Confidence 334456999999999885433 4454444444432 12234455666 59999999999999988 699996 89
Q ss_pred EEEEecCCcccccccCCCccccCCCEEEEEEEEEe----CCeEEEEeecc
Q 000449 523 KALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVK----SKRITVTHKKT 568 (1497)
Q Consensus 523 ~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~----~~~i~lS~K~~ 568 (1497)
+|++|.+++. |.+.|++|+.++|.|+.++ ..+|.||++..
T Consensus 156 ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 156 EGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred EEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 9999998775 4567999999999999992 34799999864
No 138
>PRK11642 exoribonuclease R; Provisional
Probab=97.95 E-value=2.3e-05 Score=102.87 Aligned_cols=76 Identities=25% Similarity=0.408 Sum_probs=66.6
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCC-eEEEEEccccCCCcc-c----------CCCCccCCCCEEEEEEEEEcCCCCeEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRK-LDAKVLLSNLSDGYV-E----------SPEKEFPIGKLVAGRVLSVEPLSKRVE 1444 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~-~~g~v~is~lsd~~~-~----------~~~~~~~~g~~V~~~V~~vd~~~~~i~ 1444 (1497)
++|+++.|.|++|++||+||+|... ++|+||+++|.++|. . +....|++||.|+|+|+++|...++|.
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 6899999999999999999999875 999999999998742 2 235789999999999999999999999
Q ss_pred EEEEeCCC
Q 000449 1445 VTLKTSDS 1452 (1497)
Q Consensus 1445 lslk~~~~ 1452 (1497)
|++.....
T Consensus 722 f~l~~~~~ 729 (813)
T PRK11642 722 FSLISSER 729 (813)
T ss_pred EEEecccc
Confidence 99965444
No 139
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.94 E-value=1.6e-05 Score=93.85 Aligned_cols=109 Identities=16% Similarity=0.337 Sum_probs=79.3
Q ss_pred ccccCCCEEEEEEEEEe-CCeEEEEeecchhhh-----hhhHHhhhhhccCCcEEEEEEEEEeeee-EEEEEcCceEEee
Q 000449 541 KKFKVGAELVFRVLGVK-SKRITVTHKKTLVKS-----KLAILSSYAEATDRLITHGWITKIEKHG-CFVRFYNGVQGFA 613 (1497)
Q Consensus 541 ~~~kvG~~V~~rVl~v~-~~~i~lS~K~~l~~~-----~~~~~~~~~~~~~G~~~~G~V~~i~~~G-~~V~~~~gv~gfl 613 (1497)
..+++|+.+++.+...+ .+....+.|+.+... +...+..|.+ +.|+++.|+|.++.+.| +||++ +++.|||
T Consensus 82 ~~~~vGD~I~~~I~~~~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~-k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~L 159 (341)
T TIGR01953 82 PDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSS-KEGEIISGTVKRVNRRGNLYVEL-GKTEGIL 159 (341)
T ss_pred cccccCCEEEEEecccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCEEEEEEEEEecCCcEEEEE-CCeEEEe
Confidence 36899999998874333 233334444433221 1123333322 58999999999999988 69999 6999999
Q ss_pred ecccccCCCCCCCCCCccCCCEEEEEEEEEecCC--CEEEEEEeeC
Q 000449 614 PRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPAS--RRINLSFMMK 657 (1497)
Q Consensus 614 p~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~--~ri~lS~k~~ 657 (1497)
|.+|+. |.+.|++|+.++|.|++++... ..+.||.+..
T Consensus 160 P~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 160 PKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred cHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 999987 4466999999999999999654 5799998764
No 140
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.91 E-value=4.4e-05 Score=83.61 Aligned_cols=78 Identities=19% Similarity=0.416 Sum_probs=66.5
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCccc-----------CCCCccCCCCEEEEEEEEEcCCC----
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVE-----------SPEKEFPIGKLVAGRVLSVEPLS---- 1440 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~-----------~~~~~~~~g~~V~~~V~~vd~~~---- 1440 (1497)
..+|+++.|.|++++++|+||+|+ ..+|++|.+++.+++.. +....|++||.|+++|++++...
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~ 157 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR 157 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence 456999999999999999999998 59999999999987543 34567999999999999998644
Q ss_pred -CeEEEEEEeCCCCc
Q 000449 1441 -KRVEVTLKTSDSRT 1454 (1497)
Q Consensus 1441 -~~i~lslk~~~~~~ 1454 (1497)
.+|.+|++.....+
T Consensus 158 ~~~I~ls~~~~~LG~ 172 (187)
T PRK08563 158 GSKIGLTMRQPGLGK 172 (187)
T ss_pred CCEEEEEecCCCCCc
Confidence 38999999877654
No 141
>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=97.89 E-value=3.3e-05 Score=100.10 Aligned_cols=71 Identities=23% Similarity=0.359 Sum_probs=63.7
Q ss_pred CCCcEEEEEEEEEeceeEEEEeC-CCeEEEEEccccCCCcc-----------cCCCCccCCCCEEEEEEEEEcCCCCeEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLS-RKLDAKVLLSNLSDGYV-----------ESPEKEFPIGKLVAGRVLSVEPLSKRVE 1444 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~-~~~~g~v~is~lsd~~~-----------~~~~~~~~~g~~V~~~V~~vd~~~~~i~ 1444 (1497)
++|+++.|+|++|+++|+||+|. .+++|+||++++.++|. ++....|++||.|+|+|+++|...++|.
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~ 650 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII 650 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 56999999999999999999998 77999999999998751 2345789999999999999999999999
Q ss_pred EEE
Q 000449 1445 VTL 1447 (1497)
Q Consensus 1445 lsl 1447 (1497)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 986
No 142
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.86 E-value=2.3e-05 Score=93.00 Aligned_cols=108 Identities=16% Similarity=0.243 Sum_probs=78.6
Q ss_pred cccCCCEEEEEEEEEe-CCeEEEEeecchhhhhhh--HHhhhhhc--cCCcEEEEEEEEEeeeeEEEEEcCceEEeeecc
Q 000449 542 KFKVGAELVFRVLGVK-SKRITVTHKKTLVKSKLA--ILSSYAEA--TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRS 616 (1497)
Q Consensus 542 ~~kvG~~V~~rVl~v~-~~~i~lS~K~~l~~~~~~--~~~~~~~~--~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~s 616 (1497)
..++|+.+++.+...+ .+....+.|+.+...-.. --.-|+++ +.|+++.|+|.++.++|+||++ ++++||||.+
T Consensus 86 ~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~~ 164 (362)
T PRK12327 86 AYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPPA 164 (362)
T ss_pred cccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecHH
Confidence 5789999998875442 333344445444332111 01114444 6899999999999999999999 6799999998
Q ss_pred cccCCCCCCCCCCccCCCEEEEEEEEEecCCC--EEEEEEee
Q 000449 617 ELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR--RINLSFMM 656 (1497)
Q Consensus 617 el~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~--ri~lS~k~ 656 (1497)
++. |.+.|++|+.++|.|++++.+.+ .+.||...
T Consensus 165 E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 165 EQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred HcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 874 45779999999999999996654 58888754
No 143
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.80 E-value=3.6e-05 Score=91.37 Aligned_cols=106 Identities=19% Similarity=0.300 Sum_probs=80.8
Q ss_pred ccccCCCCEEEEEEEEEecCCCeEEEEcchhhcc-----ccccccccc--CCCcEEEEEEEEEecCeeEEEeCCCeEEEE
Q 000449 454 EKKYKEGSCVRVRILGFRHLEGLATGILKASAFE-----GLVFTHSDV--KPGMVVKGKVIAVDSFGAIVQFPGGVKALC 526 (1497)
Q Consensus 454 ~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~-----~~~~~~~~l--~~G~iv~g~V~~v~~~G~~V~i~~gv~g~v 526 (1497)
....++|+.++..+.-.+ +++....+.++.... .+...++.+ +.|++|+|+|.++.++|++|+++ +++|++
T Consensus 84 ~~~~~vGD~i~~~I~~~~-fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~L 161 (362)
T PRK12327 84 NPAYELGDVIEIEVTPKD-FGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVL 161 (362)
T ss_pred CccccCCCEEEEecCcCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEe
Confidence 345899999999887543 344444444443322 234556777 89999999999999999999997 699999
Q ss_pred ecCCcccccccCCCccccCCCEEEEEEEEEe--C--CeEEEEeec
Q 000449 527 PLPHMSEFEIVKPGKKFKVGAELVFRVLGVK--S--KRITVTHKK 567 (1497)
Q Consensus 527 p~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~--~--~~i~lS~K~ 567 (1497)
|..++. |.+.|++|+.++|.|+.++ . .+|.||+-.
T Consensus 162 P~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 162 PPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred cHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 987653 4678999999999999992 2 379999764
No 144
>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=97.76 E-value=9.2e-05 Score=80.35 Aligned_cols=73 Identities=29% Similarity=0.459 Sum_probs=62.5
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc-----------CcccCcCCCCEEEEEEEEEe-----CCCC
Q 000449 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVN-----SETG 824 (1497)
Q Consensus 761 ~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~-----------~~~~~~~~Gq~V~v~V~~iD-----~e~~ 824 (1497)
.|+++.|.|++++++|+||++ +.++|++|.+++.+++.. +....|+.||.|.++|.++| ++..
T Consensus 81 ~gEvv~G~V~~v~~~GifV~l-g~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 159 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSL-GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGS 159 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEe-CCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcc
Confidence 699999999999999999999 569999999998754321 23467999999999999998 6778
Q ss_pred eEEEEeeccc
Q 000449 825 RITLSLKQSC 834 (1497)
Q Consensus 825 Ri~LSlK~~~ 834 (1497)
|+.+|+|+.-
T Consensus 160 ~I~lt~k~~~ 169 (179)
T TIGR00448 160 KIGLTMRQPL 169 (179)
T ss_pred eEEEEeccCc
Confidence 9999999764
No 145
>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=97.76 E-value=7.3e-05 Score=66.87 Aligned_cols=67 Identities=22% Similarity=0.297 Sum_probs=57.0
Q ss_pred CcEEEEEEEEEecCeeEEEeCC-CeEEEEecCCcccccccCC---CccccCCCEE-EEEEEEEeCCeEEEEee
Q 000449 499 GMVVKGKVIAVDSFGAIVQFPG-GVKALCPLPHMSEFEIVKP---GKKFKVGAEL-VFRVLGVKSKRITVTHK 566 (1497)
Q Consensus 499 G~iv~g~V~~v~~~G~~V~i~~-gv~g~vp~~~ls~~~~~~~---~~~~kvG~~V-~~rVl~v~~~~i~lS~K 566 (1497)
|++|+|+|...++++++|++.+ ++.|++|..|++| ...+. -.++++|+++ .+.||....+.|.||.|
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-HVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEEeccccEEEEecC
Confidence 7899999999999999999987 8999999999999 44332 2567899999 89999446778888875
No 146
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.75 E-value=8.3e-05 Score=71.26 Aligned_cols=76 Identities=18% Similarity=0.245 Sum_probs=63.4
Q ss_pred cCCCEEEEEEEEEecCcCeEEEEE--------CCceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEEEEE
Q 000449 1258 HEGDIVGGRISKILSGVGGLVVQI--------GPHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCKVLE 1329 (1497)
Q Consensus 1258 ~~G~~v~g~V~~v~~~~~gl~V~l--------~~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~Vl~ 1329 (1497)
++|++|.|+|+++... .+.|++ .....|.+|++|+.+.+.+. .+..+.|.+|+.|+|+|++
T Consensus 5 ~~GDiVig~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~---------~~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 5 KVGSIVIARVTRINPR--FAKVDILCVGGRPLKESFRGVIRKEDIRATEKDK---------VEMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCEEEEEEEEEcCC--EEEEEEEEecCeecCCCcccEEEHHHccccccch---------HHHHhhcCCCCEEEEEEEE
Confidence 4899999999999998 999999 77789999999998876552 0145789999999999999
Q ss_pred eecccCCccEEEEEeeccc
Q 000449 1330 ISRTVRGTFHVELSLRSSL 1348 (1497)
Q Consensus 1330 ~d~~~~g~~~i~lS~R~s~ 1348 (1497)
.+. ...+.||++...
T Consensus 74 ~~~----~~~~~Lst~~~~ 88 (92)
T cd05791 74 LGD----ASSYYLSTAENE 88 (92)
T ss_pred cCC----CCCcEEEecCCC
Confidence 974 357999998654
No 147
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.69 E-value=3.3e-05 Score=91.65 Aligned_cols=78 Identities=23% Similarity=0.302 Sum_probs=69.8
Q ss_pred hccCCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCCC
Q 000449 582 EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPT 659 (1497)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~~~ 659 (1497)
++..|-++.|+|+.+.++|+||+||++..|++|.||++.+++.+|++.+.+||.+.++-++.|+..+...+|.+....
T Consensus 665 ~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~ 742 (760)
T KOG1067|consen 665 DLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPD 742 (760)
T ss_pred ceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhhhhcCC
Confidence 344688999999999999999999999999999999999999999999999999999999999988877777665433
No 148
>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=97.68 E-value=4.9e-05 Score=64.57 Aligned_cols=59 Identities=20% Similarity=0.293 Sum_probs=54.0
Q ss_pred CcEEEEEEEEEecceEEEEecCCCceEEEEeecccC-cCCCCccCcCCCCEEEEEEEeec
Q 000449 971 HQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYN-TQKFPQKQFLNGQSVIATVMALP 1029 (1497)
Q Consensus 971 G~~v~a~V~~v~~~~~~vsl~~~~~~~g~~~~~~~n-~~~~~~~~f~~Gq~V~~~V~~~~ 1029 (1497)
++..+|.|+++..+++++||.+.+++.+|...+++| +++++++++++||++.+.+...+
T Consensus 1 ~S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~ 60 (69)
T cd05701 1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPN 60 (69)
T ss_pred CCccchhhhhhhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCc
Confidence 356789999999999999999999999999999999 78889999999999999988875
No 149
>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=97.65 E-value=0.00012 Score=96.29 Aligned_cols=75 Identities=19% Similarity=0.332 Sum_probs=64.5
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccc-----------cCcccCcCCCCEEEEEEEEEeCCC
Q 000449 756 ASHIHPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQR-----------ADLSKTYYVGQSVRSNILDVNSET 823 (1497)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~-----------~~~~~~~~~Gq~V~v~V~~iD~e~ 823 (1497)
|-.-++|+.+.|.|++|+++|+||++.+ +++||+|.+++++++. .+....|++||.|.|+|.++|.++
T Consensus 622 yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~ 701 (709)
T TIGR02063 622 YMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDT 701 (709)
T ss_pred hhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence 3345679999999999999999999987 8999999999985432 234467999999999999999999
Q ss_pred CeEEEEe
Q 000449 824 GRITLSL 830 (1497)
Q Consensus 824 ~Ri~LSl 830 (1497)
+++.+++
T Consensus 702 ~~I~~~l 708 (709)
T TIGR02063 702 GKIDFEL 708 (709)
T ss_pred CeEEEEE
Confidence 9999886
No 150
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.64 E-value=4.8e-05 Score=90.29 Aligned_cols=82 Identities=11% Similarity=0.222 Sum_probs=74.8
Q ss_pred ccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1372 KIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1372 ~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
...+|..|-+|.+.|+.+.++|+||+|.+...|++|+|+|+..++.+|.+.+.+||.|.++-+..|+ .+.+.+|-|...
T Consensus 662 ~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ralL 740 (760)
T KOG1067|consen 662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRALL 740 (760)
T ss_pred cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhhhc
Confidence 3568899999999999999999999999999999999999999999999999999999999999995 567777777777
Q ss_pred CCc
Q 000449 1452 SRT 1454 (1497)
Q Consensus 1452 ~~~ 1454 (1497)
++|
T Consensus 741 p~p 743 (760)
T KOG1067|consen 741 PDP 743 (760)
T ss_pred CCc
Confidence 665
No 151
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.48 E-value=0.0021 Score=70.66 Aligned_cols=87 Identities=24% Similarity=0.260 Sum_probs=73.2
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCc----ccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGY----VESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~----~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
.++||+|-|+|..+...+-.|+|+....|++|+|++...- -.+...+|++||.|.|+|.++| ....+.|++|+..
T Consensus 62 P~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd-~~~~~~L~~k~~~ 140 (239)
T COG1097 62 PEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVD-RDGEVELTLKDEG 140 (239)
T ss_pred CCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEcc-CCCceEEEeecCC
Confidence 4679999999999999999999999999999999995443 2467889999999999999999 6789999997644
Q ss_pred CCcccccccCCCCCCCCCCEEEE
Q 000449 1452 SRTASQSEINNLSNLHVGDIVIG 1474 (1497)
Q Consensus 1452 ~~~~~~~~~~~~~d~~~G~iv~G 1474 (1497)
. -.|+-|++|..
T Consensus 141 ~-----------GkL~~G~iv~i 152 (239)
T COG1097 141 L-----------GKLKNGQIVKI 152 (239)
T ss_pred C-----------ccccCCEEEEE
Confidence 3 45666766654
No 152
>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=97.44 E-value=0.00054 Score=65.07 Aligned_cols=62 Identities=13% Similarity=0.134 Sum_probs=53.0
Q ss_pred CCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCC-----------CCccCCCCEEEEEEEEEcCCC
Q 000449 1378 PNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESP-----------EKEFPIGKLVAGRVLSVEPLS 1440 (1497)
Q Consensus 1378 ~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~-----------~~~~~~g~~V~~~V~~vd~~~ 1440 (1497)
.|+++.|.|++++++|+||++| .+++|+|.+.+.+++..+| ...+..|+.|++||+++..+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 73 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDA 73 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEcc
Confidence 4899999999999999999998 8999999999988876654 234789999999999886543
No 153
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.43 E-value=0.00037 Score=73.43 Aligned_cols=72 Identities=24% Similarity=0.338 Sum_probs=59.1
Q ss_pred CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCC----------CCC-CCCCccCCCEEEEEEEEEecCC-----C
Q 000449 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDP----------GCE-PSSMYHVGQVVKCRIMSSIPAS-----R 648 (1497)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~----------~~~-~~~~~~vGq~v~v~Vl~vd~~~-----~ 648 (1497)
.|+++.|.|+++.++|+||.+ +-.+||+|.+++..+. +.. ....+.+|+.|++||+.++... .
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~i-gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~ 159 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRES 159 (183)
T ss_pred cccEEEEEEEEEeecceEEEe-ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccc
Confidence 499999999999999999999 5899999999996441 111 1226889999999999998665 5
Q ss_pred EEEEEEeeC
Q 000449 649 RINLSFMMK 657 (1497)
Q Consensus 649 ri~lS~k~~ 657 (1497)
++.+++++.
T Consensus 160 ~I~lTmrq~ 168 (183)
T COG1095 160 KIGLTMRQP 168 (183)
T ss_pred eEEEEeccc
Confidence 788999885
No 154
>PRK11642 exoribonuclease R; Provisional
Probab=97.37 E-value=0.00045 Score=90.95 Aligned_cols=73 Identities=23% Similarity=0.322 Sum_probs=63.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccc-c----------CcccCcCCCCEEEEEEEEEeCCCCeE
Q 000449 759 IHPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQR-A----------DLSKTYYVGQSVRSNILDVNSETGRI 826 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~-~----------~~~~~~~~Gq~V~v~V~~iD~e~~Ri 826 (1497)
-++|+.+.|.|++++++|+||++.+ +++||+|.+++.+.+. . +....|++||.|.|+|.++|.++++|
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 3689999999999999999999986 4999999999986421 1 23467999999999999999999999
Q ss_pred EEEee
Q 000449 827 TLSLK 831 (1497)
Q Consensus 827 ~LSlK 831 (1497)
.+++-
T Consensus 721 ~f~l~ 725 (813)
T PRK11642 721 DFSLI 725 (813)
T ss_pred EEEEe
Confidence 99985
No 155
>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=97.33 E-value=0.0013 Score=61.79 Aligned_cols=74 Identities=15% Similarity=0.100 Sum_probs=63.4
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
.++||.|-|+|+.++...-+|+|+....|++|++++... .++.+..|++||.|-|+|.++++. ..++||+..+.
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~~ 77 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDSS 77 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCCC
Confidence 467999999999999999999999999999999887544 445567899999999999999954 56899998743
No 156
>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=97.31 E-value=0.00079 Score=87.49 Aligned_cols=71 Identities=25% Similarity=0.383 Sum_probs=61.9
Q ss_pred cCCcEEEEEEEEEeeeeEEEEEc-CceEEeeecccccCCC-----------CCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 000449 584 TDRLITHGWITKIEKHGCFVRFY-NGVQGFAPRSELGLDP-----------GCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1497)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~-~gv~gflp~sel~~~~-----------~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~ 651 (1497)
+.|+.+.|+|+++.++|+||++. .+++||+|.+++.++. ..+....|++||+|+|+|.++|.++++|.
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~ 650 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII 650 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 57999999999999999999997 6899999999997652 12334679999999999999999999998
Q ss_pred EEE
Q 000449 652 LSF 654 (1497)
Q Consensus 652 lS~ 654 (1497)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 875
No 157
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.28 E-value=0.00068 Score=61.63 Aligned_cols=70 Identities=19% Similarity=0.267 Sum_probs=64.3
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeC-CCeEEEEE-ccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLS-RKLDAKVL-LSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~-~~~~g~v~-is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lsl 1447 (1497)
.++|+++. .|..+.+.|+||.|- .+.+|+|- .++++-.++...++.+ +|..+.++|+.+|+.++-|.||.
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 46799999 888999999999984 46999998 9999999999999999 99999999999999999999984
No 158
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.26 E-value=0.001 Score=72.89 Aligned_cols=75 Identities=28% Similarity=0.430 Sum_probs=62.3
Q ss_pred CCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccccc-----------CcccCcCCCCEEEEEEEEEeCCCC----
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVNSETG---- 824 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~-----------~~~~~~~~Gq~V~v~V~~iD~e~~---- 824 (1497)
..|+++.|.|+++.++|+||+++ .++|++|.+++.+++.. +....|+.||.|.++|.++|.+.+
T Consensus 80 ~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~ 158 (187)
T PRK08563 80 ELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRG 158 (187)
T ss_pred cCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCC
Confidence 36999999999999999999995 59999999999865321 235578999999999999996543
Q ss_pred -eEEEEeecccc
Q 000449 825 -RITLSLKQSCC 835 (1497)
Q Consensus 825 -Ri~LSlK~~~~ 835 (1497)
++.+|+++.-.
T Consensus 159 ~~I~ls~~~~~L 170 (187)
T PRK08563 159 SKIGLTMRQPGL 170 (187)
T ss_pred CEEEEEecCCCC
Confidence 89999987643
No 159
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.23 E-value=0.00078 Score=61.26 Aligned_cols=69 Identities=14% Similarity=0.266 Sum_probs=62.8
Q ss_pred CCCCEEEEEEEEEecceEEEEeCC-CeEEEEe-CCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAP-RSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp-~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSl 830 (1497)
.+|+.+. .|+.+.+.|++|.+.+ +++|++. .++++..+.....+.+ +|.++.|+|+++|.+++-|-||.
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 5688888 7999999999999964 6999999 9999999999988888 99999999999999999998874
No 160
>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=97.16 E-value=0.00099 Score=61.89 Aligned_cols=60 Identities=17% Similarity=0.189 Sum_probs=43.5
Q ss_pred CCCcEEEEEEEEEeceeEEEEeC------------------CCeEEEEEccccCCCcccC--CCCccCCCCEEEEEEEEE
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLS------------------RKLDAKVLLSNLSDGYVES--PEKEFPIGKLVAGRVLSV 1436 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~------------------~~~~g~v~is~lsd~~~~~--~~~~~~~g~~V~~~V~~v 1436 (1497)
++|++|.|+|++++..-++++|- ....|.+|.+|+...+... +.+.|++||+|+|+|+|.
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 68999999999999999998852 2578999999998877654 588999999999999984
No 161
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.08 E-value=0.0019 Score=56.86 Aligned_cols=61 Identities=20% Similarity=0.190 Sum_probs=37.4
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 000449 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1497)
Q Consensus 761 ~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK 831 (1497)
+|++....|..++++|+|++..++-+-|+|.+++.. .+++||.|.|.|.. |. ++|+.+++|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~-D~-~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE--------PLKVGDEVEVFVYL-DK-EGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE--T-TS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC--------CCCCCCEEEEEEEE-CC-CCCEEEecC
Confidence 478889999999999999999888999999998753 58899999999874 64 568888875
No 162
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.05 E-value=0.0017 Score=57.23 Aligned_cols=61 Identities=18% Similarity=0.197 Sum_probs=36.9
Q ss_pred CCCEEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeeecc
Q 000449 669 LGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAK 742 (1497)
Q Consensus 669 vG~iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS~K 742 (1497)
+|++.+.+|.++++.|+|++. +++-+.+||..++. ..+++||+++.+++.|.++ ++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~--~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~D~~~-rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDD--GEGKEVLLPKSEVP----------EPLKVGDEVEVFVYLDKEG-RLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEE--TT-EEEEEEGGG----------------TTSEEEEEEEE-TTS--EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEEC--CCCCEEEechHHcC----------CCCCCCCEEEEEEEECCCC-CEEEecC
Confidence 589999999999999999998 66789999988763 4688999999999999887 6777764
No 163
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.00 E-value=0.0012 Score=77.85 Aligned_cols=108 Identities=19% Similarity=0.215 Sum_probs=77.1
Q ss_pred hcccccCCCCEEEEEEEEEecCCCeEEEEcchhhcc-----ccccccccc--CCCcEEEEEEEEEec-CeeEEEeCCCeE
Q 000449 452 KLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFE-----GLVFTHSDV--KPGMVVKGKVIAVDS-FGAIVQFPGGVK 523 (1497)
Q Consensus 452 ~~~~~~~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~-----~~~~~~~~l--~~G~iv~g~V~~v~~-~G~~V~i~~gv~ 523 (1497)
.+...+++|+.++..+.- ..+++...-+.++.... .+...++.+ +.|++|+|+|.++.. .+++|+++ +.+
T Consensus 86 ~i~~~~~vGd~i~~~i~~-~~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~e 163 (374)
T PRK12328 86 EIDPSVEIGDELTYELSL-ENMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEID-EIR 163 (374)
T ss_pred hhCCCCCCCCEEEEecCh-hhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcC-CeE
Confidence 344568999999876542 33455544444544311 112223333 689999999999987 46999997 899
Q ss_pred EEEecCCcccccccCCCccccCCCEEEEEEEEE--eC---CeEEEEeec
Q 000449 524 ALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KS---KRITVTHKK 567 (1497)
Q Consensus 524 g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v--~~---~~i~lS~K~ 567 (1497)
|++|..+.. |.+.|++|+.++|.|..+ .. -+|.||+..
T Consensus 164 a~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~ 206 (374)
T PRK12328 164 AVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTS 206 (374)
T ss_pred EEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence 999987653 678999999999999999 22 389999864
No 164
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.99 E-value=0.00098 Score=80.27 Aligned_cols=104 Identities=18% Similarity=0.361 Sum_probs=81.3
Q ss_pred ccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCC
Q 000449 1372 KIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSD 1451 (1497)
Q Consensus 1372 ~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~ 1451 (1497)
++.|++.|..|.|.|.++..||+||+|+.++.|++|=++++.. ..|.+|+.+.+.|..+.++.+.|.|.....+
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 5788999999999999999999999999999999999998872 3488999999999999987788877766655
Q ss_pred CCcc----cccc---cCCCCCCCCCCEE--EEEEEEEeec
Q 000449 1452 SRTA----SQSE---INNLSNLHVGDIV--IGQIKRVESY 1482 (1497)
Q Consensus 1452 ~~~~----~~~~---~~~~~d~~~G~iv--~G~V~~v~~~ 1482 (1497)
.... ..+. +..+++ ..|+.| +|.|+.|.--
T Consensus 190 ~Y~~~~~~ke~~r~~i~~id~-~ig~tV~I~GeV~qikqT 228 (715)
T COG1107 190 RYREVQVEKELPRTLIDDLDE-MIGKTVRIEGEVTQIKQT 228 (715)
T ss_pred cchhhhhhhhcccccHHHHHh-hcCceEEEEEEEEEEEEc
Confidence 2110 1111 223444 788875 6999888753
No 165
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.93 E-value=0.0014 Score=77.39 Aligned_cols=108 Identities=19% Similarity=0.225 Sum_probs=76.2
Q ss_pred cccCCCEEEEEEEEEe-CCeEEEEeecchhhhh--hhHHhhhhhc--cCCcEEEEEEEEEee-eeEEEEEcCceEEeeec
Q 000449 542 KFKVGAELVFRVLGVK-SKRITVTHKKTLVKSK--LAILSSYAEA--TDRLITHGWITKIEK-HGCFVRFYNGVQGFAPR 615 (1497)
Q Consensus 542 ~~kvG~~V~~rVl~v~-~~~i~lS~K~~l~~~~--~~~~~~~~~~--~~G~~~~G~V~~i~~-~G~~V~~~~gv~gflp~ 615 (1497)
.+++|+.+...+---+ .+...-+.|+.+...- ..--.-|+++ +.|+++.|+|.++.. .++||++ +++.|+||.
T Consensus 90 ~~~vGd~i~~~i~~~~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~LP~ 168 (374)
T PRK12328 90 SVEIGDELTYELSLENMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVLPM 168 (374)
T ss_pred CCCCCCEEEEecChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEeCH
Confidence 5889999987653222 2233334444442210 0001113344 479999999999986 4599999 689999999
Q ss_pred ccccCCCCCCCCCCccCCCEEEEEEEEEecCCC---EEEEEEee
Q 000449 616 SELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR---RINLSFMM 656 (1497)
Q Consensus 616 sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~---ri~lS~k~ 656 (1497)
++.. |.+.|++|+.++|.|.+++...+ .+.||+..
T Consensus 169 ~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~ 206 (374)
T PRK12328 169 KNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTS 206 (374)
T ss_pred HHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence 8875 56789999999999999998766 78888754
No 166
>PRK05054 exoribonuclease II; Provisional
Probab=96.86 E-value=0.003 Score=81.84 Aligned_cols=69 Identities=13% Similarity=0.099 Sum_probs=58.5
Q ss_pred CcEEEEEEEEEeceeEEEEeCC-CeEEEEEccccCCC---ccc--C-------CCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIMLSR-KLDAKVLLSNLSDG---YVE--S-------PEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l~~-~~~g~v~is~lsd~---~~~--~-------~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
|+.+.|.|+.|+++|+||+|.. +++|+||++.|.++ |.. + -...|++||.|+++|.++|...++|.+
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~ 641 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA 641 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence 4599999999999999999965 59999999999874 211 1 124799999999999999999999988
Q ss_pred EE
Q 000449 1446 TL 1447 (1497)
Q Consensus 1446 sl 1447 (1497)
++
T Consensus 642 ~~ 643 (644)
T PRK05054 642 RP 643 (644)
T ss_pred EE
Confidence 75
No 167
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.86 E-value=0.0026 Score=77.61 Aligned_cols=72 Identities=17% Similarity=0.170 Sum_probs=56.8
Q ss_pred CCCcEEEEEEEEEece--eEEEEeCCCeEEEEEccccCCCc------------ccCCCCccCCCCEEEEEEEEEcCCCCe
Q 000449 1377 SPNMIVQGYVKNVTSK--GCFIMLSRKLDAKVLLSNLSDGY------------VESPEKEFPIGKLVAGRVLSVEPLSKR 1442 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~--G~fV~l~~~~~g~v~is~lsd~~------------~~~~~~~~~~g~~V~~~V~~vd~~~~~ 1442 (1497)
.+|++|.|+|.++.+. ||||+||.+..||+|++++.+.+ .++..+.+++||.|.|.|+.=-...+.
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kg 103 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKG 103 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCC
Confidence 4799999999999998 99999999999999999997532 334456799999999999883323344
Q ss_pred EEEEEE
Q 000449 1443 VEVTLK 1448 (1497)
Q Consensus 1443 i~lslk 1448 (1497)
-.||..
T Consensus 104 p~lT~~ 109 (414)
T TIGR00757 104 ARLTTD 109 (414)
T ss_pred CeEEEE
Confidence 444443
No 168
>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=96.84 E-value=0.0073 Score=51.05 Aligned_cols=64 Identities=25% Similarity=0.287 Sum_probs=53.6
Q ss_pred CcEEEEEEEEEeeceeE-EEecCCCceEEEEeeeecCCccccCCCEEEEEEEEEecCCCEEEEEe
Q 000449 875 GSVIEGKVHESNDFGVV-VSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSL 938 (1497)
Q Consensus 875 G~~V~g~V~~i~~~G~~-v~l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~Vl~vd~~~~~v~lSl 938 (1497)
|+..+..|.+.+++|.. +.-++-.+.+-....+|+.+..+.+||+++++|+++|.-+..+++|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 67889999999888865 44444456677788899999999999999999999999888888875
No 169
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.76 E-value=0.0055 Score=66.02 Aligned_cols=77 Identities=17% Similarity=0.106 Sum_probs=59.5
Q ss_pred CCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccC------------CCCccCCCCEEEEEEEEEcCC--CCe
Q 000449 1377 SPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVES------------PEKEFPIGKLVAGRVLSVEPL--SKR 1442 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~------------~~~~~~~g~~V~~~V~~vd~~--~~~ 1442 (1497)
-.|+++.|.|++++++|+||++| -.+++||.++|.+++.-+ -...+..|+.|++||+++..+ ...
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~ 158 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF 158 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence 45999999999999999999998 566999999998653222 134688999999999887643 334
Q ss_pred EEEEEEeCCCCc
Q 000449 1443 VEVTLKTSDSRT 1454 (1497)
Q Consensus 1443 i~lslk~~~~~~ 1454 (1497)
+-.|||..-.++
T Consensus 159 ~i~T~~~~~LG~ 170 (176)
T PTZ00162 159 AIATINSDYLGP 170 (176)
T ss_pred EEEEecCCCcCc
Confidence 566887765543
No 170
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.71 E-value=0.0029 Score=75.73 Aligned_cols=115 Identities=15% Similarity=0.205 Sum_probs=80.1
Q ss_pred hHHHhhcccccCCCCEEEEEEEE-EecCCCeEEEEcchhhcc-----ccccccccc--CCCcEEEEEEEEEecCeeEEEe
Q 000449 447 EEEVRKLEKKYKEGSCVRVRILG-FRHLEGLATGILKASAFE-----GLVFTHSDV--KPGMVVKGKVIAVDSFGAIVQF 518 (1497)
Q Consensus 447 ~~~~~~~~~~~~vG~~~~~rVi~-~~~~~~~~~lS~k~~~~~-----~~~~~~~~l--~~G~iv~g~V~~v~~~G~~V~i 518 (1497)
......+...+++|+.+...|.- ...++++..-+.++.... ++...++.+ +.|++|+|+|.++...+++|++
T Consensus 93 L~eAk~i~~~~~iGD~v~~~v~~~~~~fgRiAAq~aKQvi~Qkire~ER~~i~~ef~~~~GeIV~G~V~r~e~~~viv~l 172 (449)
T PRK12329 93 LAEVQQVADEAQLGDTVVLDVTPEQEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAV 172 (449)
T ss_pred HHHHHhhCCCCcCCCEEEEecCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEcCCCEEEEe
Confidence 33334444568999999877742 123455554444443221 122333444 5899999999999999999999
Q ss_pred C---C--CeEEEEecCCcccccccCCCccccCCCEEEEEEEEE-eC----CeEEEEeec
Q 000449 519 P---G--GVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-KS----KRITVTHKK 567 (1497)
Q Consensus 519 ~---~--gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v-~~----~~i~lS~K~ 567 (1497)
+ + +++|++|..+. -|.+.|++|+.++|.|..| .. -+|.||+-.
T Consensus 173 ~~~~g~~~~EaiLP~~Eq------ip~E~y~~Gdrika~i~~V~~~~~kGpqIilSRt~ 225 (449)
T PRK12329 173 SSGFGQPEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSRAN 225 (449)
T ss_pred cccCCCcceEEEecHHHc------CCCCcCCCCCEEEEEEEEeecCCCCCCEEEEEcCC
Confidence 4 2 39999998765 3678999999999999999 32 379999763
No 171
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.66 E-value=0.0096 Score=56.64 Aligned_cols=64 Identities=16% Similarity=0.252 Sum_probs=48.4
Q ss_pred CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccccCCCCCCC-----------CCCccCCCEEEEEEEEEecCCCE
Q 000449 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEP-----------SSMYHVGQVVKCRIMSSIPASRR 649 (1497)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel~~~~~~~~-----------~~~~~vGq~v~v~Vl~vd~~~~r 649 (1497)
.|+++.|+|+++.+.|+||++ +.+++|++.+.+......+| ...+..|+.|++||+.+..+.+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~-Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 75 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEV-GPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATD 75 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEE-cCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCc
Confidence 489999999999999999999 78999999988843222122 23467788888888887655433
No 172
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.55 E-value=0.0054 Score=57.08 Aligned_cols=61 Identities=18% Similarity=0.337 Sum_probs=41.0
Q ss_pred CCCEEEEEEEEEecCcCeEEEEE-C-----------------CceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCC
Q 000449 1259 EGDIVGGRISKILSGVGGLVVQI-G-----------------PHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEG 1320 (1497)
Q Consensus 1259 ~G~~v~g~V~~v~~~~~gl~V~l-~-----------------~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g 1320 (1497)
+|++|.|||+++++. .+.+.+ . ....|.++..|+-..+.+. -++.+.|++|
T Consensus 4 vGdiV~~rVtrv~~~--~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dk---------v~~~~~FrpG 72 (82)
T PF10447_consen 4 VGDIVIARVTRVNPR--QAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDK---------VKMYDCFRPG 72 (82)
T ss_dssp TT-EEEEEEEEE-SS--EEEEEEEES----------SSS----SS-S-EEEEGGGT-SS-------------GGGT--SS
T ss_pred CCCEEEEEEEEEecc--EEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccch---------hhHHhccCCC
Confidence 899999999999998 888776 2 2467899998887654332 1146789999
Q ss_pred CEEEEEEEEe
Q 000449 1321 QFVKCKVLEI 1330 (1497)
Q Consensus 1321 ~~v~~~Vl~~ 1330 (1497)
++|+|+|++.
T Consensus 73 DIVrA~ViSl 82 (82)
T PF10447_consen 73 DIVRARVISL 82 (82)
T ss_dssp SEEEEEEEEE
T ss_pred CEEEEEEeeC
Confidence 9999999974
No 173
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.48 E-value=0.0015 Score=71.46 Aligned_cols=77 Identities=21% Similarity=0.302 Sum_probs=71.7
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeC--CCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeCCC
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLS--RKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~--~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~~~ 1452 (1497)
..++++|.+.|.+|.+.|+||.|- ++++|+|-+|+||..++...++..++|..=.|.|+.+|++.+-|.||.|....
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 467999999999999999999985 58999999999999999999999999999999999999999999999987654
No 174
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.43 E-value=0.021 Score=69.39 Aligned_cols=155 Identities=18% Similarity=0.302 Sum_probs=105.5
Q ss_pred cccCCCCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 755 DASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 755 ~~~~~~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
.+.++..|..+.|.|.++..||+||++...+.||+|.++++.. ..|.+|+.+.+.+..+-++++.+.+.....+
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 5788999999999999999999999999999999999998751 3688999999999999998888877765554
Q ss_pred cCCCCcchhhhhhhH--HHHHHHhhccccCCcccccccccCCCcEE--EEEEEEEeece--eEEEecCCCceEEEEeeee
Q 000449 835 CSSTDASFMQEHFLL--EEKIAMLQSSKHNGSELKWVEGFIIGSVI--EGKVHESNDFG--VVVSFEEHSDVYGFITHHQ 908 (1497)
Q Consensus 835 ~~~~~~~~~~~y~~~--~~~~~~~~~~~~~~~~~~~~~~~~vG~~V--~g~V~~i~~~G--~~v~l~~~~~~~G~i~~~~ 908 (1497)
... ..++-++ +..+.. ..+ .+|+.| +|+|+.++..+ -++.+.+. +|++..--
T Consensus 190 ~Y~-----~~~~~ke~~r~~i~~-------------id~-~ig~tV~I~GeV~qikqT~GPTVFtltDe---tg~i~aAA 247 (715)
T COG1107 190 RYR-----EVQVEKELPRTLIDD-------------LDE-MIGKTVRIEGEVTQIKQTSGPTVFTLTDE---TGAIWAAA 247 (715)
T ss_pred cch-----hhhhhhhcccccHHH-------------HHh-hcCceEEEEEEEEEEEEcCCCEEEEEecC---CCceehhh
Confidence 210 0111111 101111 122 678765 58999997754 44566653 33333322
Q ss_pred cC--C----ccccCCCEEEEEEEEEecCCCEEEEEe
Q 000449 909 LA--G----ATVESGSVIQAAILDVAKAERLVDLSL 938 (1497)
Q Consensus 909 l~--~----~~~~~G~~v~~~Vl~vd~~~~~v~lSl 938 (1497)
+. + -..++|+.|+.. =.++..++++.+-+
T Consensus 248 Fe~aGvRAyP~IevGdiV~Vi-G~V~~r~g~lQiE~ 282 (715)
T COG1107 248 FEEAGVRAYPEIEVGDIVEVI-GEVTRRDGRLQIEI 282 (715)
T ss_pred hccCCcccCCCCCCCceEEEE-EEEeecCCcEEEee
Confidence 21 1 267889988754 24556677776654
No 175
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.42 E-value=0.0069 Score=79.65 Aligned_cols=75 Identities=28% Similarity=0.362 Sum_probs=64.3
Q ss_pred CCCCCcEEEEEEEEEeceeEEEEeCCC-eEEEEEccccCCCcc-cC----------CCCccCCCCEEEEEEEEEcCCCCe
Q 000449 1375 DLSPNMIVQGYVKNVTSKGCFIMLSRK-LDAKVLLSNLSDGYV-ES----------PEKEFPIGKLVAGRVLSVEPLSKR 1442 (1497)
Q Consensus 1375 ~l~~G~~v~G~V~~v~~~G~fV~l~~~-~~g~v~is~lsd~~~-~~----------~~~~~~~g~~V~~~V~~vd~~~~~ 1442 (1497)
.-.+|+.+.|+|++|+.+|+||.|... ++|+||++.|.++|. .+ ....|+.||.|+++|.+++...++
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 346799999999999999999999875 999999999997543 22 234799999999999999999999
Q ss_pred EEEEEEe
Q 000449 1443 VEVTLKT 1449 (1497)
Q Consensus 1443 i~lslk~ 1449 (1497)
|.+++..
T Consensus 699 i~~~~v~ 705 (706)
T COG0557 699 IDFELVE 705 (706)
T ss_pred eEEEecC
Confidence 9988754
No 176
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.38 E-value=0.03 Score=59.42 Aligned_cols=73 Identities=21% Similarity=0.331 Sum_probs=59.7
Q ss_pred ccCCCEEEEEEEEEecCcCeEEEEEC----------CceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEE
Q 000449 1257 IHEGDIVGGRISKILSGVGGLVVQIG----------PHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCK 1326 (1497)
Q Consensus 1257 l~~G~~v~g~V~~v~~~~~gl~V~l~----------~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~ 1326 (1497)
++.|++|-|+|+++... .++|.+. ....|-+|++++.+.|..+ ..+.|.+|++|+|+
T Consensus 62 ~K~GdiV~grV~~v~~~--~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~-----------~~d~f~~GDivrA~ 128 (188)
T COG1096 62 PKGGDIVYGRVTDVREQ--RALVRIVGVEGKERELATSGAADIHVSQVRDGYVEK-----------LSDAFRIGDIVRAR 128 (188)
T ss_pred CCCCCEEEEEEeeccce--EEEEEEEEEecccccCCCCceeeEEEEecccccccc-----------cccccccccEEEEE
Confidence 44999999999999987 8888762 1256789999999999887 57899999999999
Q ss_pred EEEeecccCCccEEEEEeeccc
Q 000449 1327 VLEISRTVRGTFHVELSLRSSL 1348 (1497)
Q Consensus 1327 Vl~~d~~~~g~~~i~lS~R~s~ 1348 (1497)
|++.- ..+.||.+...
T Consensus 129 Vis~~------~~~~Lst~~~d 144 (188)
T COG1096 129 VISTG------DPIQLSTKGND 144 (188)
T ss_pred EEecC------CCeEEEecCCc
Confidence 99984 25788876543
No 177
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.31 E-value=0.0096 Score=77.05 Aligned_cols=68 Identities=15% Similarity=0.142 Sum_probs=56.4
Q ss_pred CcEEEEEEEEEeceeEEEEe-CCCeEEEEEccccCC--C-cccCC---------CCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1379 NMIVQGYVKNVTSKGCFIML-SRKLDAKVLLSNLSD--G-YVESP---------EKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~fV~l-~~~~~g~v~is~lsd--~-~~~~~---------~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
|+.+.|.|+.++.+|+||+| ..+++|+||++.|.+ + |.-+. ...|++||.|+++|.++|...++|.+
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 45999999999999999999 557999999999976 3 32111 12699999999999999998888876
Q ss_pred E
Q 000449 1446 T 1446 (1497)
Q Consensus 1446 s 1446 (1497)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 4
No 178
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.11 E-value=0.018 Score=62.05 Aligned_cols=71 Identities=20% Similarity=0.154 Sum_probs=55.2
Q ss_pred CCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCccccc-----------c-cCCCccccCCCEEEEEEEEE--e--CCe
Q 000449 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFE-----------I-VKPGKKFKVGAELVFRVLGV--K--SKR 560 (1497)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~-----------~-~~~~~~~kvG~~V~~rVl~v--~--~~~ 560 (1497)
-.|+++.|+|++++++|++|++| -+++|||.+.|.+.. . .+-+..++.|+.|++||..+ + +-.
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~ 158 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF 158 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence 36999999999999999999997 788999999887421 1 11134578999999999998 2 235
Q ss_pred EEEEeecc
Q 000449 561 ITVTHKKT 568 (1497)
Q Consensus 561 i~lS~K~~ 568 (1497)
+..|+|+-
T Consensus 159 ~i~T~~~~ 166 (176)
T PTZ00162 159 AIATINSD 166 (176)
T ss_pred EEEEecCC
Confidence 66677753
No 179
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.93 E-value=0.0066 Score=66.61 Aligned_cols=76 Identities=25% Similarity=0.335 Sum_probs=70.8
Q ss_pred CCCCEEEEEEEEEecceEEEEeC--CCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~--~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
.+++++-+.|.+|.+-|++|.+. ++++|++..|++|..++.......++|-.=.|.|+++|.+++-|-||.+...+
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 36899999999999999999994 79999999999999999999999999999999999999999999999987754
No 180
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=95.92 E-value=0.018 Score=70.28 Aligned_cols=73 Identities=19% Similarity=0.200 Sum_probs=56.6
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEeCCCeEEEEeCCCCCcc------------cccCcccCcCCCCEEEEEEEEEeCCCC
Q 000449 759 IHPNSVVHGYVCNIIET--GCFVRFLGRLTGFAPRSKAVDG------------QRADLSKTYYVGQSVRSNILDVNSETG 824 (1497)
Q Consensus 759 ~~~G~~v~G~V~~i~~~--G~FV~~~~gl~Glvp~sels~~------------~~~~~~~~~~~Gq~V~v~V~~iD~e~~ 824 (1497)
..+|+++.|.|.++.+. ||||+++.+..||+|.+++.+. ...++.+.+++||.|.|.|..=....+
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~K 102 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNK 102 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCC
Confidence 56899999999999999 9999999999999999998653 123455679999999999998322333
Q ss_pred eEEEEee
Q 000449 825 RITLSLK 831 (1497)
Q Consensus 825 Ri~LSlK 831 (1497)
.-.||..
T Consensus 103 gp~lT~~ 109 (414)
T TIGR00757 103 GARLTTD 109 (414)
T ss_pred CCeEEEE
Confidence 3334443
No 181
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.85 E-value=0.045 Score=60.55 Aligned_cols=74 Identities=23% Similarity=0.308 Sum_probs=63.9
Q ss_pred CCCCEEEEEEEEEecceEEEEeCCCeEEEEeCCCCCccc----ccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 000449 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ----RADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1497)
Q Consensus 760 ~~G~~v~G~V~~i~~~G~FV~~~~gl~Glvp~sels~~~----~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~ 834 (1497)
.+|+.+-|.|..+...+-.|++.....+++|.|++.+.. ..+....|.+||.|.|+|..+|+ .....|++|...
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~~ 140 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDEG 140 (239)
T ss_pred CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEeecCC
Confidence 469999999999999999999999999999999996544 24667789999999999999995 677888886554
No 182
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.81 E-value=0.0076 Score=77.96 Aligned_cols=81 Identities=28% Similarity=0.343 Sum_probs=73.3
Q ss_pred cCCCCCCcEEEEEEEEEecee---EEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEe
Q 000449 1373 IEDLSPNMIVQGYVKNVTSKG---CFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKT 1449 (1497)
Q Consensus 1373 ~~~l~~G~~v~G~V~~v~~~G---~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~ 1449 (1497)
.+.+.+|.+|.+.|++|+..- +=|.+.++++|+|+..++|+.-+.+|...+++||.|.|+|+++|.++=.+.||++.
T Consensus 980 ~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 980 PETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred hhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhh
Confidence 456889999999999997765 46789999999999999999999999999999999999999999888888999999
Q ss_pred CCCC
Q 000449 1450 SDSR 1453 (1497)
Q Consensus 1450 ~~~~ 1453 (1497)
++..
T Consensus 1060 sdlk 1063 (1299)
T KOG1856|consen 1060 SDLK 1063 (1299)
T ss_pred HHhh
Confidence 8763
No 183
>PRK05054 exoribonuclease II; Provisional
Probab=95.74 E-value=0.028 Score=73.03 Aligned_cols=71 Identities=20% Similarity=0.215 Sum_probs=57.9
Q ss_pred CCC--CEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcc---cc--cC-------cccCcCCCCEEEEEEEEEeCCCC
Q 000449 760 HPN--SVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDG---QR--AD-------LSKTYYVGQSVRSNILDVNSETG 824 (1497)
Q Consensus 760 ~~G--~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~---~~--~~-------~~~~~~~Gq~V~v~V~~iD~e~~ 824 (1497)
++| +.+.|.|++++++|+||++.+ +++||+|.+.+.+. +. .+ -...|+.||.|.|+|.++|.+++
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 455 599999999999999999964 79999999998642 11 11 12469999999999999999999
Q ss_pred eEEEEe
Q 000449 825 RITLSL 830 (1497)
Q Consensus 825 Ri~LSl 830 (1497)
+|.+.+
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 988764
No 184
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.66 E-value=0.01 Score=76.74 Aligned_cols=76 Identities=25% Similarity=0.298 Sum_probs=66.6
Q ss_pred hccCCcEEEEEEEEEeee--eE-EEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 000449 582 EATDRLITHGWITKIEKH--GC-FVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1497)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~--G~-~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~vd~~~~ri~lS~k~~ 657 (1497)
.+..|.++.++|+++... +| -|.+.+|+.||+|.++++...+.+|...+++||+|.|+|+++|.++=...|||+.+
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 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 356799999999999853 34 56888999999999999988888999999999999999999999888888898864
No 185
>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=95.16 E-value=0.097 Score=49.36 Aligned_cols=70 Identities=17% Similarity=0.091 Sum_probs=57.3
Q ss_pred CCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE-eCCeEEEEeec
Q 000449 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-KSKRITVTHKK 567 (1497)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v-~~~~i~lS~K~ 567 (1497)
++|++|=|+|+.+...+..|+|+....|++|..++... ..+....+++|+-|-|||..+ ......||...
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~ 75 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVD 75 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeC
Confidence 58999999999999999999999889999999877432 223344689999999999998 45567888753
No 186
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.74 E-value=0.07 Score=69.24 Aligned_cols=72 Identities=14% Similarity=0.162 Sum_probs=55.3
Q ss_pred CCCcEEEEEEEEEec--eeEEEEeCCCeEEEEEccccCCCcccC---------CCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1377 SPNMIVQGYVKNVTS--KGCFIMLSRKLDAKVLLSNLSDGYVES---------PEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~--~G~fV~l~~~~~g~v~is~lsd~~~~~---------~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
.+|+||.|+|.+|.+ .++||+||.+..||+|++++...+..+ ....+++||.|.|.|..=...++-..|
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~L 116 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAAL 116 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCce
Confidence 479999999999955 579999999999999999997554322 244689999999999885444444444
Q ss_pred EEE
Q 000449 1446 TLK 1448 (1497)
Q Consensus 1446 slk 1448 (1497)
|.+
T Consensus 117 Tt~ 119 (1068)
T PRK10811 117 TTF 119 (1068)
T ss_pred eee
Confidence 433
No 187
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=94.49 E-value=0.096 Score=67.99 Aligned_cols=68 Identities=21% Similarity=0.273 Sum_probs=55.2
Q ss_pred CCEEEEEEEEEecceEEEEeC-CCeEEEEeCCCCCc--c-c--ccCc-------ccCcCCCCEEEEEEEEEeCCCCeEEE
Q 000449 762 NSVVHGYVCNIIETGCFVRFL-GRLTGFAPRSKAVD--G-Q--RADL-------SKTYYVGQSVRSNILDVNSETGRITL 828 (1497)
Q Consensus 762 G~~v~G~V~~i~~~G~FV~~~-~gl~Glvp~sels~--~-~--~~~~-------~~~~~~Gq~V~v~V~~iD~e~~Ri~L 828 (1497)
|..+.|.|..++.+|+||++. .+++||+|.+.+.+ . + ..+. ...|+.||.|.++|.++|.++++|.+
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 458999999999999999994 58999999999865 1 1 1111 12599999999999999999998876
Q ss_pred E
Q 000449 829 S 829 (1497)
Q Consensus 829 S 829 (1497)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 4
No 188
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.30 E-value=0.13 Score=62.14 Aligned_cols=72 Identities=19% Similarity=0.305 Sum_probs=59.8
Q ss_pred CCcEEEEEEEEEEeCeEEEEe----CCCCeEEEeeCCCCCCCCCCcCCCCcEEEEEEEEEcCC---CcEEEEccCccccc
Q 000449 232 EGMVLTAYVKSIEDHGYILHF----GLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRT---RKVVYLSSDPDTVS 304 (1497)
Q Consensus 232 ~g~~l~~~V~svedhG~ivd~----Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~---~~~v~ls~~~~~~~ 304 (1497)
.|.+++|.|..++.++++||+ |-.++.|+||+++.-+.. .+++|+.+.|.|.++... |-.+.||+....+.
T Consensus 152 ~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E--~y~~Gdrika~i~~V~~~~~kGpqIilSRt~p~lv 229 (449)
T PRK12329 152 EDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPND--NYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLV 229 (449)
T ss_pred cCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCC--cCCCCCEEEEEEEEeecCCCCCCEEEEEcCCHHHH
Confidence 599999999999999999999 433589999999865555 899999999999999554 45789998666655
Q ss_pred c
Q 000449 305 K 305 (1497)
Q Consensus 305 ~ 305 (1497)
.
T Consensus 230 ~ 230 (449)
T PRK12329 230 V 230 (449)
T ss_pred H
Confidence 4
No 189
>PRK11712 ribonuclease G; Provisional
Probab=93.78 E-value=0.13 Score=63.97 Aligned_cols=71 Identities=17% Similarity=0.119 Sum_probs=52.6
Q ss_pred CCCcEEEEEEEEEec--eeEEEEeCCCeEEEEEccccCCC--c----------ccCCCCccCCCCEEEEEEEEEcCCCCe
Q 000449 1377 SPNMIVQGYVKNVTS--KGCFIMLSRKLDAKVLLSNLSDG--Y----------VESPEKEFPIGKLVAGRVLSVEPLSKR 1442 (1497)
Q Consensus 1377 ~~G~~v~G~V~~v~~--~G~fV~l~~~~~g~v~is~lsd~--~----------~~~~~~~~~~g~~V~~~V~~vd~~~~~ 1442 (1497)
.+|+||.|+|.+|.+ .+|||+||.+..||+|++++... + .....+.+++||.|.|.|+.=-...+.
T Consensus 37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG 116 (489)
T PRK11712 37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKG 116 (489)
T ss_pred ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCC
Confidence 469999999999966 57999999999999999998421 1 111234589999999999874433343
Q ss_pred EEEEE
Q 000449 1443 VEVTL 1447 (1497)
Q Consensus 1443 i~lsl 1447 (1497)
-.||.
T Consensus 117 ~~lT~ 121 (489)
T PRK11712 117 ARLTT 121 (489)
T ss_pred CeEEE
Confidence 44444
No 190
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=93.17 E-value=0.22 Score=65.82 Aligned_cols=75 Identities=21% Similarity=0.313 Sum_probs=62.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEeCC-CeEEEEeCCCCCcccc-----------cCcccCcCCCCEEEEEEEEEeCCC
Q 000449 756 ASHIHPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQR-----------ADLSKTYYVGQSVRSNILDVNSET 823 (1497)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~G~FV~~~~-gl~Glvp~sels~~~~-----------~~~~~~~~~Gq~V~v~V~~iD~e~ 823 (1497)
|-.-++|+...|+|.+++.+|+||.+.+ +++|++|.+.+...+. ......|..||.|.+++.++|...
T Consensus 617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~ 696 (706)
T COG0557 617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE 696 (706)
T ss_pred HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence 4456789999999999999999999977 4999999999985221 122346999999999999999988
Q ss_pred CeEEEEe
Q 000449 824 GRITLSL 830 (1497)
Q Consensus 824 ~Ri~LSl 830 (1497)
+++.+++
T Consensus 697 ~~i~~~~ 703 (706)
T COG0557 697 RKIDFEL 703 (706)
T ss_pred cceEEEe
Confidence 8888775
No 191
>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=92.33 E-value=0.55 Score=45.01 Aligned_cols=62 Identities=23% Similarity=0.443 Sum_probs=50.2
Q ss_pred ccccccccccCCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE
Q 000449 487 EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1497)
Q Consensus 487 ~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1497)
..++..+-+ ..|.+|.|+|..+.++-+++++|+.+.++|+.... ..++|..|.+|..|+...
T Consensus 13 ~S~fi~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~-------~~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 13 NSPFIQLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAV-------NGEKYVRGSRVRLRLKDL 74 (104)
T ss_pred CChhhhcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecccc-------cccccccCCEEEEEECCH
Confidence 345555656 68999999999999999999999999999986533 225799999999998554
No 192
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=91.53 E-value=0.71 Score=48.16 Aligned_cols=76 Identities=13% Similarity=0.106 Sum_probs=59.2
Q ss_pred CCCCcEEEEEEEEEeceeEEEEe--------CCCeEEEEEccccCCC--cccCCCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIML--------SRKLDAKVLLSNLSDG--YVESPEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l--------~~~~~g~v~is~lsd~--~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
..+|+||..+|.+++..-+=|+| .....|+||-.++-.. -.-++.+.|++||+|.|+|++.+ .+...-|
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~-~~~~y~L 144 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG-DGSNYLL 144 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC-CCCcEEE
Confidence 36799999999999888777775 3478999998887532 12246678999999999999966 5677888
Q ss_pred EEEeCCC
Q 000449 1446 TLKTSDS 1452 (1497)
Q Consensus 1446 slk~~~~ 1452 (1497)
|.-+.+.
T Consensus 145 TtAeneL 151 (193)
T KOG3409|consen 145 TTAENEL 151 (193)
T ss_pred EEecccc
Confidence 8876654
No 193
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=89.83 E-value=1.3 Score=44.95 Aligned_cols=59 Identities=24% Similarity=0.242 Sum_probs=43.1
Q ss_pred CCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCccccc------------c-cCCCccccCCCEEEEEEEEE
Q 000449 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFE------------I-VKPGKKFKVGAELVFRVLGV 556 (1497)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~------------~-~~~~~~~kvG~~V~~rVl~v 556 (1497)
+|+++.|+|.+.+..|+.|.++-.-+-+||...|.... . ..-+-.|..|++|++||..+
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEE
Confidence 69999999999999999999985567899998886321 1 11222358999999999887
No 194
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=88.13 E-value=2.1 Score=44.89 Aligned_cols=72 Identities=18% Similarity=0.252 Sum_probs=56.2
Q ss_pred CCCCEEEEEEEEEeCCEEEEEEc--------CCeEEEEEeeccCCCCchhhhccccCCCCCEEEEEEEEEeccCcEEEEE
Q 000449 1162 SIGQRVTGYVYKVDNEWALLTIS--------RHLKAQLFILDSAYEPSELQEFQRRFHIGKAVTGHVLSINKEKKLLRLV 1233 (1497)
Q Consensus 1162 ~~G~~v~g~V~~v~~~~l~V~ls--------~~~~g~i~~~~~s~~~~~~~~~~~~f~vG~~v~~~V~~~~~~~~~l~LS 1233 (1497)
..|++|++.|..++..++.++|. ...+|.|+..|+-.-..+.-++.++|.||+-|.|+|++.++..+. .|+
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y-~LT 145 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNY-LLT 145 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcE-EEE
Confidence 57999999999999988877763 456799998887555444556789999999999999997655554 454
Q ss_pred e
Q 000449 1234 L 1234 (1497)
Q Consensus 1234 ~ 1234 (1497)
.
T Consensus 146 t 146 (193)
T KOG3409|consen 146 T 146 (193)
T ss_pred E
Confidence 3
No 195
>PRK10811 rne ribonuclease E; Reviewed
Probab=88.03 E-value=2.7 Score=55.28 Aligned_cols=86 Identities=23% Similarity=0.297 Sum_probs=61.9
Q ss_pred CCCEEEEEEEEEecCcCeEEEEECCceEEEEecccccccccCCCCCCCCC-CCCCCCCCcCCCCEEEEEEEEeecccCCc
Q 000449 1259 EGDIVGGRISKILSGVGGLVVQIGPHLYGRVHFTELKNICVSDPLSGYDE-GQFDPLSGYDEGQFVKCKVLEISRTVRGT 1337 (1497)
Q Consensus 1259 ~G~~v~g~V~~v~~~~~gl~V~l~~~~~G~v~~tdl~d~~~~~~~~~~d~-~~~~~~~~~~~g~~v~~~Vl~~d~~~~g~ 1337 (1497)
+|.|+.|+|.+|.++-+++||+||.+..||+|+.|+...+..+. +.- +.......+++||.|-|.|..-.. |+
T Consensus 38 vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~---~~~~~~~~i~~~Lk~GqeILVQV~KEa~---gt 111 (1068)
T PRK10811 38 KANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPAN---YSAHGRPNIKDVLREGQEVIVQIDKEER---GN 111 (1068)
T ss_pred ccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccc---cccccccccccccCCCCEEEEEEeeccc---CC
Confidence 89999999999999888999999999999999999975443220 000 000012347789999988877544 35
Q ss_pred cEEEEEeeccccC
Q 000449 1338 FHVELSLRSSLDG 1350 (1497)
Q Consensus 1338 ~~i~lS~R~s~~~ 1350 (1497)
|-..||.+-+..|
T Consensus 112 KGp~LTt~ISLpG 124 (1068)
T PRK10811 112 KGAALTTFISLAG 124 (1068)
T ss_pred CCCceeeeEEecc
Confidence 6667777776633
No 196
>PRK11712 ribonuclease G; Provisional
Probab=87.66 E-value=1.1 Score=56.09 Aligned_cols=59 Identities=15% Similarity=0.167 Sum_probs=45.5
Q ss_pred cCCcEEEEEEEEEee--eeEEEEEcCceEEeeecccccCC------------CCCCCCCCccCCCEEEEEEEE
Q 000449 584 TDRLITHGWITKIEK--HGCFVRFYNGVQGFAPRSELGLD------------PGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 584 ~~G~~~~G~V~~i~~--~G~~V~~~~gv~gflp~sel~~~------------~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.+|.++.|+|.++.+ .+|||+++.+-.||+|.+++... ...+..+.++.||.+-|.|..
T Consensus 37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~K 109 (489)
T PRK11712 37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVK 109 (489)
T ss_pred ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEe
Confidence 479999999999997 68999999999999999987310 011123447788888888876
No 197
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=87.50 E-value=0.78 Score=57.69 Aligned_cols=74 Identities=18% Similarity=0.178 Sum_probs=58.5
Q ss_pred CCCCcEEEEEEEEEece--eEEEEeCCCeEEEEEccccCCCcccCC-----CCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1376 LSPNMIVQGYVKNVTSK--GCFIMLSRKLDAKVLLSNLSDGYVESP-----EKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~--G~fV~l~~~~~g~v~is~lsd~~~~~~-----~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
..+|.+|.|+|++|.+. .+||++|....||+|++++.+ |...+ +..++.||.+-+.|+.-...++--.||..
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~~ 113 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTTD 113 (487)
T ss_pred eeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCccccccceeE
Confidence 35699999999999764 689999999999999999999 54443 34899999999999886655554455544
Q ss_pred eC
Q 000449 1449 TS 1450 (1497)
Q Consensus 1449 ~~ 1450 (1497)
-+
T Consensus 114 Is 115 (487)
T COG1530 114 IS 115 (487)
T ss_pred Ee
Confidence 43
No 198
>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=86.51 E-value=2.8 Score=40.43 Aligned_cols=52 Identities=13% Similarity=0.232 Sum_probs=43.9
Q ss_pred CCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEE
Q 000449 320 VPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILF 379 (1497)
Q Consensus 320 ~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~ 379 (1497)
-.|-+|.|.|..|..+.++++|+++|..+....... .+.|..|..|+.|+..
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~--------~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN--------GEKYVRGSRVRLRLKD 73 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc--------ccccccCCEEEEEECC
Confidence 368899999999999999999999999998755432 1369999999999854
No 199
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=85.76 E-value=3.2 Score=43.22 Aligned_cols=64 Identities=16% Similarity=0.100 Sum_probs=42.3
Q ss_pred CCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCC----------CcccCCCCccCCCCEEEEEEEEEcCCCC
Q 000449 1378 PNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSD----------GYVESPEKEFPIGKLVAGRVLSVEPLSK 1441 (1497)
Q Consensus 1378 ~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd----------~~~~~~~~~~~~g~~V~~~V~~vd~~~~ 1441 (1497)
.|+++.|.|+.+...|+|++.|+---......-.+| .|..+-.+...+|..|+.+|+.+.-...
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~ 154 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET 154 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence 399999999999999999999953322222222211 2333333467888899999988753333
No 200
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=82.69 E-value=7.4 Score=40.65 Aligned_cols=64 Identities=25% Similarity=0.401 Sum_probs=44.0
Q ss_pred CCcEEEEEEEEEeeeeEEEEEcCceEEeeecccc----cCCCCCCCC-------CCccCCCEEEEEEEEEecCCCE
Q 000449 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSEL----GLDPGCEPS-------SMYHVGQVVKCRIMSSIPASRR 649 (1497)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~gflp~sel----~~~~~~~~~-------~~~~vGq~v~v~Vl~vd~~~~r 649 (1497)
.|++++|+|+++.+.|+|++. +-++-|+..-.+ ...+.++|. ....+|.+|+++|+..-.+...
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~-GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~ 155 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARS-GPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE 155 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEec-cceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeee
Confidence 599999999999999999998 677777654332 222333311 1467788888888876544433
No 201
>PRK06386 replication factor A; Reviewed
Probab=79.48 E-value=1.5e+02 Score=35.84 Aligned_cols=114 Identities=20% Similarity=0.156 Sum_probs=67.0
Q ss_pred cCccCCCCCCcE---EEEEEEEEeceeEEEEeCCCeEEEEEccccCCC----cccCCCCccCCCCEEEEEEEEEcCCCCe
Q 000449 1370 LEKIEDLSPNMI---VQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDG----YVESPEKEFPIGKLVAGRVLSVEPLSKR 1442 (1497)
Q Consensus 1370 ~~~~~~l~~G~~---v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~----~~~~~~~~~~~g~~V~~~V~~vd~~~~~ 1442 (1497)
...+.||++|+. +.|+|..+.+. .++ ..+-.|.|.---|.|+ ++..|.+.+..|+.++..=..++.-+++
T Consensus 107 ~~KI~DL~~g~~~v~V~akVle~~e~--e~~-~~g~~~~v~sg~lgDeTGrIr~TlW~~~l~eGd~v~i~na~v~e~~G~ 183 (358)
T PRK06386 107 LVKIRDLSLVTPYVSVIGKITGITKK--EYD-SDGTSKIVYQGYIEDDTARVRISSFGKPLEDNRFVRIENARVSQYNGY 183 (358)
T ss_pred ccEeEeccCCCCceEEEEEEEEccCc--eEe-cCCCccEEEEEEEEcCCCeEEEEEccccccCCCEEEEeeeEEEccCCe
Confidence 457889998854 79999888654 223 3333333333333332 2334555688999998765556655788
Q ss_pred EEEEEEeCCCC-c-cccc----ccCCCCCCCCCC---EEEEEEEEEee-ceeEE
Q 000449 1443 VEVTLKTSDSR-T-ASQS----EINNLSNLHVGD---IVIGQIKRVES-YGLFI 1486 (1497)
Q Consensus 1443 i~lslk~~~~~-~-~~~~----~~~~~~d~~~G~---iv~G~V~~v~~-~GvFV 1486 (1497)
++|++-....- + ..+. ....+.|+..++ -+.|.|..|.+ -|+|=
T Consensus 184 ~el~v~~~t~I~~~~~~iev~~~~~~I~di~~~~g~v~i~G~iv~i~~gsgli~ 237 (358)
T PRK06386 184 IEISVGNKSVIKEVESDINLESRNIFIFEIKSPVGGITIMGFIVSVGQGSRIFT 237 (358)
T ss_pred EEEEeCCeEEEEECCCCcccCccccchhhhhccCCeEEEEEEEEEEcCCcEeEe
Confidence 88887543220 0 0111 123455677765 78888888885 45443
No 202
>PRK14699 replication factor A; Provisional
Probab=78.71 E-value=2e+02 Score=36.58 Aligned_cols=255 Identities=16% Similarity=0.174 Sum_probs=129.0
Q ss_pred cCCCCCEEEEEEEEEeccCcEEEEEeccccCCC--CCcccccccccccccccCCC---EEEEEEEEEecCc-----Ce--
Q 000449 1209 RFHIGKAVTGHVLSINKEKKLLRLVLRPFQDGI--SDKTVDISNDNMQTFIHEGD---IVGGRISKILSGV-----GG-- 1276 (1497)
Q Consensus 1209 ~f~vG~~v~~~V~~~~~~~~~l~LS~~~~~~~~--~~~~~~~~~~~~~~~l~~G~---~v~g~V~~v~~~~-----~g-- 1276 (1497)
.+.+|+.|+.+=. +-...+.++|++....... ..+........+...|.+|+ .+.|+|..+.+-. .|
T Consensus 123 ~l~~GDvv~I~~~-~r~~~~g~el~~~~~~~i~~~~~~i~v~~~~~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~ 201 (484)
T PRK14699 123 KIKAGQTLQISGY-AKQGYSGVEVNIGNNGVLTESEEEIDVAANSQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTS 201 (484)
T ss_pred CCCCCCEEEEcce-eccCCCCceEEeCCCceeeccCcccccCCCCcchhhcCCCCCceEEEEEEEeccCceEEecCCCCc
Confidence 5899999887432 2222334677765311111 11111111112233444654 6899998876520 01
Q ss_pred --EE-EEECCceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEE--EEEeecccCCccEEEEEeeccccCC
Q 000449 1277 --LV-VQIGPHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCK--VLEISRTVRGTFHVELSLRSSLDGM 1351 (1497)
Q Consensus 1277 --l~-V~l~~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~--Vl~~d~~~~g~~~i~lS~R~s~~~~ 1351 (1497)
+. +-|+. -.|.|.+|-..+.- + ....+.+|+.|+.. -.... ..+++++|+.=.... .
T Consensus 202 g~v~~~~igD-eTG~ir~tlW~~~a--~-----------~~~~l~~Gd~v~I~~a~vr~~---~~~~~~el~~~~~s~-i 263 (484)
T PRK14699 202 GKVGNLLLGD-ETGTLRVTLWDDKT--D-----------FLNQIEYGDTVELINAYAREN---AFTQKVELQVGNRSI-I 263 (484)
T ss_pred eEEEEEEEEc-CCceEEEEEECccc--c-----------cccccCCCCEEEEecceEeec---ccCCceEEEecCceE-e
Confidence 11 23342 35667766554421 1 23346789988743 11211 123577777633210 0
Q ss_pred CCCCCCCCCCCCCCCCCccCccCCCCCCc---EEEEEEEEEeceeEEE------------EeCCCeEEEEEccccCCCcc
Q 000449 1352 SSTNSSDLSTDVDTPGKHLEKIEDLSPNM---IVQGYVKNVTSKGCFI------------MLSRKLDAKVLLSNLSDGYV 1416 (1497)
Q Consensus 1352 ~~~~~~~~~~~~~~~~~~~~~~~~l~~G~---~v~G~V~~v~~~G~fV------------~l~~~~~g~v~is~lsd~~~ 1416 (1497)
..... ... ..+....+.+|++++ .+.|+|.++.+---|- .|+ .-+|.|+++-..+.-
T Consensus 264 --~~~~~---~~e-~~~~~~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~-DeTG~Ir~T~W~~~a- 335 (484)
T PRK14699 264 --RKSEK---KVE-YEEEFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLG-DSTGKIRLTLWDEKT- 335 (484)
T ss_pred --ecccc---ccc-ccccccCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEE-CCCCeEEEEEeCccc-
Confidence 00000 000 112345577787764 4899999887643333 233 345556665444321
Q ss_pred cCCCCccCCCCEEEEEEEEEc--CCCCeEEEEEEeCCC-Cc-----ccccccCCCCCCCCCCEE--EEEEEEEeeceeEE
Q 000449 1417 ESPEKEFPIGKLVAGRVLSVE--PLSKRVEVTLKTSDS-RT-----ASQSEINNLSNLHVGDIV--IGQIKRVESYGLFI 1486 (1497)
Q Consensus 1417 ~~~~~~~~~g~~V~~~V~~vd--~~~~~i~lslk~~~~-~~-----~~~~~~~~~~d~~~G~iv--~G~V~~v~~~GvFV 1486 (1497)
+....+.+|+.++..-..+. .-+++++|++-.... .+ .-......+.+|..|+.+ .|.|+.+.+--=|.
T Consensus 336 -~~~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~~~~~~~I~die~~~~vdV~G~V~~v~~~~~~~ 414 (484)
T PRK14699 336 -NFLDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEYREKFTDIADIIPGESYSVQGKVSEIGELREFE 414 (484)
T ss_pred -ccccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcceeeeccccHHHccCCCeeEEEEEEEEcCCcceEE
Confidence 12224567886553222222 124678888755432 11 001123346788888875 79999999988888
Q ss_pred EECCe
Q 000449 1487 TIENT 1491 (1497)
Q Consensus 1487 ~l~~s 1491 (1497)
+-+++
T Consensus 415 ~~~g~ 419 (484)
T PRK14699 415 REDGT 419 (484)
T ss_pred ecCCC
Confidence 87766
No 203
>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=77.63 E-value=7.8 Score=39.31 Aligned_cols=61 Identities=10% Similarity=0.041 Sum_probs=43.0
Q ss_pred CCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCC---C---------CCCcccCCCCCEEEEEEEEEe
Q 000449 321 PGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFP---T---------TNWKNDYNQHKKVNARILFVD 381 (1497)
Q Consensus 321 pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~---~---------~~~~~~~~vG~~v~arVl~~~ 381 (1497)
.|.++.|+|.+.+++|+.|+++-+-+=+||...|..... . .+-+-.|..|+.|+.||..+.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 588999999999999999999665567799888875431 0 122334588999999998763
No 204
>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=73.36 E-value=3 Score=36.37 Aligned_cols=59 Identities=15% Similarity=0.301 Sum_probs=45.0
Q ss_pred CEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccCCCCchhhhc-cccCCCCCEEEEEEEEEec
Q 000449 1165 QRVTGYVYKVDNEWALLTISRHLKAQLFILDSAYEPSELQEF-QRRFHIGKAVTGHVLSINK 1225 (1497)
Q Consensus 1165 ~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s~~~~~~~~~-~~~f~vG~~v~~~V~~~~~ 1225 (1497)
...++.|+.+.++...|+|.. .|++.....+.+.+....+ .+++++|+.+.+++...+-
T Consensus 2 S~htA~VQh~~kdfAvvSL~~--t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 2 SRHTAIVQHADKDFAIVSLAT--TGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred CccchhhhhhhhceEEEEeec--cccEEEEEchhhccccccccceeeeccceEEEEEecCcc
Confidence 456788999999999999954 4666666666666655555 5789999999999887654
No 205
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=70.92 E-value=12 Score=47.18 Aligned_cols=80 Identities=28% Similarity=0.375 Sum_probs=58.9
Q ss_pred CCCEEEEEEEEEecCcCeEEEEECCceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEEEEEeecccCCcc
Q 000449 1259 EGDIVGGRISKILSGVGGLVVQIGPHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCKVLEISRTVRGTF 1338 (1497)
Q Consensus 1259 ~G~~v~g~V~~v~~~~~gl~V~l~~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~Vl~~d~~~~g~~ 1338 (1497)
+|.++.|+|++|.|+-..++|++|....||+|+.|+.+ |...++. + +-...++.|+.+-+.|+.-.. |++
T Consensus 37 ~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~---~---~i~~~lr~~~~~~Vqv~ke~~---G~K 106 (487)
T COG1530 37 VGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLE---E---KIKVRLRGGQATLVQVVKEPR---GTK 106 (487)
T ss_pred ecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhccc---c---cceeeecCCceEEEEEEeecC---ccc
Confidence 79999999999999888999999999999999999999 5444210 0 011356678888777776654 455
Q ss_pred EEEEEeeccc
Q 000449 1339 HVELSLRSSL 1348 (1497)
Q Consensus 1339 ~i~lS~R~s~ 1348 (1497)
-..||.--+.
T Consensus 107 ga~lT~~Is~ 116 (487)
T COG1530 107 GARLTTDISL 116 (487)
T ss_pred cccceeEEee
Confidence 5555555444
No 206
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=66.19 E-value=8 Score=43.18 Aligned_cols=75 Identities=21% Similarity=0.227 Sum_probs=60.7
Q ss_pred CCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccC--CCccc--------CCCCccCCCCEEEEEEEEEcCCCCeEEE
Q 000449 1376 LSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLS--DGYVE--------SPEKEFPIGKLVAGRVLSVEPLSKRVEV 1445 (1497)
Q Consensus 1376 l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~ls--d~~~~--------~~~~~~~~g~~V~~~V~~vd~~~~~i~l 1445 (1497)
.++||+|-|+|..|..+--=|+++...++.+.+|.+. ..-.. ....+|+.||+|.+.|.++- .++-+.|
T Consensus 83 pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~-~dGs~sL 161 (301)
T KOG3013|consen 83 PEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF-HDGSLSL 161 (301)
T ss_pred CccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhc-cCCeEEE
Confidence 3679999999999999999999999999999998653 32111 25678999999999999887 5677888
Q ss_pred EEEeCC
Q 000449 1446 TLKTSD 1451 (1497)
Q Consensus 1446 slk~~~ 1451 (1497)
-.|...
T Consensus 162 hTRS~K 167 (301)
T KOG3013|consen 162 HTRSLK 167 (301)
T ss_pred Eecchh
Confidence 777654
No 207
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=63.24 E-value=34 Score=32.35 Aligned_cols=66 Identities=17% Similarity=0.163 Sum_probs=51.4
Q ss_pred EEEEEEEEEecceEEE-EeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecc
Q 000449 764 VVHGYVCNIIETGCFV-RFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1497)
Q Consensus 764 ~v~G~V~~i~~~G~FV-~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~ 833 (1497)
.+.|.|..+.+.+.|- .+.+|..-++|.|-=-. .-.-.+.+||.|.+-+-..|.+++||.--.+..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR----~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~~ 74 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMR----KHRIRILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecccee----eeeEEecCCCEEEEEECcccCCceeEEEEecCC
Confidence 4789999998888775 88899988888763211 111246689999999999999999999888743
No 208
>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=61.22 E-value=36 Score=30.82 Aligned_cols=60 Identities=18% Similarity=0.172 Sum_probs=46.2
Q ss_pred EEEEEEEEEecceEEE-EeCCCeEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEE
Q 000449 764 VVHGYVCNIIETGCFV-RFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRIT 827 (1497)
Q Consensus 764 ~v~G~V~~i~~~G~FV-~~~~gl~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~ 827 (1497)
.+.|.|....+.|.|- .+.+|..-++|.+-=-. .-.-...+||.|.+-+-..|.+++||.
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 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEE
Confidence 4789999999888775 88899998888763211 112246789999999999999888885
No 209
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=60.82 E-value=36 Score=29.62 Aligned_cols=62 Identities=24% Similarity=0.277 Sum_probs=42.0
Q ss_pred CceEEEEEEEEeCCeEEEEeCCCeEEE---EeccccccCCCCCCCcccCCCCCEEEEEEEEEeCCCceEEEec
Q 000449 322 GMMVSTRVQSILENGVMLSFLTYFTGT---VDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTL 391 (1497)
Q Consensus 322 G~~V~g~V~~v~~~Gl~v~~~~~~~G~---v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~~~~~i~LSl 391 (1497)
|+.+.-.|..++++|-..--++.+.|. ....|... ....+|++++|-|+.+|--+-.+.+||
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~AtryH~~g--------~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEG--------VNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEEEecc--------eecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 566777888888877554444444433 33445432 257799999999999987666666664
No 210
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=53.96 E-value=29 Score=35.15 Aligned_cols=52 Identities=19% Similarity=0.316 Sum_probs=43.4
Q ss_pred CCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEE
Q 000449 321 PGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFV 380 (1497)
Q Consensus 321 pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~ 380 (1497)
.|-+|-|.|-.+..+.++++|+++|...-....+. .+.|..|..|+.|++..
T Consensus 82 ~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n--------~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 82 KGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN--------GEAYQKGARVRLRLIDL 133 (173)
T ss_pred CCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC--------HHHhhcCceEEEEEcCh
Confidence 58899999999999999999999998776554442 24799999999999754
No 211
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=53.37 E-value=42 Score=36.80 Aligned_cols=62 Identities=19% Similarity=0.228 Sum_probs=48.2
Q ss_pred CCCCCEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccCCCCchhhhccccCCCCCEEEEEEEEEec
Q 000449 1161 VSIGQRVTGYVYKVDNEWALLTISRHLKAQLFILDSAYEPSELQEFQRRFHIGKAVTGHVLSINK 1225 (1497)
Q Consensus 1161 ~~~G~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s~~~~~~~~~~~~f~vG~~v~~~V~~~~~ 1225 (1497)
-.+|+.|.|.|.....+..||+|+...-|-++.+..- ... +.-.-.+++|+.|-|+|...++
T Consensus 63 P~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe-~At--krNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE-GAT--KRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCCEEEEEEEeccCceEEEecCCCCeeeeeecccc-Ccc--ccCCCccccccEEEEEEEecCC
Confidence 3689999999999999999999998888888876531 111 1222368999999999988753
No 212
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=53.35 E-value=1.3e+02 Score=34.95 Aligned_cols=114 Identities=13% Similarity=0.164 Sum_probs=67.6
Q ss_pred EEEEEEEEEeCc----eEEEEcCCC---cEEEEeccccCChhhcccccccccCCCCCccCCCCEEEEEEEEEecCCcccc
Q 000449 136 KLWGVVAEVNEK----DLVICLPGG---LRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIG 208 (1497)
Q Consensus 136 ~vlG~V~~i~~~----~l~vslp~~---l~G~v~~~~is~~~~~~~~~~~~~~~L~~~f~vGq~v~~~V~~~~~~~~~~~ 208 (1497)
.+-|+|.+|... .+.|.|..+ +...|.-..+.+ | -..+|+.|++.|.+.
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~~--------------L--~l~~G~~v~~~Ika~-------- 184 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAER--------------L--GLDEGKEVLVLIKAP-------- 184 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHhh--------------c--CCCCCCeEEEEEECC--------
Confidence 678899999754 234555432 334333322221 1 246899999998752
Q ss_pred eeEEEEecchhhHhcCCCcccccCCcEEEEEEEEEEeCeEEE----EeC-CCCeEEEeeCCCCCCCCCCcCCCCcEEEEE
Q 000449 209 KRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYIL----HFG-LPSFTGFLPRNNLAENSGIDVKPGLLLQGV 283 (1497)
Q Consensus 209 ~~~i~LSl~p~~vn~~l~~~~l~~g~~l~~~V~svedhG~iv----d~G-i~~~~gFl~~~~~~~~~~~~l~~G~~~~~~ 283 (1497)
.|.|+..+. .....-..++|+|.+++.+|..+ +++ -..+.+-++...+ ....|.+|+.+.+.
T Consensus 185 --~V~l~~~~~--------~~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~---~~L~L~~G~~V~a~ 251 (263)
T PRK10676 185 --WVGITQDPA--------VAQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEA---ARLSLQQGDAVTAY 251 (263)
T ss_pred --EEEEEcCCC--------CCCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHH---HhcCCCCCCEEEEE
Confidence 466664321 11223357999999999876543 442 1124555554332 22378999999999
Q ss_pred EEE
Q 000449 284 VRS 286 (1497)
Q Consensus 284 V~~ 286 (1497)
+..
T Consensus 252 iKa 254 (263)
T PRK10676 252 FNA 254 (263)
T ss_pred EEc
Confidence 865
No 213
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=52.96 E-value=2e+02 Score=33.63 Aligned_cols=119 Identities=17% Similarity=0.214 Sum_probs=73.3
Q ss_pred CCCCEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccCCCCchhhhccccCCCCCEEEEEEEEEeccCcEEEEEeccccCCC
Q 000449 1162 SIGQRVTGYVYKVDNEWALLTISRHLKAQLFILDSAYEPSELQEFQRRFHIGKAVTGHVLSINKEKKLLRLVLRPFQDGI 1241 (1497)
Q Consensus 1162 ~~G~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s~~~~~~~~~~~~f~vG~~v~~~V~~~~~~~~~l~LS~~~~~~~~ 1241 (1497)
+.|..+.|.|...++.+-.-.+.-. .+.+.+ +....++|+.++.+|-.-| +.|.++.++
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~-~~~l~v------------~~~~a~~g~~~R~~I~a~D-----Vslal~~P~--- 288 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALG-DQHLWV------------PKLDAPVGARLRIRIQARD-----VSLALQKPE--- 288 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecC-ceEEEe------------eccCCCCCCcEEEEEEccc-----eEEEecCcc---
Confidence 4577778888776665443333211 222222 1223478999999998876 667766542
Q ss_pred CCcccccccccccccccCCCEEEEEEEEEecCcCeEEEEECCc-eEEEEecccccccccCCCCCCCCCCCCCCCCCcCCC
Q 000449 1242 SDKTVDISNDNMQTFIHEGDIVGGRISKILSGVGGLVVQIGPH-LYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEG 1320 (1497)
Q Consensus 1242 ~~~~~~~~~~~~~~~l~~G~~v~g~V~~v~~~~~gl~V~l~~~-~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g 1320 (1497)
... .=.+++|+|+.+.+..+.+-|++..+ ..=-..+|+.+ -+ .-.+++|
T Consensus 289 ---------~~S-----irNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~s----rd------------~L~l~~G 338 (352)
T COG4148 289 ---------QTS-----IRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWA----RD------------ELALKPG 338 (352)
T ss_pred ---------ccc-----hhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhh----HH------------hhcCCCC
Confidence 222 45678999999987766777777322 22233344443 22 2357799
Q ss_pred CEEEEEEEEee
Q 000449 1321 QFVKCKVLEIS 1331 (1497)
Q Consensus 1321 ~~v~~~Vl~~d 1331 (1497)
+.|-|.|.++.
T Consensus 339 ~~v~AqIKsVs 349 (352)
T COG4148 339 QWVYAQIKSVS 349 (352)
T ss_pred CeEEEEEEEEE
Confidence 99999998875
No 214
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=52.44 E-value=19 Score=38.98 Aligned_cols=84 Identities=19% Similarity=0.274 Sum_probs=63.3
Q ss_pred ccCccCCCCCCcEEEEEEEEEec--eeEEEEeC----CCeEEEEEccccCCCcccCC----CCc--cCCCCEEEEEEEEE
Q 000449 1369 HLEKIEDLSPNMIVQGYVKNVTS--KGCFIMLS----RKLDAKVLLSNLSDGYVESP----EKE--FPIGKLVAGRVLSV 1436 (1497)
Q Consensus 1369 ~~~~~~~l~~G~~v~G~V~~v~~--~G~fV~l~----~~~~g~v~is~lsd~~~~~~----~~~--~~~g~~V~~~V~~v 1436 (1497)
++.++.+++.|+++.|+.....+ ||++|+++ +..+|+|+.-.|.-.+-..| ... +-....|.+.|..+
T Consensus 66 ei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~ev 145 (247)
T COG4044 66 EIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEV 145 (247)
T ss_pred CCCccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEec
Confidence 56688999999999999999965 67888876 35889999988887765444 222 23567889999999
Q ss_pred cCCCCeEEEEEEeCCC
Q 000449 1437 EPLSKRVEVTLKTSDS 1452 (1497)
Q Consensus 1437 d~~~~~i~lslk~~~~ 1452 (1497)
|...+.|..-|-+...
T Consensus 146 nk~~~EIea~ltd~qv 161 (247)
T COG4044 146 NKLAQEIEARLTDKQV 161 (247)
T ss_pred cchhhhhhhhhhHHHH
Confidence 8766777766655444
No 215
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=51.68 E-value=35 Score=34.62 Aligned_cols=53 Identities=23% Similarity=0.536 Sum_probs=45.0
Q ss_pred CCCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE
Q 000449 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1497)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1497)
..|.+|-|+|-.+...-+++++++.+.+++....+ ..+.|..|..|..|++..
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~-------n~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPAL-------NGEAYQKGARVRLRLIDL 133 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCc-------CHHHhhcCceEEEEEcCh
Confidence 36999999999999999999999999999975543 235899999999998765
No 216
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=47.84 E-value=1.9e+02 Score=33.79 Aligned_cols=115 Identities=12% Similarity=0.139 Sum_probs=73.2
Q ss_pred CCCEEEEEEEEEecCcCeEEEEECCceEEEEecccccccccCCCCCCCCCCCCCCCCCcCCCCEEEEEEEEeecccCCcc
Q 000449 1259 EGDIVGGRISKILSGVGGLVVQIGPHLYGRVHFTELKNICVSDPLSGYDEGQFDPLSGYDEGQFVKCKVLEISRTVRGTF 1338 (1497)
Q Consensus 1259 ~G~~v~g~V~~v~~~~~gl~V~l~~~~~G~v~~tdl~d~~~~~~~~~~d~~~~~~~~~~~~g~~v~~~Vl~~d~~~~g~~ 1338 (1497)
.|.++.|.|....+.++-..+.++. ..+ |+.. ....+|+.+|.+|-+-|.
T Consensus 231 ~~~vl~~~V~~hd~~y~lt~l~l~~---~~l--------~v~~-------------~~a~~g~~~R~~I~a~DV------ 280 (352)
T COG4148 231 QSSVLEGTVLEHDPRYGLTALALGD---QHL--------WVPK-------------LDAPVGARLRIRIQARDV------ 280 (352)
T ss_pred cceEEEEEehhcCCCcceEEEecCc---eEE--------Eeec-------------cCCCCCCcEEEEEEccce------
Confidence 6999999999999985334444442 122 2222 122489999999877764
Q ss_pred EEEEEeeccccCCCCCCCCCCCCCCCCCCCccCccCCCCCCcEEEEEEEEEecee----EEEEeCCCeEEEEEccccCCC
Q 000449 1339 HVELSLRSSLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSPNMIVQGYVKNVTSKG----CFIMLSRKLDAKVLLSNLSDG 1414 (1497)
Q Consensus 1339 ~i~lS~R~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~G~V~~v~~~G----~fV~l~~~~~g~v~is~lsd~ 1414 (1497)
.|.+++.. -.+ .-.+++|+|+.+.+.+ ++++++ +-.=.-.|+..+-+
T Consensus 281 --slal~~P~---------------------~~S-----irNiLp~~v~~i~~~~~~V~v~ld~~-g~~l~Arit~~srd 331 (352)
T COG4148 281 --SLALQKPE---------------------QTS-----IRNILPGKVVGIEDDDGQVDVQLDCG-GKTLWARITPWARD 331 (352)
T ss_pred --EEEecCcc---------------------ccc-----hhhccceeEEEEEcCCCcEEEEEEcC-CcEEEEEccHhhHH
Confidence 45665432 112 2456889999996654 234444 44445566666644
Q ss_pred cccCCCCccCCCCEEEEEEEEEc
Q 000449 1415 YVESPEKEFPIGKLVAGRVLSVE 1437 (1497)
Q Consensus 1415 ~~~~~~~~~~~g~~V~~~V~~vd 1437 (1497)
-+ .+++||.|-+.|.++.
T Consensus 332 ~L-----~l~~G~~v~AqIKsVs 349 (352)
T COG4148 332 EL-----ALKPGQWVYAQIKSVS 349 (352)
T ss_pred hh-----cCCCCCeEEEEEEEEE
Confidence 33 4899999999998764
No 217
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=47.11 E-value=99 Score=29.37 Aligned_cols=65 Identities=15% Similarity=0.198 Sum_probs=51.7
Q ss_pred EEEEEEEEEeceeEE-EEeCCCeEEEEEcccc-CCCcccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEEeC
Q 000449 1381 IVQGYVKNVTSKGCF-IMLSRKLDAKVLLSNL-SDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTS 1450 (1497)
Q Consensus 1381 ~v~G~V~~v~~~G~f-V~l~~~~~g~v~is~l-sd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk~~ 1450 (1497)
.+.|.|+.+...+.| |+|.++..-+.||+-= --.|+ .+.+||.|.+.+...|...++|..-.++.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rI-----rIl~GD~V~VE~spYDltkGRIiyR~~~~ 74 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRI-----RILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeE-----EecCCCEEEEEECcccCCceeEEEEecCC
Confidence 489999999888876 5899888888887631 12233 36789999999999999999999988854
No 218
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=46.13 E-value=36 Score=36.45 Aligned_cols=59 Identities=27% Similarity=0.281 Sum_probs=41.8
Q ss_pred CCcEEEEEEEEEecCeeEEEeCCCeEEEEecCCccc-----------ccccC----C-C-ccccCCCEEEEEEEEE
Q 000449 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSE-----------FEIVK----P-G-KKFKVGAELVFRVLGV 556 (1497)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~gv~g~vp~~~ls~-----------~~~~~----~-~-~~~kvG~~V~~rVl~v 556 (1497)
.|+++.|+|...+..|+.|.++-.=+-|||..-|.. ...-. | . -.|.+|..|++||...
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 589999999999999999999744467787765533 21111 2 1 2247899999999765
No 219
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=45.50 E-value=91 Score=28.31 Aligned_cols=60 Identities=13% Similarity=0.125 Sum_probs=44.3
Q ss_pred EEEEEEEEEeceeEE-EEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEcCCCCeEE
Q 000449 1381 IVQGYVKNVTSKGCF-IMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVE 1444 (1497)
Q Consensus 1381 ~v~G~V~~v~~~G~f-V~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~ 1444 (1497)
.+.|.|+.....+.| |+|.++.+-+.||+-= +..-.-...+||.|.+.+...|.+.++|-
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GK----mr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGK----IRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCc----chhccEEECCCCEEEEEECcccCCcEeEE
Confidence 478999999988876 5899888888888641 22112236789999998888777766663
No 220
>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=44.49 E-value=1.7e+02 Score=25.85 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=35.5
Q ss_pred EEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.|+|+...+ ||.+..-.++-+-|+|.+++.... -..+..|+.|++.+..
T Consensus 2 ~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 2 TGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred eEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 689999884 676665444558999999997542 2357899999999987
No 221
>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=42.37 E-value=38 Score=29.75 Aligned_cols=49 Identities=24% Similarity=0.342 Sum_probs=34.3
Q ss_pred cEEEEEEEEEEeCe----EEEEeCCCC-eEEEeeCCCCCCCCCCcCCCCcEEEEEEE
Q 000449 234 MVLTAYVKSIEDHG----YILHFGLPS-FTGFLPRNNLAENSGIDVKPGLLLQGVVR 285 (1497)
Q Consensus 234 ~~l~~~V~svedhG----~ivd~Gi~~-~~gFl~~~~~~~~~~~~l~~G~~~~~~V~ 285 (1497)
..+.|.|..+|+.| +.+++|-.. +.+.++..... ...|++|+.+.+.+.
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 36899999999999 667776444 77777765432 226899999998875
No 222
>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=42.22 E-value=2.5e+02 Score=24.89 Aligned_cols=50 Identities=22% Similarity=0.102 Sum_probs=36.4
Q ss_pred EEEEEEEEec---eeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEE
Q 000449 1382 VQGYVKNVTS---KGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLS 1435 (1497)
Q Consensus 1382 v~G~V~~v~~---~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~ 1435 (1497)
.+|+|+...+ ||....-+..-+-++|++++.... ...+..|+.|.-.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 4799999965 554444444569999999998775 2457899999999877
No 223
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=41.70 E-value=4.3e+02 Score=29.11 Aligned_cols=46 Identities=17% Similarity=0.165 Sum_probs=31.2
Q ss_pred CCEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccCCCCchhhhccccCCCCCEEEEE
Q 000449 1164 GQRVTGYVYKVDNEWALLTISRHLKAQLFILDSAYEPSELQEFQRRFHIGKAVTGH 1219 (1497)
Q Consensus 1164 G~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s~~~~~~~~~~~~f~vG~~v~~~ 1219 (1497)
=+++.|.|..+.++.+.|..-.. ..+.+..-+....+++|+.|+|+
T Consensus 39 ~~tiEGrVvEV~~~~i~iesk~y----------n~~v~i~~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 39 FSTIEGRVVEVDNGVIVIKSKQY----------EEPVSVYIDSLSNVKVGDEVKAT 84 (213)
T ss_pred cceeeeEEEEEeCCEEEEEeccC----------CCceEEEecCCCCcccCcEEEEc
Confidence 46899999999999998876311 11111122345567999999985
No 224
>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=41.67 E-value=1.4e+02 Score=26.12 Aligned_cols=55 Identities=20% Similarity=0.152 Sum_probs=34.4
Q ss_pred CCCCEEEEEEEEEecCCCeEEEEcchhhcccccccccccCC--CcEEEEEEEEEecCeeEEE
Q 000449 458 KEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKP--GMVVKGKVIAVDSFGAIVQ 517 (1497)
Q Consensus 458 ~vG~~~~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~--G~iv~g~V~~v~~~G~~V~ 517 (1497)
++|+++++.|.+.. .++..+.-.+. -....+..-.| |+.++.+|++..++-++-+
T Consensus 3 ~~G~~~~VlVe~~~-~~g~~~gr~~~----~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 3 YVGKTLEVLVEELG-DEGQGIGRTDN----GKVVFVPGGLPLIGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -TTEEEEEEEEEE--TTSEEEEEET-----TEEEEETT--T--TEEEEEEEEEE-SSEEEEE
T ss_pred cCCcEEEEEEEEec-CCCEEEEEeCC----CeEEEECCCCCCCCCEEEEEEEEeeCCcEEEE
Confidence 58999999999998 55555544332 11122233355 9999999999998877654
No 225
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=38.40 E-value=1.2e+02 Score=33.59 Aligned_cols=61 Identities=10% Similarity=0.026 Sum_probs=50.7
Q ss_pred CCCceEEEEEEEEeCCeEEEEeCCCeEEEEeccccccCCCCCCCcccCCCCCEEEEEEEEEeC
Q 000449 320 VPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDP 382 (1497)
Q Consensus 320 ~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~~~~~~~vG~~v~arVl~~~~ 382 (1497)
.+|+.|-|.|++-..++..|++++.-.+.++...+.... +.....+++|+-|.|+|...++
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~At--krNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGAT--KRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCcc--ccCCCccccccEEEEEEEecCC
Confidence 469999999999999999999999888888888776653 2345679999999999976543
No 226
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=38.24 E-value=1.7e+02 Score=34.06 Aligned_cols=116 Identities=9% Similarity=0.041 Sum_probs=66.5
Q ss_pred CEEEEEEEEEecc--eEEEE--eCCC---eEEEEeCCCCCcccccCcccCcCCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 000449 763 SVVHGYVCNIIET--GCFVR--FLGR---LTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1497)
Q Consensus 763 ~~v~G~V~~i~~~--G~FV~--~~~g---l~Glvp~sels~~~~~~~~~~~~~Gq~V~v~V~~iD~e~~Ri~LSlK~~~~ 835 (1497)
..+.|+|.+|... ...|+ +..+ +...+.. ....+ -.+.+|+.|.+.|-.-| +.+.....
T Consensus 128 N~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~-----~s~~~--L~l~~G~~v~~~Ika~~-----V~l~~~~~-- 193 (263)
T PRK10676 128 NQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITA-----QSAER--LGLDEGKEVLVLIKAPW-----VGITQDPA-- 193 (263)
T ss_pred hcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCH-----HHHhh--cCCCCCCeEEEEEECCE-----EEEEcCCC--
Confidence 4688999999755 55555 4332 3333322 21122 24678999888876533 33332110
Q ss_pred CCCCcchhhhhhhHHHHHHHhhccccCCcccccccccCCCcEEEEEEEEEeeceeE--EEec--CCCceEEEEeeeecCC
Q 000449 836 SSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVV--VSFE--EHSDVYGFITHHQLAG 911 (1497)
Q Consensus 836 ~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~vG~~V~g~V~~i~~~G~~--v~l~--~~~~~~G~i~~~~l~~ 911 (1497)
.....-+.+.|+|.++...|.. |.+. ++..+...|+...+..
T Consensus 194 ----------------------------------~~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~~ 239 (263)
T PRK10676 194 ----------------------------------VAQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAAR 239 (263)
T ss_pred ----------------------------------CCCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHHh
Confidence 1123346889999999876653 3333 3223445555544444
Q ss_pred ccccCCCEEEEEEEE
Q 000449 912 ATVESGSVIQAAILD 926 (1497)
Q Consensus 912 ~~~~~G~~v~~~Vl~ 926 (1497)
-.+.+|+.|.+.+-.
T Consensus 240 L~L~~G~~V~a~iKa 254 (263)
T PRK10676 240 LSLQQGDAVTAYFNA 254 (263)
T ss_pred cCCCCCCEEEEEEEc
Confidence 478899999887743
No 227
>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=36.37 E-value=1.6e+02 Score=25.92 Aligned_cols=47 Identities=21% Similarity=0.385 Sum_probs=33.3
Q ss_pred EEEEEEEEEecCeeEEEeCC-CeEEEEecCCcccccccCCCccccCCCEEEEEEEEE
Q 000449 501 VVKGKVIAVDSFGAIVQFPG-GVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1497)
Q Consensus 501 iv~g~V~~v~~~G~~V~i~~-gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1497)
-++|+|..+.+..++++.++ |.+-++|...+. .+..+++++..+.-+
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 47899999999999999986 678888866443 334555666655444
No 228
>PRK10943 cold shock-like protein CspC; Provisional
Probab=34.21 E-value=1.3e+02 Score=27.32 Aligned_cols=51 Identities=16% Similarity=0.092 Sum_probs=36.5
Q ss_pred EEEEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 588 ITHGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 588 ~~~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.+.|+|....+ ||.+-.-.++-+-|+|+|.+.... ...+..||.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC----CCCCCCCCEEEEEEEE
Confidence 46799999874 555544445678999999996331 1246799999998765
No 229
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=33.36 E-value=1e+02 Score=27.22 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=32.9
Q ss_pred eEEEEEEEEecCeEEEEeCCCceeeEEeeeecCCccccccccccCcCCCCEEEEEE
Q 000449 1066 LVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARI 1121 (1497)
Q Consensus 1066 ~v~~~V~~vk~~~l~V~L~~~~~GrVhvsev~d~~~~~~~~Pl~~fk~G~~V~~rV 1121 (1497)
-++|+|++|.+..+.+.|.+|..=.+ .. .--++.+++|.+|.+.-
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~l-----p~------ef~~~~L~~G~kV~V~y 48 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKL-----PE------EFDFDGLKPGMKVVVFY 48 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEEC-----CC------cccccccCCCCEEEEEE
Confidence 37899999999999999999854322 11 12257889999887543
No 230
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=32.43 E-value=91 Score=35.27 Aligned_cols=74 Identities=16% Similarity=0.217 Sum_probs=58.6
Q ss_pred CCCCEEEEEEEEEeCCEEEEEEcCCeEEEEEeeccCCCCchhh--------hccccCCCCCEEEEEEEEEeccCcEEEEE
Q 000449 1162 SIGQRVTGYVYKVDNEWALLTISRHLKAQLFILDSAYEPSELQ--------EFQRRFHIGKAVTGHVLSINKEKKLLRLV 1233 (1497)
Q Consensus 1162 ~~G~~v~g~V~~v~~~~l~V~ls~~~~g~i~~~~~s~~~~~~~--------~~~~~f~vG~~v~~~V~~~~~~~~~l~LS 1233 (1497)
++|+.|.|.|..|..+-..|+++.+..+.+.+..+......+. ....-|+.|+.+.|.|-.+- ..|.+.|-
T Consensus 84 EvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~-~dGs~sLh 162 (301)
T KOG3013|consen 84 EVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF-HDGSLSLH 162 (301)
T ss_pred ccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhc-cCCeEEEE
Confidence 6899999999999999999999999999998877655432221 23466999999999887774 45777777
Q ss_pred ecc
Q 000449 1234 LRP 1236 (1497)
Q Consensus 1234 ~~~ 1236 (1497)
.|+
T Consensus 163 TRS 165 (301)
T KOG3013|consen 163 TRS 165 (301)
T ss_pred ecc
Confidence 665
No 231
>PRK15464 cold shock-like protein CspH; Provisional
Probab=32.37 E-value=1.3e+02 Score=27.40 Aligned_cols=50 Identities=12% Similarity=0.087 Sum_probs=35.4
Q ss_pred EEEEEEEEee-eeE-EEEEc-CceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 589 THGWITKIEK-HGC-FVRFY-NGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 589 ~~G~V~~i~~-~G~-~V~~~-~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
..|+|...++ .|. |+.-. ++-+-|+|+|.+.... ...+..||.|.+.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC----CCCCCCCCEEEEEEEE
Confidence 3799999974 444 45443 4568999999995321 1246899999998875
No 232
>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=31.28 E-value=2.6e+02 Score=24.38 Aligned_cols=56 Identities=16% Similarity=0.145 Sum_probs=33.9
Q ss_pred CCCcEEEEEEEEEcCCCcEEEEccCccccccccccccccccccccCC--CceEEEEEEEEeCCeEEEEe
Q 000449 275 KPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVP--GMMVSTRVQSILENGVMLSF 341 (1497)
Q Consensus 275 ~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~s~~~l~p--G~~V~g~V~~v~~~Gl~v~~ 341 (1497)
.+|+.+.+.|.+....+..+-=+-+ .....+..-.| |+.+..+|++..++.+...+
T Consensus 3 ~~G~~~~VlVe~~~~~g~~~gr~~~-----------~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 3 YVGKTLEVLVEELGDEGQGIGRTDN-----------GKVVFVPGGLPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -TTEEEEEEEEEE-TTSEEEEEET------------TEEEEETT--T--TEEEEEEEEEE-SSEEEEEE
T ss_pred cCCcEEEEEEEEecCCCEEEEEeCC-----------CeEEEECCCCCCCCCEEEEEEEEeeCCcEEEEE
Confidence 5799999999998744332211110 01223444478 99999999999999887654
No 233
>PRK15463 cold shock-like protein CspF; Provisional
Probab=30.98 E-value=1.4e+02 Score=27.16 Aligned_cols=50 Identities=14% Similarity=0.092 Sum_probs=35.5
Q ss_pred EEEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 589 THGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 589 ~~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
..|+|+.... ||.+-.-.++-+-|+|++.+...- ...+..||.|.+.+..
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 3799999874 555444444678999999996321 1246799999998765
No 234
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=30.08 E-value=1.8e+02 Score=26.47 Aligned_cols=51 Identities=16% Similarity=0.103 Sum_probs=36.0
Q ss_pred EEEEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 588 ITHGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 588 ~~~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.+.|+|+...+ ||.+-.-.++-+-|+|+|.+.... -..+.+||.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccC----CCCCCCCCEEEEEEEE
Confidence 45799999874 555544444578999999996331 1246899999997765
No 235
>PRK15464 cold shock-like protein CspH; Provisional
Probab=28.99 E-value=2.3e+02 Score=25.88 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=35.3
Q ss_pred EEEEEEEEec---CeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEE
Q 000449 502 VKGKVIAVDS---FGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1497)
Q Consensus 502 v~g~V~~v~~---~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1497)
++|+|+-..+ +|.+..-.++-+-|+|.+.+... ..+.+.+|+.|.+.+-.-
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNG 58 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEEC
Confidence 4799998865 34443334467999998877532 223578999999988553
No 236
>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=28.55 E-value=1.2e+02 Score=26.53 Aligned_cols=49 Identities=18% Similarity=0.298 Sum_probs=32.0
Q ss_pred cEEEEEEEEEeece----eEEEecCCCceEEEEeeeecCCccccCCCEEEEEE
Q 000449 876 SVIEGKVHESNDFG----VVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAI 924 (1497)
Q Consensus 876 ~~V~g~V~~i~~~G----~~v~l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~V 924 (1497)
..+.|+|..+.+.| +.+.+++...+...++......=.+++|++|.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEE
Confidence 56799999999999 33445553226667766555433577899987766
No 237
>PRK10943 cold shock-like protein CspC; Provisional
Probab=27.95 E-value=1.6e+02 Score=26.74 Aligned_cols=51 Identities=20% Similarity=0.298 Sum_probs=36.0
Q ss_pred EEEEEEEEEec---CeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEE
Q 000449 501 VVKGKVIAVDS---FGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLG 555 (1497)
Q Consensus 501 iv~g~V~~v~~---~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~ 555 (1497)
.++|+|+...+ +|.+-.-.++-+-|+|.+.+.... ...+.+|+.|.+.+-.
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g----~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC----CCCCCCCCEEEEEEEE
Confidence 46899998865 455554455789999888775321 1356799999998754
No 238
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=27.82 E-value=1.8e+02 Score=26.92 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=35.3
Q ss_pred EEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.|+|...+. ||.+..-.++-+-|+|+|.+...- ...+..||.|.+.+..
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~ 54 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQ 54 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence 488888874 555544455688999999996331 1246899999999876
No 239
>PRK06386 replication factor A; Reviewed
Probab=27.23 E-value=1.2e+03 Score=28.40 Aligned_cols=46 Identities=22% Similarity=0.202 Sum_probs=29.1
Q ss_pred cEEEEEEEEEEe---------CeEEEEeCCCCeEEEeeCCCCCCCCCCcCCCCcEEEE
Q 000449 234 MVLTAYVKSIED---------HGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQG 282 (1497)
Q Consensus 234 ~~l~~~V~sved---------hG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~ 282 (1497)
-.+.|.|.++.. +++..-+ +.+=+|-+++..|.+.. .+++|+.+..
T Consensus 15 V~v~akVl~~~~r~i~~~~g~~~~~~gl-lgDeTG~I~fT~W~~~~--~l~~Gd~v~i 69 (358)
T PRK06386 15 VDLKVKVLSLNKRTIKNDRGETIYYYGI-IGDETGTVPFTAWEFPD--AVKSGDVIEI 69 (358)
T ss_pred EEEEEEEEEccceEEecCCCCeEEEEEE-EECCcceEEEEecCCcc--cCCCCCEEEE
Confidence 457777777762 2232222 23458888888876433 7899998765
No 240
>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=26.63 E-value=3.4e+02 Score=23.92 Aligned_cols=50 Identities=26% Similarity=0.182 Sum_probs=37.4
Q ss_pred EEEEEEEec-eeE-EEEeCC-CeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEE
Q 000449 1383 QGYVKNVTS-KGC-FIMLSR-KLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSV 1436 (1497)
Q Consensus 1383 ~G~V~~v~~-~G~-fV~l~~-~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~v 1436 (1497)
.|+|+...+ .|- ||.-.. +-+-++|++++...- ...+.+||.|...+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 588888855 443 666655 899999999988652 24578999999888664
No 241
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=26.32 E-value=88 Score=26.71 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=21.7
Q ss_pred cCCCCEE---------EEEEEEEeCceEEEEcCCC
Q 000449 131 ISAGMKL---------WGVVAEVNEKDLVICLPGG 156 (1497)
Q Consensus 131 l~~G~~v---------lG~V~~i~~~~l~vslp~~ 156 (1497)
|.|||+| +|||.+....-+.|++++.
T Consensus 1 l~pG~~VrHP~~pdWG~GqVqS~i~~rvTVnF~~a 35 (52)
T PF12073_consen 1 LEPGMLVRHPDHPDWGIGQVQSNIGGRVTVNFEHA 35 (52)
T ss_pred CCCCCEEeCCCCCCCcceEEEEecCCeEEEeeccC
Confidence 4577776 7999999999999999874
No 242
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=25.96 E-value=2.9e+02 Score=25.69 Aligned_cols=56 Identities=18% Similarity=0.194 Sum_probs=41.1
Q ss_pred cEEEEEEEEEeeceeE-EEecCCCceEEEEeeeecCC------ccccCCCEEEEEEEEEecCCCEEEE
Q 000449 876 SVIEGKVHESNDFGVV-VSFEEHSDVYGFITHHQLAG------ATVESGSVIQAAILDVAKAERLVDL 936 (1497)
Q Consensus 876 ~~V~g~V~~i~~~G~~-v~l~~~~~~~G~i~~~~l~~------~~~~~G~~v~~~Vl~vd~~~~~v~l 936 (1497)
-.+.|+|.+....+.| |.++++ ..-..|+++ -.+.+||.|.+..-..+..++.|..
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg-----~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENG-----HERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCC-----cEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEE
Confidence 4678999999998887 888763 333344543 2678899999998888877666654
No 243
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=25.38 E-value=2.4e+02 Score=25.61 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=35.8
Q ss_pred EEEEEEEEEec---CeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEE
Q 000449 501 VVKGKVIAVDS---FGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLG 555 (1497)
Q Consensus 501 iv~g~V~~v~~---~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~ 555 (1497)
.++|+|+...+ +|.+-.-.++-+-|+|.+.+... ....+.+|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEE
Confidence 46799998865 45554445567999998877532 12457899999997754
No 244
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=25.34 E-value=3.3e+02 Score=24.25 Aligned_cols=56 Identities=14% Similarity=0.282 Sum_probs=36.6
Q ss_pred EEEEEEEEEecCcEEEEEEecCcEEEEEcCCccccccccccccccccCCCCeEeEEEEeeccCCceeee
Q 000449 672 LVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLS 740 (1497)
Q Consensus 672 iv~g~V~~i~~~Gv~V~l~~~~~v~g~ip~~hLsd~~~~~~~~~~~~k~G~~l~~vl~~d~~~~~i~lS 740 (1497)
-++|+|.++.+...-+.| ++|-.=-+|..-= .+.+++|.++- +.+-+..++|++-.
T Consensus 4 ~veG~I~~id~~~~titL--dDGksy~lp~ef~----------~~~L~~G~kV~-V~yd~~~gk~vitd 59 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITL--DDGKSYKLPEEFD----------FDGLKPGMKVV-VFYDEVDGKRVITD 59 (61)
T ss_pred cceEEEEEEcCCceEEEe--cCCCEEECCCccc----------ccccCCCCEEE-EEEEccCCcEEeee
Confidence 368899999999888888 6666555554311 35788999886 33444455555433
No 245
>PRK14998 cold shock-like protein CspD; Provisional
Probab=24.45 E-value=2.2e+02 Score=26.26 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=35.2
Q ss_pred EEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.|+|..... ||.+..-.++-+-|+|+|.+...- ...+..|+.|.+.+..
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~ 54 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQ 54 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC----CCCCCCCCEEEEEEEE
Confidence 488888874 555544445678999999986331 1346899999999876
No 246
>PRK15463 cold shock-like protein CspF; Provisional
Probab=24.07 E-value=2.2e+02 Score=26.00 Aligned_cols=50 Identities=16% Similarity=0.248 Sum_probs=35.3
Q ss_pred EEEEEEEEec---CeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEE
Q 000449 502 VKGKVIAVDS---FGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLG 555 (1497)
Q Consensus 502 v~g~V~~v~~---~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~ 555 (1497)
++|+|+-..+ +|++-.-.++-+.|+|.+.+.... ...+++|+.|.+.+..
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 355444455689999988775421 2357799999998754
No 247
>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=24.01 E-value=2.4e+02 Score=27.72 Aligned_cols=64 Identities=16% Similarity=0.280 Sum_probs=38.0
Q ss_pred EEEEEEEEEecee--EEEEeCCCeEEEEEc----cccCCCcccCCCCccCCCCEEEEE--EEEEcCCCCeEEEEE
Q 000449 1381 IVQGYVKNVTSKG--CFIMLSRKLDAKVLL----SNLSDGYVESPEKEFPIGKLVAGR--VLSVEPLSKRVEVTL 1447 (1497)
Q Consensus 1381 ~v~G~V~~v~~~G--~fV~l~~~~~g~v~i----s~lsd~~~~~~~~~~~~g~~V~~~--V~~vd~~~~~i~lsl 1447 (1497)
.+.|.|.++...| +|++|..+. |.+++ .++.+....++...++.|+.|.++ +..- ..+.++|..
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~-~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~--~~g~~El~~ 74 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDES-GKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKT--KTGELSIFV 74 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECC-eEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEec--CCCCEEEEe
Confidence 4889999998776 899997543 45553 222122222333448899988654 4432 335555543
No 248
>PRK09890 cold shock protein CspG; Provisional
Probab=23.95 E-value=2.7e+02 Score=25.30 Aligned_cols=50 Identities=12% Similarity=0.053 Sum_probs=34.9
Q ss_pred EEEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 589 THGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 589 ~~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
..|+|....+ ||.+-.-.++-+-|+|+|.+..... ..+.+||.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 4799998874 5554443345789999999964311 246799999997754
No 249
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.93 E-value=1.1e+02 Score=33.60 Aligned_cols=79 Identities=14% Similarity=0.149 Sum_probs=54.1
Q ss_pred ccccccCCcccCCCCCCEEEEEEEEEec--ceEEEEeC----CCeEEEEeCCCCCcccccCc------ccCcCCCCEEEE
Q 000449 747 NSAQQLPSDASHIHPNSVVHGYVCNIIE--TGCFVRFL----GRLTGFAPRSKAVDGQRADL------SKTYYVGQSVRS 814 (1497)
Q Consensus 747 ~~~~~~~~~~~~~~~G~~v~G~V~~i~~--~G~FV~~~----~gl~Glvp~sels~~~~~~~------~~~~~~Gq~V~v 814 (1497)
+.|-.++ ++.++..|+++-|+.....+ ||++|+++ .-.++|+|.-++...+-+.| ...+-..-.+.|
T Consensus 62 eefgei~-sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV 140 (247)
T COG4044 62 EEFGEIP-SLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEV 140 (247)
T ss_pred HHhCCCC-ccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEE
Confidence 3344455 67789999999999999965 55666653 13678898777765443344 345566778888
Q ss_pred EEEEEeCCCCeE
Q 000449 815 NILDVNSETGRI 826 (1497)
Q Consensus 815 ~V~~iD~e~~Ri 826 (1497)
.|.++|...+.|
T Consensus 141 ~V~evnk~~~EI 152 (247)
T COG4044 141 EVNEVNKLAQEI 152 (247)
T ss_pred EEEeccchhhhh
Confidence 899888654443
No 250
>PRK07218 replication factor A; Provisional
Probab=22.90 E-value=1.6e+03 Score=28.17 Aligned_cols=113 Identities=13% Similarity=0.087 Sum_probs=68.2
Q ss_pred cCccCCCCCCc---EEEEEEEEEece---------eEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEc
Q 000449 1370 LEKIEDLSPNM---IVQGYVKNVTSK---------GCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVE 1437 (1497)
Q Consensus 1370 ~~~~~~l~~G~---~v~G~V~~v~~~---------G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd 1437 (1497)
...+.+|++|+ .+.|+|..+.+. ++.--+=..-+|.|+++-+.+. ..+.+|+.|+..=..++
T Consensus 162 ~~kI~DL~~g~~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~------~~l~~Gd~v~I~na~v~ 235 (423)
T PRK07218 162 DKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPL------PEIEIGASIRIEDAYVR 235 (423)
T ss_pred ccchhhccCCCCceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEeccc------ccCCCCCEEEEeeeEEe
Confidence 34567777775 679999988542 1111111256777777665531 24789999987766666
Q ss_pred CCCCeEEEEEEeCCC---Cc-----ccccccCCCCCCCCCC-----EEEEEEEEEeeceeEEEE
Q 000449 1438 PLSKRVEVTLKTSDS---RT-----ASQSEINNLSNLHVGD-----IVIGQIKRVESYGLFITI 1488 (1497)
Q Consensus 1438 ~~~~~i~lslk~~~~---~~-----~~~~~~~~~~d~~~G~-----iv~G~V~~v~~~GvFV~l 1488 (1497)
.-+++++|++-.... .+ ...+....+.++..++ -|+|.|..|.+--.|++.
T Consensus 236 e~~G~~elnv~~~t~I~~~d~~i~v~~~~~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~r 299 (423)
T PRK07218 236 EFRGVPSVNVSEFTTVEALDREVSVSKDPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIER 299 (423)
T ss_pred ccCCeEEEEECCceEEEECCCCccccCCccccchhhhhccCCcceEEEEEEEEEeccCCcceec
Confidence 567888888764321 11 0112222344554333 589999999987455554
No 251
>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=22.86 E-value=1.8e+02 Score=26.21 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=34.2
Q ss_pred EEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.|+|..... ||.+..-.++-+-|+|+|.+...- ...+..||.|.+.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEE
Confidence 488888863 555544444688999999995321 1346899999997765
No 252
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=22.75 E-value=1.1e+03 Score=26.22 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=30.5
Q ss_pred cEEEEEEEEEeeceeEEEecCCCceEEEEeeeecCCccccCCCEEEEE
Q 000449 876 SVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAA 923 (1497)
Q Consensus 876 ~~V~g~V~~i~~~G~~v~l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~ 923 (1497)
+.++|+|.++.+.-+.++.....+ -+....=....+++||.|+|.
T Consensus 40 ~tiEGrVvEV~~~~i~iesk~yn~---~v~i~~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSKQYEE---PVSVYIDSLSNVKVGDEVKAT 84 (213)
T ss_pred ceeeeEEEEEeCCEEEEEeccCCC---ceEEEecCCCCcccCcEEEEc
Confidence 689999999998877787765322 122222223467999999875
No 253
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=21.99 E-value=2.9e+02 Score=25.07 Aligned_cols=49 Identities=20% Similarity=0.121 Sum_probs=34.9
Q ss_pred EEEEEEEee---eeEEEEEcCceEEeeecccccCCCCCCCCCCccCCCEEEEEEEE
Q 000449 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1497)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~gflp~sel~~~~~~~~~~~~~vGq~v~v~Vl~ 642 (1497)
.|+|....+ ||.+-.-.++-+-|+|+|.+.... ...+.+|+.|.+.+..
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 57 (70)
T ss_pred eEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence 799988863 565544344578999999996331 1346899999998765
No 254
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=21.92 E-value=3.1e+02 Score=27.96 Aligned_cols=95 Identities=22% Similarity=0.295 Sum_probs=59.4
Q ss_pred CCCcEEEEEEEEEecC-eeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEEEeCCeEEEEeecchhhhhhh
Q 000449 497 KPGMVVKGKVIAVDSF-GAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLA 575 (1497)
Q Consensus 497 ~~G~iv~g~V~~v~~~-G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~lS~K~~l~~~~~~ 575 (1497)
+-|--..|+|.+..+. -++|++..+-.-.+|..++-...... ...+++||.|-|+. +...
T Consensus 10 ~DG~YY~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~-~~~L~~GD~VLA~~---~~~~--------------- 70 (124)
T PF15057_consen 10 EDGFYYPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAM-RHSLQVGDKVLAPW---EPDD--------------- 70 (124)
T ss_pred CCCcEEeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcc-cCcCCCCCEEEEec---CcCC---------------
Confidence 3456667788877554 46778865666666666553322111 34678999998872 1100
Q ss_pred HHhhhhhccCCcEEEEEEE------EEeeeeEEEEEcCceEEeeecccccC
Q 000449 576 ILSSYAEATDRLITHGWIT------KIEKHGCFVRFYNGVQGFAPRSELGL 620 (1497)
Q Consensus 576 ~~~~~~~~~~G~~~~G~V~------~i~~~G~~V~~~~gv~gflp~sel~~ 620 (1497)
-.-..|+|. ...+.-+.|.|++|-...+|..++-|
T Consensus 71 ----------~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~ 111 (124)
T PF15057_consen 71 ----------CRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIW 111 (124)
T ss_pred ----------CEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEE
Confidence 112345555 33456688999999999999888854
No 255
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=21.83 E-value=4.9e+02 Score=23.65 Aligned_cols=45 Identities=18% Similarity=0.081 Sum_probs=30.4
Q ss_pred EEEEEecCCCEEEEEEeeCCC-Cc------------ccccccCCCCEEEEEEEEEecC
Q 000449 639 RIMSSIPASRRINLSFMMKPT-RV------------SEDDLVKLGSLVSGVVDVVTPN 683 (1497)
Q Consensus 639 ~Vl~vd~~~~ri~lS~k~~~~-~~------------~~~~~~~vG~iv~g~V~~i~~~ 683 (1497)
+|.++|++.+.+.++..+-.. .| .....+++|+.|...+....+.
T Consensus 2 ~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~~ 59 (70)
T PF11604_consen 2 VVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDDG 59 (70)
T ss_dssp EEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETTC
T ss_pred EEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCCC
Confidence 688999999999999987543 12 2235789999999988765444
No 256
>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=21.65 E-value=2.3e+02 Score=25.04 Aligned_cols=50 Identities=22% Similarity=0.246 Sum_probs=32.9
Q ss_pred cEEEEEEEEEeeceeEEE----ecCCCceEEEEeeeecCCccccCCCEEEEEEE
Q 000449 876 SVIEGKVHESNDFGVVVS----FEEHSDVYGFITHHQLAGATVESGSVIQAAIL 925 (1497)
Q Consensus 876 ~~V~g~V~~i~~~G~~v~----l~~~~~~~G~i~~~~l~~~~~~~G~~v~~~Vl 925 (1497)
+.+.|+|.++...|..+. +++...+...++...+..-.+++|+.+.+.+-
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik 60 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIK 60 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEE
Confidence 578999999988775533 32211345556555554457889999887763
No 257
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=21.40 E-value=2.4e+02 Score=25.59 Aligned_cols=50 Identities=18% Similarity=0.261 Sum_probs=35.1
Q ss_pred EEEEEEEEec---CeeEEEeCCCeEEEEecCCcccccccCCCccccCCCEEEEEEEE
Q 000449 502 VKGKVIAVDS---FGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLG 555 (1497)
Q Consensus 502 v~g~V~~v~~---~G~~V~i~~gv~g~vp~~~ls~~~~~~~~~~~kvG~~V~~rVl~ 555 (1497)
++|+|+...+ +|.+-.-.++-+-|+|.+.+... ....+.+|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEE
Confidence 4799998854 46554445568999998877532 22457899999997654
No 258
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=21.17 E-value=2.4e+02 Score=32.68 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=43.8
Q ss_pred cCccCCCCCCcEEEEEEEEEeceeEEEEeCCCeEEEEEccccCCCcccCCCCccCCCCEEEEEEEEEc
Q 000449 1370 LEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLDAKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVE 1437 (1497)
Q Consensus 1370 ~~~~~~l~~G~~v~G~V~~v~~~G~fV~l~~~~~g~v~is~lsd~~~~~~~~~~~~g~~V~~~V~~vd 1437 (1497)
-......++|.+-.|+|.+....|.+|++|.+.-+.++ ..+++|..|+++|.+..
T Consensus 97 h~~~~~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~-------------~~~~~~~RvTvri~~~~ 151 (272)
T COG2106 97 HTVSTSPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLS-------------SPAPPGARVTVRIISRS 151 (272)
T ss_pred ccCcCCccceeecceEEEEecCCceEEEecCCcceecc-------------CCCCCCceEEEEEEecc
Confidence 33445678899999999999999999999865555544 12889999999998863
No 259
>TIGR03833 conserved hypothetical protein. A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895. The function is unknown.
Probab=20.31 E-value=1e+02 Score=27.15 Aligned_cols=31 Identities=23% Similarity=0.504 Sum_probs=25.4
Q ss_pred CCcceEEEEEEEEe------cCeEEEEeCCCceeeEE
Q 000449 1062 DVGSLVQAEITEIK------PLELRLKFGIGFHGRIH 1092 (1497)
Q Consensus 1062 ~~G~~v~~~V~~vk------~~~l~V~L~~~~~GrVh 1092 (1497)
..|..+.|.|..+- |.++.|+|.++.-|||.
T Consensus 23 ~tG~lt~G~V~diLT~s~~Hp~GIKVrL~dG~VGRV~ 59 (62)
T TIGR03833 23 RTGKLTRGIVKDILTNSPTHPHGIKVRLEDGQVGRVK 59 (62)
T ss_pred CCCceeeEEhhhhhcCCCCCCCceEEEEecCCeeeEE
Confidence 46788888888763 55799999999999985
No 260
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=20.23 E-value=1.1e+02 Score=27.08 Aligned_cols=32 Identities=22% Similarity=0.479 Sum_probs=25.2
Q ss_pred CCCcceEEEEEEEEe------cCeEEEEeCCCceeeEE
Q 000449 1061 YDVGSLVQAEITEIK------PLELRLKFGIGFHGRIH 1092 (1497)
Q Consensus 1061 ~~~G~~v~~~V~~vk------~~~l~V~L~~~~~GrVh 1092 (1497)
-..|..++|.|..|- |.++.|.|.+|.-|||.
T Consensus 23 Q~tg~lt~GiV~~iLT~s~~HP~GIKVrL~~G~VGRV~ 60 (62)
T PF09962_consen 23 QRTGKLTEGIVKDILTNSPTHPHGIKVRLEDGQVGRVQ 60 (62)
T ss_pred CCcCccccEEhheeecCCCCCCCCcEEEecCCCeeeEE
Confidence 345677888888764 55799999999999984
No 261
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=20.04 E-value=6.2e+02 Score=23.60 Aligned_cols=65 Identities=14% Similarity=0.134 Sum_probs=48.2
Q ss_pred CcEEEEEEEEEeceeE-EEEeCCCeEEEEEccccCCC-cccCCCCccCCCCEEEEEEEEEcCCCCeEEEEEE
Q 000449 1379 NMIVQGYVKNVTSKGC-FIMLSRKLDAKVLLSNLSDG-YVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLK 1448 (1497)
Q Consensus 1379 G~~v~G~V~~v~~~G~-fV~l~~~~~g~v~is~lsd~-~~~~~~~~~~~g~~V~~~V~~vd~~~~~i~lslk 1448 (1497)
.-.+.|.|...-..+- -|++.++..-+-||+.=-.. |+ .+.+||.|.+.....|...++|.--.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i-----~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRI-----RILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeE-----EeCCCCEEEEEecccccccccEEEEec
Confidence 3458899999988875 58898888888888752222 33 377999999999888877777765544
Done!