Query 001115
Match_columns 1152
No_of_seqs 464 out of 3607
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 16:14:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001115hhsearch_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-102 3E-107 935.2 46.8 1028 41-1144 25-1141(1710)
2 KOG1070 rRNA processing protei 100.0 1.4E-81 3E-86 755.1 37.1 884 120-1150 48-977 (1710)
3 COG0539 RpsA Ribosomal protein 100.0 1.7E-64 3.7E-69 585.2 43.4 491 314-834 14-515 (541)
4 COG0539 RpsA Ribosomal protein 100.0 2.5E-62 5.3E-67 567.2 46.4 484 491-1044 14-514 (541)
5 PRK06299 rpsA 30S ribosomal pr 100.0 3.1E-58 6.8E-63 565.4 48.7 496 317-835 26-534 (565)
6 PRK12269 bifunctional cytidyla 100.0 1.1E-57 2.4E-62 565.1 52.1 490 402-944 316-830 (863)
7 PRK06299 rpsA 30S ribosomal pr 100.0 1E-57 2.2E-62 560.8 51.2 495 403-944 26-535 (565)
8 PRK12269 bifunctional cytidyla 100.0 6.9E-58 1.5E-62 567.0 48.4 493 313-834 313-828 (863)
9 TIGR00717 rpsA ribosomal prote 100.0 1.5E-57 3.3E-62 554.7 47.4 490 317-831 14-516 (516)
10 TIGR00717 rpsA ribosomal prote 100.0 1.6E-56 3.4E-61 545.9 47.6 496 126-655 11-516 (516)
11 PRK13806 rpsA 30S ribosomal pr 100.0 1.6E-49 3.5E-54 475.1 46.1 401 495-941 31-451 (491)
12 PRK13806 rpsA 30S ribosomal pr 100.0 7.8E-50 1.7E-54 477.9 42.7 411 404-833 31-451 (491)
13 PRK07899 rpsA 30S ribosomal pr 100.0 4.1E-44 8.9E-49 421.0 34.6 328 493-835 30-367 (486)
14 PRK06676 rpsA 30S ribosomal pr 100.0 2.4E-42 5.2E-47 406.2 36.1 334 488-835 7-351 (390)
15 PRK07899 rpsA 30S ribosomal pr 100.0 2.9E-40 6.2E-45 388.5 33.6 329 315-658 29-366 (486)
16 PRK00087 4-hydroxy-3-methylbut 100.0 1.4E-38 3E-43 393.5 34.6 333 489-835 293-636 (647)
17 PRK06676 rpsA 30S ribosomal pr 100.0 4.8E-38 1E-42 369.7 34.3 331 315-658 11-350 (390)
18 PRK00087 4-hydroxy-3-methylbut 100.0 2.7E-36 5.9E-41 373.1 32.5 332 314-658 295-635 (647)
19 PRK07400 30S ribosomal protein 100.0 1.1E-32 2.3E-37 311.2 27.9 237 583-835 29-269 (318)
20 PRK07400 30S ribosomal protein 100.0 3.2E-30 6.9E-35 291.0 26.9 243 495-751 28-274 (318)
21 PTZ00248 eukaryotic translatio 99.4 3.5E-13 7.5E-18 149.5 11.1 126 757-909 12-145 (319)
22 COG1098 VacB Predicted RNA bin 99.4 1.6E-13 3.4E-18 127.6 5.4 77 758-835 2-78 (129)
23 COG2996 Predicted RNA-bindinin 99.4 2.8E-11 6.2E-16 127.9 22.0 214 667-944 3-221 (287)
24 cd05705 S1_Rrp5_repeat_hs14 S1 99.4 9.4E-13 2E-17 116.7 8.5 71 759-829 1-74 (74)
25 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 1.5E-12 3.2E-17 115.3 9.1 70 229-300 1-70 (74)
26 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 3.5E-12 7.7E-17 112.9 10.3 71 758-834 1-72 (74)
27 PTZ00248 eukaryotic translatio 99.3 5.9E-13 1.3E-17 147.6 5.1 144 494-641 12-171 (319)
28 cd05693 S1_Rrp5_repeat_hs1_sc1 99.3 2.9E-12 6.2E-17 120.3 8.1 90 131-222 1-100 (100)
29 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 4.2E-12 9.1E-17 115.6 8.5 79 752-830 5-83 (83)
30 cd05703 S1_Rrp5_repeat_hs12_sc 99.3 6.4E-12 1.4E-16 111.2 8.9 70 762-831 1-72 (73)
31 cd05705 S1_Rrp5_repeat_hs14 S1 99.3 7.9E-12 1.7E-16 110.8 8.9 70 584-653 2-74 (74)
32 COG1098 VacB Predicted RNA bin 99.3 1.7E-12 3.6E-17 120.9 4.4 75 583-658 3-77 (129)
33 PF00575 S1: S1 RNA binding do 99.3 1.8E-11 4E-16 108.8 10.5 73 759-831 2-74 (74)
34 COG2996 Predicted RNA-bindinin 99.3 5.5E-10 1.2E-14 118.2 23.0 212 405-657 3-218 (287)
35 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 1.1E-11 2.5E-16 112.8 8.7 79 576-654 5-83 (83)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 99.3 1.9E-11 4.1E-16 107.5 8.6 70 762-831 1-70 (70)
37 cd05703 S1_Rrp5_repeat_hs12_sc 99.2 3.1E-11 6.6E-16 106.8 8.9 70 586-655 1-72 (73)
38 PF00575 S1: S1 RNA binding do 99.2 3.6E-11 7.9E-16 106.9 9.5 73 583-655 2-74 (74)
39 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 3.5E-11 7.6E-16 105.8 8.7 70 586-655 1-70 (70)
40 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 6.8E-11 1.5E-15 104.1 9.0 69 586-654 1-71 (71)
41 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 6.5E-11 1.4E-15 103.8 8.8 69 762-830 1-69 (69)
42 cd05707 S1_Rrp5_repeat_sc11 S1 99.2 6.1E-11 1.3E-15 103.6 8.0 68 762-829 1-68 (68)
43 cd05704 S1_Rrp5_repeat_hs13 S1 99.2 7.2E-11 1.6E-15 104.2 8.2 71 759-831 1-72 (72)
44 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 1.8E-10 3.8E-15 102.2 10.5 73 759-831 1-73 (73)
45 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 1E-10 2.3E-15 102.5 8.7 69 586-654 1-69 (69)
46 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.1 1.5E-10 3.2E-15 102.0 8.8 69 762-830 1-71 (71)
47 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 1.7E-10 3.7E-15 100.8 8.0 68 586-653 1-68 (68)
48 PRK08582 hypothetical protein; 99.1 3.6E-10 7.9E-15 112.4 10.7 75 759-834 3-77 (139)
49 PRK07252 hypothetical protein; 99.1 3.9E-10 8.4E-15 109.2 10.6 76 760-835 2-77 (120)
50 cd04452 S1_IF2_alpha S1_IF2_al 99.1 4.6E-10 1E-14 100.3 9.9 73 760-832 2-76 (76)
51 cd05706 S1_Rrp5_repeat_sc10 S1 99.1 6.8E-10 1.5E-14 98.4 10.4 72 584-655 2-73 (73)
52 cd05704 S1_Rrp5_repeat_hs13 S1 99.1 3.4E-10 7.3E-15 100.0 8.2 70 584-655 2-72 (72)
53 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 5.5E-10 1.2E-14 100.1 9.7 74 760-833 1-75 (77)
54 cd05690 S1_RPS1_repeat_ec5 S1_ 99.1 3.9E-10 8.5E-15 98.8 8.0 68 762-829 1-69 (69)
55 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 2.5E-10 5.4E-15 107.2 6.8 75 759-833 1-97 (100)
56 cd05686 S1_pNO40 S1_pNO40: pNO 99.1 8.2E-10 1.8E-14 97.9 9.7 70 760-830 2-72 (73)
57 cd05691 S1_RPS1_repeat_ec6 S1_ 99.0 9.3E-10 2E-14 97.5 9.5 72 762-833 1-72 (73)
58 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 9.1E-10 2E-14 95.4 8.9 66 586-653 1-66 (66)
59 cd04452 S1_IF2_alpha S1_IF2_al 99.0 1.1E-09 2.5E-14 97.8 9.7 73 584-656 2-76 (76)
60 PRK07252 hypothetical protein; 99.0 1.2E-09 2.7E-14 105.7 10.6 74 584-657 2-75 (120)
61 cd05690 S1_RPS1_repeat_ec5 S1_ 99.0 7.6E-10 1.6E-14 97.0 8.1 68 586-653 1-69 (69)
62 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.0 9.2E-10 2E-14 95.4 8.3 66 762-829 1-66 (66)
63 cd05689 S1_RPS1_repeat_ec4 S1_ 99.0 1.1E-09 2.4E-14 96.8 8.9 71 759-829 1-72 (72)
64 cd05708 S1_Rrp5_repeat_sc12 S1 99.0 1.7E-09 3.6E-14 96.9 10.0 73 585-657 2-75 (77)
65 cd05699 S1_Rrp5_repeat_hs7 S1_ 99.0 7.3E-10 1.6E-14 95.1 6.9 72 670-742 1-72 (72)
66 cd05691 S1_RPS1_repeat_ec6 S1_ 99.0 1.9E-09 4E-14 95.6 9.8 71 586-656 1-71 (73)
67 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 1.6E-09 3.5E-14 95.2 9.1 70 762-831 1-70 (70)
68 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 2.2E-09 4.7E-14 94.4 9.4 70 586-655 1-70 (70)
69 cd04465 S1_RPS1_repeat_ec2_hs2 99.0 2.1E-09 4.6E-14 93.6 9.1 67 586-655 1-67 (67)
70 PRK08582 hypothetical protein; 99.0 2.5E-09 5.4E-14 106.5 10.7 75 583-658 3-77 (139)
71 cd05686 S1_pNO40 S1_pNO40: pNO 99.0 2.9E-09 6.4E-14 94.3 9.2 70 584-654 2-72 (73)
72 PRK08059 general stress protei 99.0 3.2E-09 7E-14 103.9 10.1 80 756-835 2-81 (123)
73 PRK05807 hypothetical protein; 98.9 3.9E-09 8.5E-14 104.8 10.6 74 759-834 3-76 (136)
74 cd05689 S1_RPS1_repeat_ec4 S1_ 98.9 3.7E-09 8.1E-14 93.4 9.0 70 584-653 2-72 (72)
75 cd04465 S1_RPS1_repeat_ec2_hs2 98.9 3.9E-09 8.5E-14 91.9 8.9 67 762-831 1-67 (67)
76 cd05692 S1_RPS1_repeat_hs4 S1_ 98.9 4.2E-09 9.1E-14 91.9 8.9 69 762-831 1-69 (69)
77 cd05692 S1_RPS1_repeat_hs4 S1_ 98.9 4.2E-09 9.1E-14 91.9 8.6 69 586-655 1-69 (69)
78 cd05685 S1_Tex S1_Tex: The C-t 98.9 4.4E-09 9.5E-14 91.6 7.6 68 762-829 1-68 (68)
79 cd05684 S1_DHX8_helicase S1_DH 98.9 9.4E-09 2E-13 92.6 9.8 71 762-834 1-75 (79)
80 PRK08059 general stress protei 98.9 8.7E-09 1.9E-13 100.9 10.1 77 581-657 3-79 (123)
81 PHA02945 interferon resistance 98.9 9.7E-09 2.1E-13 90.6 9.1 72 760-834 10-85 (88)
82 PRK05807 hypothetical protein; 98.9 1.3E-08 2.7E-13 101.2 10.6 73 583-657 3-75 (136)
83 cd05684 S1_DHX8_helicase S1_DH 98.8 1.6E-08 3.6E-13 91.1 9.9 70 586-657 1-74 (79)
84 cd05685 S1_Tex S1_Tex: The C-t 98.8 8.8E-09 1.9E-13 89.6 7.7 68 586-653 1-68 (68)
85 cd04472 S1_PNPase S1_PNPase: P 98.8 1.3E-08 2.8E-13 88.7 8.3 68 586-654 1-68 (68)
86 smart00316 S1 Ribosomal protei 98.8 1.7E-08 3.7E-13 88.4 9.1 71 761-831 2-72 (72)
87 cd04472 S1_PNPase S1_PNPase: P 98.8 1.7E-08 3.6E-13 88.0 8.6 68 762-830 1-68 (68)
88 PHA02945 interferon resistance 98.8 2.2E-08 4.7E-13 88.5 8.9 71 584-657 10-84 (88)
89 smart00316 S1 Ribosomal protei 98.8 2.4E-08 5.1E-13 87.5 8.9 71 585-655 2-72 (72)
90 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2.1E-08 4.5E-13 87.4 8.4 68 585-653 1-68 (68)
91 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2.5E-08 5.5E-13 86.8 8.3 68 761-829 1-68 (68)
92 PLN00207 polyribonucleotide nu 98.8 2E-08 4.4E-13 125.0 10.4 78 757-835 749-827 (891)
93 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.7 3.1E-08 6.8E-13 90.8 8.5 74 759-833 4-81 (86)
94 cd05702 S1_Rrp5_repeat_hs11_sc 98.7 3.8E-08 8.3E-13 86.5 7.9 61 1064-1126 1-62 (70)
95 cd04453 S1_RNase_E S1_RNase_E: 98.7 7.4E-08 1.6E-12 88.4 8.9 75 758-832 4-83 (88)
96 COG1093 SUI2 Translation initi 98.7 2.2E-08 4.7E-13 105.9 5.5 75 761-835 11-87 (269)
97 cd04471 S1_RNase_R S1_RNase_R: 98.7 1.2E-07 2.7E-12 86.1 9.7 70 761-830 1-82 (83)
98 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.7 7E-08 1.5E-12 88.5 7.9 73 584-657 5-81 (86)
99 cd04453 S1_RNase_E S1_RNase_E: 98.6 1.1E-07 2.4E-12 87.2 8.5 73 583-655 5-82 (88)
100 PRK03987 translation initiatio 98.6 1E-07 2.2E-12 104.9 9.6 76 760-835 7-84 (262)
101 cd05702 S1_Rrp5_repeat_hs11_sc 98.6 1.2E-07 2.5E-12 83.4 7.9 63 762-824 1-65 (70)
102 cd04473 S1_RecJ_like S1_RecJ_l 98.6 2.1E-07 4.6E-12 83.4 9.7 71 575-654 6-76 (77)
103 cd04473 S1_RecJ_like S1_RecJ_l 98.6 2.7E-07 5.9E-12 82.6 10.4 67 755-830 10-76 (77)
104 TIGR02696 pppGpp_PNP guanosine 98.6 6.3E-08 1.4E-12 118.3 8.3 71 758-829 644-718 (719)
105 PLN00207 polyribonucleotide nu 98.6 1.1E-07 2.3E-12 118.7 10.0 81 582-663 750-832 (891)
106 COG2183 Tex Transcriptional ac 98.6 6.5E-08 1.4E-12 117.0 7.2 82 754-835 651-732 (780)
107 cd00164 S1_like S1_like: Ribos 98.6 1.3E-07 2.9E-12 81.0 7.1 64 590-653 2-65 (65)
108 cd00164 S1_like S1_like: Ribos 98.6 1.3E-07 2.8E-12 81.0 6.9 65 765-829 1-65 (65)
109 cd04454 S1_Rrp4_like S1_Rrp4_l 98.6 2.5E-07 5.5E-12 84.0 9.0 73 760-833 5-77 (82)
110 PRK03987 translation initiatio 98.6 2E-07 4.3E-12 102.7 9.8 74 584-657 7-82 (262)
111 cd04471 S1_RNase_R S1_RNase_R: 98.6 3.2E-07 7E-12 83.4 9.6 69 586-654 2-82 (83)
112 TIGR02696 pppGpp_PNP guanosine 98.6 2.5E-07 5.5E-12 113.1 11.4 98 555-653 612-718 (719)
113 COG1093 SUI2 Translation initi 98.5 5.7E-08 1.2E-12 102.8 4.4 73 585-657 11-85 (269)
114 cd04454 S1_Rrp4_like S1_Rrp4_l 98.5 3.1E-07 6.6E-12 83.4 8.4 72 584-656 5-76 (82)
115 PRK11824 polynucleotide phosph 98.5 4E-07 8.6E-12 114.1 10.4 76 757-833 617-692 (693)
116 PRK09521 exosome complex RNA-b 98.4 1.2E-06 2.6E-11 92.7 10.2 94 727-833 40-143 (189)
117 PRK11824 polynucleotide phosph 98.4 1.1E-06 2.4E-11 110.1 11.6 74 582-656 618-691 (693)
118 COG2183 Tex Transcriptional ac 98.4 5.2E-07 1.1E-11 109.3 7.8 80 579-658 652-731 (780)
119 PRK09202 nusA transcription el 98.4 8.2E-07 1.8E-11 105.4 8.8 122 524-657 73-201 (470)
120 PRK09521 exosome complex RNA-b 98.4 2.8E-06 6.1E-11 89.9 11.9 102 541-656 25-142 (189)
121 PRK09202 nusA transcription el 98.3 9.4E-07 2E-11 104.9 7.4 119 437-568 72-201 (470)
122 PRK04163 exosome complex RNA-b 98.3 8E-06 1.7E-10 89.2 13.4 73 584-657 62-138 (235)
123 cd04460 S1_RpoE S1_RpoE: RpoE, 98.3 3.9E-06 8.5E-11 79.1 9.3 71 763-834 1-87 (99)
124 cd04455 S1_NusA S1_NusA: N-uti 98.3 3.5E-06 7.7E-11 73.3 8.2 62 497-565 2-67 (67)
125 TIGR03591 polynuc_phos polyrib 98.2 3.2E-06 6.9E-11 105.8 10.6 70 582-652 615-684 (684)
126 cd04455 S1_NusA S1_NusA: N-uti 98.2 4.7E-06 1E-10 72.5 8.6 63 760-829 2-66 (67)
127 TIGR03591 polynuc_phos polyrib 98.2 2.1E-06 4.6E-11 107.4 7.8 71 757-828 614-684 (684)
128 COG1185 Pnp Polyribonucleotide 98.1 4.5E-06 9.8E-11 99.8 7.0 76 757-833 615-690 (692)
129 cd04460 S1_RpoE S1_RpoE: RpoE, 98.1 1.3E-05 2.8E-10 75.6 8.5 71 587-658 1-87 (99)
130 COG1185 Pnp Polyribonucleotide 98.0 1.5E-05 3.2E-10 95.5 8.3 99 557-656 589-689 (692)
131 PRK04163 exosome complex RNA-b 98.0 2.2E-05 4.8E-10 85.8 8.9 73 760-833 62-138 (235)
132 TIGR01953 NusA transcription t 97.9 2.2E-05 4.8E-10 89.7 8.7 109 541-657 82-199 (341)
133 TIGR00448 rpoE DNA-directed RN 97.9 4.4E-05 9.5E-10 80.1 9.7 72 761-833 81-168 (179)
134 TIGR01953 NusA transcription t 97.9 2.2E-05 4.8E-10 89.8 7.3 108 453-568 80-199 (341)
135 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.9 5E-05 1.1E-09 65.7 7.5 62 875-939 1-72 (72)
136 PRK12327 nusA transcription el 97.9 3E-05 6.5E-10 89.2 7.9 109 541-656 85-200 (362)
137 TIGR00448 rpoE DNA-directed RN 97.9 6.3E-05 1.4E-09 78.9 9.6 73 585-658 81-169 (179)
138 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.8 8.3E-05 1.8E-09 68.9 8.2 77 1062-1145 5-89 (92)
139 TIGR02063 RNase_R ribonuclease 97.7 8.7E-05 1.9E-09 94.4 10.1 74 757-830 623-708 (709)
140 KOG1067 Predicted RNA-binding 97.7 4.4E-05 9.6E-10 88.1 5.0 76 582-657 665-740 (760)
141 KOG1067 Predicted RNA-binding 97.6 4.8E-05 1E-09 87.9 5.2 73 757-829 664-736 (760)
142 TIGR02063 RNase_R ribonuclease 97.6 0.00015 3.2E-09 92.3 10.2 71 584-654 626-708 (709)
143 PRK12327 nusA transcription el 97.6 7E-05 1.5E-09 86.2 5.7 104 455-566 85-199 (362)
144 COG1095 RPB7 DNA-directed RNA 97.6 0.00022 4.8E-09 72.8 7.9 73 585-658 81-169 (183)
145 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.5 0.00022 4.7E-09 66.1 6.9 71 497-567 5-86 (92)
146 COG1095 RPB7 DNA-directed RNA 97.5 0.0003 6.4E-09 71.8 8.0 73 761-834 81-169 (183)
147 PRK11642 exoribonuclease R; Pr 97.5 0.00032 7E-09 89.4 10.0 73 760-832 642-726 (813)
148 PRK11642 exoribonuclease R; Pr 97.5 0.00038 8.1E-09 88.8 10.2 72 584-655 642-725 (813)
149 TIGR00358 3_prime_RNase VacB a 97.4 0.00039 8.4E-09 87.5 10.0 72 759-830 570-653 (654)
150 PRK08563 DNA-directed RNA poly 97.4 0.00066 1.4E-08 71.9 9.8 73 761-834 81-169 (187)
151 PRK08563 DNA-directed RNA poly 97.4 0.00068 1.5E-08 71.8 9.6 73 585-658 81-169 (187)
152 TIGR00358 3_prime_RNase VacB a 97.4 0.00052 1.1E-08 86.3 10.2 71 584-654 571-653 (654)
153 PF10447 EXOSC1: Exosome compo 97.3 0.0011 2.3E-08 59.6 7.7 62 1062-1124 3-82 (82)
154 PHA02858 EIF2a-like PKR inhibi 97.1 0.0013 2.8E-08 58.0 6.4 69 760-830 15-85 (86)
155 PHA02858 EIF2a-like PKR inhibi 97.0 0.0012 2.6E-08 58.1 5.6 69 584-654 15-85 (86)
156 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.0 0.0047 1E-07 56.7 9.2 64 585-649 1-75 (88)
157 COG1107 Archaea-specific RecJ- 96.9 0.0039 8.4E-08 73.2 10.3 143 755-923 116-268 (715)
158 PRK12328 nusA transcription el 96.9 0.0018 4E-08 74.0 7.4 109 541-656 89-206 (374)
159 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.7 0.0088 1.9E-07 55.0 8.5 58 498-556 1-69 (88)
160 cd05701 S1_Rrp5_repeat_hs10 S1 96.6 0.0024 5.2E-08 52.9 3.9 60 971-1030 1-61 (69)
161 PF13509 S1_2: S1 domain; PDB: 96.5 0.0096 2.1E-07 50.7 7.2 61 498-566 1-61 (61)
162 COG1107 Archaea-specific RecJ- 96.4 0.013 2.7E-07 69.1 9.8 147 578-737 115-278 (715)
163 COG1096 Predicted RNA-binding 96.4 0.015 3.2E-07 59.7 9.1 77 1057-1144 58-144 (188)
164 KOG2916 Translation initiation 96.4 0.0022 4.7E-08 68.2 3.0 75 760-834 15-91 (304)
165 PRK12329 nusA transcription el 96.3 0.0047 1E-07 71.8 5.5 108 453-566 99-224 (449)
166 COG1097 RRP4 RNA-binding prote 96.3 0.079 1.7E-06 56.8 14.0 104 541-656 28-138 (239)
167 PTZ00162 DNA-directed RNA poly 96.3 0.015 3.2E-07 60.7 8.3 71 498-569 81-167 (176)
168 PRK05054 exoribonuclease II; P 96.1 0.018 3.9E-07 72.3 9.9 69 762-830 562-643 (644)
169 COG1096 Predicted RNA-binding 96.1 0.045 9.8E-07 56.2 10.7 105 541-656 25-142 (188)
170 PF10447 EXOSC1: Exosome compo 96.1 0.015 3.2E-07 52.4 6.4 62 132-200 3-82 (82)
171 KOG1856 Transcription elongati 96.1 0.0061 1.3E-07 76.6 5.0 78 757-834 981-1061(1299)
172 PTZ00162 DNA-directed RNA poly 95.9 0.031 6.6E-07 58.4 8.8 72 761-833 81-166 (176)
173 PRK05054 exoribonuclease II; P 95.9 0.024 5.1E-07 71.3 9.4 71 584-654 558-643 (644)
174 PF13509 S1_2: S1 domain; PDB: 95.9 0.027 5.7E-07 48.0 6.8 61 669-742 1-61 (61)
175 KOG1856 Transcription elongati 95.9 0.0075 1.6E-07 75.9 4.8 76 583-658 983-1061(1299)
176 PRK12328 nusA transcription el 95.7 0.029 6.2E-07 64.5 8.3 70 232-305 138-211 (374)
177 COG1097 RRP4 RNA-binding prote 95.7 0.057 1.2E-06 57.8 9.9 73 760-833 63-139 (239)
178 TIGR00757 RNaseEG ribonuclease 95.6 0.029 6.3E-07 66.4 8.2 60 759-818 23-96 (414)
179 TIGR00757 RNaseEG ribonuclease 95.6 0.028 6.1E-07 66.5 7.8 59 584-642 24-96 (414)
180 cd05790 S1_Rrp40 S1_Rrp40: Rrp 95.6 0.067 1.5E-06 48.7 8.3 69 497-566 5-74 (86)
181 cd05790 S1_Rrp40 S1_Rrp40: Rrp 95.5 0.083 1.8E-06 48.1 8.8 72 760-833 5-76 (86)
182 cd05700 S1_Rrp5_repeat_hs9 S1_ 95.3 0.14 3.1E-06 42.1 8.4 64 875-938 1-65 (65)
183 TIGR02062 RNase_B exoribonucle 95.2 0.062 1.4E-06 67.5 9.3 68 762-829 558-638 (639)
184 TIGR02062 RNase_B exoribonucle 94.7 0.071 1.5E-06 67.0 7.9 68 586-653 558-638 (639)
185 PRK12329 nusA transcription el 94.6 0.1 2.2E-06 61.0 8.4 71 232-304 152-229 (449)
186 COG0557 VacB Exoribonuclease R 94.3 0.11 2.4E-06 66.3 8.7 75 756-830 617-703 (706)
187 KOG2916 Translation initiation 93.9 0.027 5.8E-07 60.2 1.6 73 585-657 16-90 (304)
188 COG0557 VacB Exoribonuclease R 93.7 0.18 3.9E-06 64.4 8.8 71 584-654 621-703 (706)
189 KOG3409 Exosomal 3'-5' exoribo 93.0 0.34 7.4E-06 48.8 7.6 63 1062-1125 67-137 (193)
190 PF10246 MRP-S35: Mitochondria 91.9 0.65 1.4E-05 43.1 7.3 61 488-556 14-74 (104)
191 PF08292 RNA_pol_Rbc25: RNA po 91.6 0.67 1.4E-05 45.3 7.6 59 498-556 3-74 (122)
192 PRK10811 rne ribonuclease E; R 89.7 0.78 1.7E-05 58.3 7.6 71 584-654 37-118 (1068)
193 PRK10811 rne ribonuclease E; R 89.4 0.89 1.9E-05 57.8 7.8 61 760-820 37-108 (1068)
194 KOG3409 Exosomal 3'-5' exoribo 89.3 1.1 2.4E-05 45.3 6.9 68 498-565 68-146 (193)
195 cd05701 S1_Rrp5_repeat_hs10 S1 87.9 0.72 1.6E-05 38.7 3.8 59 762-821 1-61 (69)
196 PRK11712 ribonuclease G; Provi 86.9 1.1 2.4E-05 54.2 6.4 59 584-642 37-109 (489)
197 KOG3298 DNA-directed RNA polym 85.9 4.6 0.0001 40.7 8.9 64 585-649 81-155 (170)
198 PRK11712 ribonuclease G; Provi 84.8 2.2 4.7E-05 51.8 7.4 61 759-819 36-110 (489)
199 KOG3298 DNA-directed RNA polym 84.4 5.1 0.00011 40.4 8.4 58 498-556 81-149 (170)
200 PF10246 MRP-S35: Mitochondria 82.1 5.5 0.00012 37.1 7.1 54 760-820 22-75 (104)
201 PF08292 RNA_pol_Rbc25: RNA po 76.6 12 0.00026 36.6 8.1 60 761-820 3-75 (122)
202 cd05700 S1_Rrp5_repeat_hs9 S1_ 64.1 32 0.0007 28.9 6.5 62 322-391 1-65 (65)
203 PRK10676 DNA-binding transcrip 62.8 78 0.0017 35.5 11.9 114 136-286 129-254 (263)
204 TIGR00008 infA translation ini 59.8 41 0.00089 29.3 6.9 59 588-651 6-66 (68)
205 PRK12442 translation initiatio 57.5 53 0.0012 30.0 7.4 66 764-833 8-74 (87)
206 PF03459 TOBE: TOBE domain; I 56.8 17 0.00037 30.8 4.2 49 234-285 5-58 (64)
207 TIGR00008 infA translation ini 56.7 51 0.0011 28.8 7.0 60 764-827 6-66 (68)
208 PRK12442 translation initiatio 55.4 56 0.0012 29.9 7.2 64 588-656 8-73 (87)
209 COG1530 CafA Ribonucleases G a 51.2 21 0.00046 43.6 5.3 64 757-821 33-103 (487)
210 COG1530 CafA Ribonucleases G a 48.8 22 0.00048 43.5 5.0 60 495-555 34-100 (487)
211 KOG3013 Exosomal 3'-5' exoribo 48.0 12 0.00027 40.5 2.3 68 133-203 85-156 (301)
212 PF01938 TRAM: TRAM domain; I 47.9 1.1E+02 0.0023 25.8 7.6 56 458-518 3-60 (61)
213 KOG4078 Putative mitochondrial 46.9 45 0.00098 32.8 5.6 53 497-556 81-133 (173)
214 KOG3297 DNA-directed RNA polym 45.9 39 0.00085 35.0 5.3 59 498-556 81-156 (202)
215 KOG4078 Putative mitochondrial 44.6 47 0.001 32.6 5.4 61 761-829 82-142 (173)
216 PRK06763 F0F1 ATP synthase sub 41.7 2.9E+02 0.0062 29.4 10.8 121 876-1027 40-177 (213)
217 PF01330 RuvA_N: RuvA N termin 41.7 1.4E+02 0.0029 25.3 7.3 47 501-556 4-51 (61)
218 PF00313 CSD: 'Cold-shock' DNA 40.7 2.3E+02 0.0049 24.1 9.5 49 590-642 2-53 (66)
219 PRK10676 DNA-binding transcrip 39.5 1.7E+02 0.0037 32.8 9.8 115 764-926 129-254 (263)
220 PF07076 DUF1344: Protein of u 38.4 1.3E+02 0.0028 25.7 6.3 49 279-333 4-52 (61)
221 KOG1004 Exosomal 3'-5' exoribo 38.1 1.4E+02 0.0031 31.8 8.1 61 968-1030 63-124 (230)
222 PF11604 CusF_Ec: Copper bindi 38.0 2E+02 0.0043 25.2 7.9 46 638-683 1-59 (70)
223 PLN02741 riboflavin synthase 36.1 5.6E+02 0.012 27.3 12.7 135 237-412 9-182 (194)
224 PF03459 TOBE: TOBE domain; I 34.7 62 0.0013 27.3 4.2 49 876-924 5-57 (64)
225 PF00313 CSD: 'Cold-shock' DNA 33.1 3E+02 0.0066 23.3 9.1 50 765-818 1-53 (66)
226 cd04322 LysRS_N LysRS_N: N-ter 32.1 2.1E+02 0.0046 27.1 7.9 68 764-831 3-75 (108)
227 PRK15463 cold shock-like prote 32.0 1.9E+02 0.0042 25.3 6.9 51 236-287 5-58 (70)
228 PRK06386 replication factor A; 31.5 9.2E+02 0.02 28.4 18.9 189 777-995 38-244 (358)
229 PF12073 DUF3553: Protein of u 31.4 66 0.0014 26.4 3.4 19 138-156 17-35 (52)
230 COG4148 ModC ABC-type molybdat 31.4 5.3E+02 0.012 29.3 11.4 117 969-1125 230-349 (352)
231 PF01938 TRAM: TRAM domain; I 30.9 2.7E+02 0.0058 23.3 7.5 56 275-341 3-60 (61)
232 PRK07211 replication factor A; 30.8 1.1E+03 0.023 29.0 21.0 258 124-430 52-357 (485)
233 PF11580 DUF3239: Protein of u 30.2 1.4E+02 0.0031 29.5 6.3 81 1060-1143 10-94 (128)
234 KOG1004 Exosomal 3'-5' exoribo 29.9 1.8E+02 0.0039 31.1 7.2 58 497-556 64-122 (230)
235 COG0361 InfA Translation initi 29.8 2.4E+02 0.0051 25.2 6.9 57 876-937 7-70 (75)
236 PRK10943 cold shock-like prote 29.4 2.1E+02 0.0046 25.0 6.7 51 588-642 3-56 (69)
237 PRK15464 cold shock-like prote 28.7 2.4E+02 0.0052 24.8 6.9 51 236-287 5-58 (70)
238 PRK09507 cspE cold shock prote 28.5 2.4E+02 0.0051 24.6 6.8 51 588-642 3-56 (69)
239 COG0361 InfA Translation initi 28.0 2.5E+02 0.0054 25.1 6.7 66 586-655 6-72 (75)
240 PRK09289 riboflavin synthase s 28.0 7.6E+02 0.016 26.3 17.4 48 638-689 10-62 (194)
241 PRK15464 cold shock-like prote 27.7 2E+02 0.0044 25.2 6.2 50 589-642 5-57 (70)
242 KOG1999 RNA polymerase II tran 27.6 6.7E+02 0.015 33.0 12.9 56 496-551 408-468 (1024)
243 PRK10943 cold shock-like prote 25.9 3E+02 0.0065 24.0 7.0 53 234-287 2-57 (69)
244 PRK15463 cold shock-like prote 25.3 2.4E+02 0.0052 24.7 6.3 49 590-642 6-57 (70)
245 PRK13020 riboflavin synthase s 24.5 9.1E+02 0.02 26.0 16.1 50 637-689 9-63 (206)
246 PRK06763 F0F1 ATP synthase sub 24.3 7.8E+02 0.017 26.3 10.6 51 876-926 118-177 (213)
247 COG4044 Uncharacterized protei 24.3 92 0.002 33.0 4.0 80 747-827 62-153 (247)
248 PRK09937 stationary phase/star 23.5 2.9E+02 0.0064 24.5 6.5 49 590-642 3-54 (74)
249 TIGR00638 Mop molybdenum-pteri 22.7 1.9E+02 0.0042 24.5 5.3 50 876-925 7-60 (69)
250 PF11813 DUF3334: Protein of u 22.2 58 0.0013 34.4 2.1 19 774-792 49-67 (229)
251 PRK09838 periplasmic copper-bi 21.9 4E+02 0.0087 25.9 7.6 54 636-689 45-111 (115)
252 COG4148 ModC ABC-type molybdat 21.7 1.2E+03 0.027 26.5 14.3 114 760-928 230-349 (352)
253 PRK09890 cold shock protein Cs 21.6 4E+02 0.0086 23.3 7.0 50 589-642 5-57 (70)
No 1
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=100.00 E-value=1.6e-102 Score=935.23 Aligned_cols=1028 Identities=23% Similarity=0.289 Sum_probs=805.4
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCchhhccchhc--ccchhhhccccc-----ccccccccccccccccccccccCCccCC
Q 001115 41 QDLALPPDDDVPVFPRGGGHSLTQRERDEIHAE--VDAEFEAVERGL-----HKKNKKKKKKTERKANETVDDLGSLFGD 113 (1152)
Q Consensus 41 ~~~~~~~~~~e~~fpRGg~~~lt~~e~~~~~~~--~d~lf~~~~~~~-----~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (1152)
+..-+..++++++|||||+|.|||+|++++..| .|.+|+....+. .++++..++...+-. ..+++
T Consensus 25 s~~~l~~~t~~~~fprgg~s~lt~~e~~kv~~E~~~e~l~~~~~vke~~~~~~~~~k~vk~~~s~~s--------~~~~~ 96 (1710)
T KOG1070|consen 25 SKSSLKRKTAAPDFPRGGASKLTPLEIEKVEEEAFIEGLTGFGVVKEVFDDGRPKKKTVKKSASKVS--------KKFTE 96 (1710)
T ss_pred ccccccccccccccccccccccChHHHHHHHHHHHhhhhhcccceecccCCCCccccccccchhhHH--------Hhhhc
Confidence 334456678899999999999999999999555 455555322110 111111111111100 01111
Q ss_pred CcCCCCCeeecccccCCCCCCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChhh------cccc---cc-------
Q 001115 114 GISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPIL------DNEI---EA------- 177 (1152)
Q Consensus 114 ~~~~~~~~~ve~l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~------~~~~---~~------- 177 (1152)
+....-+.++++++++++.|||+++|+|++|+..|+.+++|++++|+++.+++|+.++ +.+. +|
T Consensus 97 ~~~~~k~~~~~~~~~k~isPG~~llgvIs~i~~~Dl~isv~~~l~g~v~~t~lS~~~~~~~~~l~~~v~S~ed~g~~l~~ 176 (1710)
T KOG1070|consen 97 NFNEEKPEIINAFQLKNISPGMLLLGVISKINGNDLKISVKGGLNGYVLNTHLSDEMLAAGEVLDTAVVSIEDHGAILDV 176 (1710)
T ss_pred cccccchhhhhhccccccCCcceeeeeeeeccccceeEEccCcccccccccccCHhHhhhhhhhccccccccccccchhc
Confidence 1111226678999999999999999999999999999999999999999999999851 2210 10
Q ss_pred --cc---------cCCCCCccCCCCEEEEEEEEEecCC-cccceeEEEEecchHHHhcCCCccccCCCCEEEEEEEEEec
Q 001115 178 --NE---------DNLLPTIFHVGQLVSCIVLQLDDDK-KEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIED 245 (1152)
Q Consensus 178 --~~---------~~~l~~~f~vGq~v~~~V~~~~~~~-~~~~~~~i~LS~~p~~vn~~l~~~~l~~g~~l~~~V~sved 245 (1152)
++ ..++.+.|++|||++|.|++..... ....++++++++.|...| +|..++|.|||+|+|.|+||+|
T Consensus 177 g~~~~~~~~e~~q~pn~~~~lKvGq~l~~~V~k~~s~~v~ks~~~~~~~t~~~t~~~-~~~~~~LvpGt~vqa~V~sv~~ 255 (1710)
T KOG1070|consen 177 GLDEITGFIEKSQFPNLGAKLKVGQWLRVSVTKSTSERVVKSTKFVEVLTLNPTSCN-GLALNDLVPGTMVQAEVQSVED 255 (1710)
T ss_pred CCccccchhhhccCchhhhhcccCceEEEEEEeccCceEEecccceeeecccchhcc-ccchhhcCCcceEEEEecceec
Confidence 11 1156688999999999999864410 111367999999999999 7999999999999999999999
Q ss_pred CeEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEEeCCCCEEEEccCccccccccccccccccccccCCCcEE
Q 001115 246 HGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMV 325 (1152)
Q Consensus 246 hG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~pG~~V 325 (1152)
||+++|| +.+++|||++.|+++.. .+..||.++|+|+.. +.|++.+.+-.. ..+... -...++.+.||..+
T Consensus 256 ~Gi~~di-l~~ftG~l~~~hl~~~~--~~~~~~~~l~~vi~~--s~Rv~~~~f~~k--a~ki~~--l~~~v~ai~p~~~~ 326 (1710)
T KOG1070|consen 256 HGITLDI-LNGFTGFLDKKHLPPFL--RYFENQEKLGKVIHK--SDRVFVVDFFDK--ASKILV--LKAGVDAIAPSRIE 326 (1710)
T ss_pred CcEEEEe-cccccceeehhhCCchh--hccccHHHhhcccch--hhheeeechhhc--cceEEE--ecCccceEccCCcc
Confidence 9999999 79999999999998665 688999999997663 456665553111 111111 12356778888888
Q ss_pred EEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeC--CC-CEEEEecchhhhcCCC--
Q 001115 326 STRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDP--TS-RAVGLTLNPYLLHNRA-- 400 (1152)
Q Consensus 326 ~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~--~~-k~v~LSl~p~~~~~~~-- 400 (1152)
.....++.+.|..++..+--.+..+..|+..... .+++.+|..+..|++|++..-| .+ -.+.|+-.||+.....
T Consensus 327 ~~~~~e~~k~G~~~K~~vi~~~~~~~~~~~tl~~-s~ie~k~~~~s~V~~r~l~~~~~svdt~~~~l~~L~hv~~f~~a~ 405 (1710)
T KOG1070|consen 327 KVLSFEIFKIGNKVKCRVIDVLQMDSLALFTLKE-SAIEGKFSLVSDVSPRGLLKKPVSVDTEEVGLSPLPHVLGFEYAD 405 (1710)
T ss_pred cccchhhcccCceEEEEEEEEeeccceEEeecch-hhccCceEEEeccCCceEEEecccCChhhhhccccchhhceeecC
Confidence 8888888888888888776667777777765443 4688999999999999998766 23 3789999999987432
Q ss_pred C----CCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhh----ccccCCCCEEEEEEEEEec
Q 001115 401 P----PSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKL----EKKYKEGSCVRVRILGFRH 472 (1152)
Q Consensus 401 ~----~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~----~~~~~vG~~v~~rVi~~~~ 472 (1152)
+ ....++|.++-.|..+..+-.++.++....+ -+.+|.+...+.+..+... ...|++|+.+.|||..|.+
T Consensus 406 p~~~~~~~~di~~~vl~~~ak~~~vt~~v~~~sK~p--vis~y~~~~~~t~~~l~~v~q~~v~~~e~~te~~~rv~~v~~ 483 (1710)
T KOG1070|consen 406 PSKKISDGKDIGFRVLTCKAKCGSVTLKVLCVSKLP--VISMYADAVKLTHGMLSKVPQGMVPIYEVGTEVKSRVWQVFY 483 (1710)
T ss_pred CCcccccccceeeEEeeccceeeeeeeeeeEeecCc--ceEEEeeccccCcchhhccccCCCCceecCCcccCccceecc
Confidence 2 2456777777777777776555667776543 3689999988776665443 2359999999999999999
Q ss_pred CCCeEEEEccccccccccccccccCCCCEEEEEEEEEeCCeEEEEeCCC-eEEEEeCCccccccccCCCCccccCCEEEE
Q 001115 473 LEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGG-VKALCPLPHMSEFEIVKPGKKFKVGAELVF 551 (1152)
Q Consensus 473 ~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~-v~g~vp~~hls~~~~~~~~~~~kvG~~V~~ 551 (1152)
.+..++|++.++.+...+++.+||+.|+.|.|+|.++++.|+.|.+..+ +.|++|..|++|.+...|...|++|..+++
T Consensus 484 v~~v~~v~~~~svl~lk~~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~ 563 (1710)
T KOG1070|consen 484 VGKVVIVSVRESVLGLKFLRVNDIEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKL 563 (1710)
T ss_pred cCcEEEEEEehHhhcccccccccccccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEE
Confidence 9999999999999999999999999999999999999999999999765 999999999999999999999999999999
Q ss_pred EEEEE--eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCC
Q 001115 552 RVLGV--KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSM 629 (1152)
Q Consensus 552 rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~ 629 (1152)
|||.+ +.+++.||+|++|++...|...+|++++||+++.|+|.++.++||||+|++|+.||+|.++|++.++.+++++
T Consensus 564 RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~eh 643 (1710)
T KOG1070|consen 564 RVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEH 643 (1710)
T ss_pred EEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhh
Confidence 99999 6899999999999999889999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCEEEEEEEEEecCCCEEEEEEeeCCCC----ccccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcC
Q 001115 630 YHVGQVVKCRIMSSIPASRRINLSFMMKPTR----VSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLA 705 (1152)
Q Consensus 630 f~vGq~v~vrV~~vd~~~~ri~lS~k~~~~~----~~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hls 705 (1152)
|.+||++.+.|+++|++++|+.++++.+.+. ....+.+..|.+..+.+.+.+.+.++|++. ..++.|++...||.
T Consensus 644 f~vGqTv~~~i~nvd~ek~rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~-~~~~~~v~~~~~L~ 722 (1710)
T KOG1070|consen 644 FPVGQTVRAKIVNVDDEKRRMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIVEIV-DQGITGVGVFGELV 722 (1710)
T ss_pred cccccEEEEEEEecCchhceeehhhhhhhhHHHHHHHHHHHhhccccccceeehhccccEEEEcc-CcceEEEEEEEEEc
Confidence 9999999999999999999999999988752 223457788988899999999999999994 24799999999999
Q ss_pred Ccc-ccccccccc---------cCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEec
Q 001115 706 DHL-EHATVMKSV---------IKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIE 774 (1152)
Q Consensus 706 d~~-~~~~~~~~~---------lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~ 774 (1152)
|.. ..+..+..+ +.+|+... +|+.++..+.-+.+++++. +|....++..|....++|.+|.+
T Consensus 723 dg~v~~~~~~~~kl~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~-------L~~~~~~l~k~~~~~~~v~~is~ 795 (1710)
T KOG1070|consen 723 DGSVVVNKVLENKLRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTD-------LPNNATKLLKGSYALALVRSISK 795 (1710)
T ss_pred cCceEEccchhhhhhhcchhheeeecceeEEEEEEeehhhhhhhcccccc-------ccchHHHHhcCchhHHHHHhhhh
Confidence 832 122222222 44666666 6655554444444444443 45556778899999999999999
Q ss_pred ceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHH
Q 001115 775 TGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIA 854 (1152)
Q Consensus 775 ~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~ 854 (1152)
.|.|+.|.+++.++++.+++.+....+.. ....||.|.|+++++++......++++......+.. + +..+
T Consensus 796 ~~~~~a~~~~~i~~v~~s~~v~s~~~d~~-~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~------~---~~~~ 865 (1710)
T KOG1070|consen 796 EGKFVAFVSNLIALVKVSHLVDSELDDLT-KAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKK------F---IKVS 865 (1710)
T ss_pred heeheeecccccceeeccccccccccccc-eeeeecccceEEEecChhHHHHHHhhcchhhcccee------E---EEec
Confidence 99999999999999999998876666544 344469999999999987777777765542211000 0 0000
Q ss_pred HhhcCcCCCcccccccCcccccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCC---------CcccCCCEEEEEEE
Q 001115 855 MLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG---------ATVESGSVIQAAIL 925 (1152)
Q Consensus 855 ~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~---------~~~~~G~~v~a~Vl 925 (1152)
.-...+++|...+..+++.+|++|.|+|++++++|+.|.+.. ++.|+||.+|+-+ .+|++||.|.|+|+
T Consensus 866 ~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~v~l~~--~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrvi 943 (1710)
T KOG1070|consen 866 SNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLNVLLAA--NHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVI 943 (1710)
T ss_pred cccCCCccccccccccceeeeeEEEEEEeeecccceEEeccc--cccCceehHHhhccccccCChhhhcccCCeEEEEEE
Confidence 012236677777767999999999999999999999888875 8999999999853 58999999999999
Q ss_pred EEECCC-----------CEEEEEEcccchhhhhcccchhhhhhhccccccccccCCCCEEEEEEEEEecCEEEEEEcCCC
Q 001115 926 DVAKAE-----------RLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVHQTVNAIVEIVKENYLVLSLPEYN 994 (1152)
Q Consensus 926 ~vd~~~-----------~~v~LSlk~s~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~~l~V~l~~~~ 994 (1152)
+.++-+ ..++||+||+.++... ....+..+++.||+++|||+++..+|+|++++|..
T Consensus 944 G~~D~k~lpith~i~k~~v~ElSvkps~les~~------------~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v 1011 (1710)
T KOG1070|consen 944 GGHDVKDLPITHLISKEQVLELSVKPSELESDE------------FNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFV 1011 (1710)
T ss_pred cCCccccCccccccchhhhhhhccChhhhcccc------------ccccchhhhhcCCeEEEEEEccccceeEEEccccc
Confidence 996533 6799999999998432 11234468999999999999999999999997755
Q ss_pred ce-EEEEEec-ccccccCCcCCCCCCCEEEEEEEeecCCCCccEEEEEecccccccccccccccccCCCcCCcEEEEEEE
Q 001115 995 HS-IGYASVS-DYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISETETSSSKRAKKKSSYDVGSLVQAEIT 1072 (1152)
Q Consensus 995 ~~-~~~~~~s-~~~~~~~~~~~f~~Gq~v~~~V~~~d~~~~~~~l~l~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~V~ 1072 (1152)
.+ +.++.++ ++....++++.|+.|+++.+.|+..|. ++. ++.-.. .++.....+|+++.|||.
T Consensus 1012 ~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~---~~t--v~~iG~----------~~~~k~~s~G~~l~Grv~ 1076 (1710)
T KOG1070|consen 1012 DGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDK---SKT--VRAIGF----------SKSDKNPSPGDILFGRVS 1076 (1710)
T ss_pred cceeeeeeccchhhhhhCchhhcccccceeeEEecccc---eeE--EEeccc----------ccCCCCCCcchhhcceee
Confidence 54 5666665 444455688999999999999999883 332 332110 111223349999999999
Q ss_pred EEeCCeEEEEeCCCeeEEEEee-eccCCccccccccccCCCCCCEEEEEEEeeecCCCCCCCceEEEEeecCC
Q 001115 1073 EIKPLELRLKFGIGFHGRIHIT-EVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPSM 1144 (1152)
Q Consensus 1073 ~i~~~~l~V~L~~~~~G~v~~t-e~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~~~~~~~k~~~~~LSlr~s~ 1144 (1152)
++.+.++.|+++.+..||++.+ ++.|+|+. +|...|..+++|.+++|.++. .|++ ++||+|.|+
T Consensus 1077 kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~---~P~~~f~~~~~v~~~~L~vs~--~n~~---leLslr~sr 1141 (1710)
T KOG1070|consen 1077 KVLPGYLILQLPFKVFGRVSFIEDMSDSYSM---TPVEHFTKIQIVYVCVLSVSA--LNKG---LELSLRESR 1141 (1710)
T ss_pred eeccceeEEecCCccccceEEeeehhccccC---ChHHhcccccEEEEEEEEEec--cccc---ceeeccccc
Confidence 9999999999999999988877 99999987 899999999999999999997 6676 999999555
No 2
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=100.00 E-value=1.4e-81 Score=755.06 Aligned_cols=884 Identities=29% Similarity=0.398 Sum_probs=691.5
Q ss_pred CeeecccccCCCCCCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChh--hcccccccc-----cCCCCCccCCCCE
Q 001115 120 PRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPI--LDNEIEANE-----DNLLPTIFHVGQL 192 (1152)
Q Consensus 120 ~~~ve~l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~--~~~~~~~~~-----~~~l~~~f~vGq~ 192 (1152)
+..++.+....+.+||...|+|+++.+.... .+ ..++...+.+ ...+..+++ ..-....|.+|+.
T Consensus 48 ~~e~~kv~~E~~~e~l~~~~~vke~~~~~~~--~~------k~vk~~~s~~s~~~~~~~~~~k~~~~~~~~~k~isPG~~ 119 (1710)
T KOG1070|consen 48 PLEIEKVEEEAFIEGLTGFGVVKEVFDDGRP--KK------KTVKKSASKVSKKFTENFNEEKPEIINAFQLKNISPGML 119 (1710)
T ss_pred hHHHHHHHHHHHhhhhhcccceecccCCCCc--cc------cccccchhhHHHhhhccccccchhhhhhccccccCCcce
Confidence 3446667777888999999999999999875 33 2233332221 011111111 1123457899999
Q ss_pred EEEEEEEEecCCcccceeEEEEecchHHHhcCCCccccCCCCEEEEEEEEEecCeEEEEeCCCceeeeecCCCCCCCCCC
Q 001115 193 VSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGI 272 (1152)
Q Consensus 193 v~~~V~~~~~~~~~~~~~~i~LS~~p~~vn~~l~~~~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~~~~ 272 (1152)
|.|.|.++...+. +..+..+|+|..+|.+++.+.+.+|+.+.+.|.|+||||+++|+|++..+||+..++++. .+.
T Consensus 120 llgvIs~i~~~Dl---~isv~~~l~g~v~~t~lS~~~~~~~~~l~~~v~S~ed~g~~l~~g~~~~~~~~e~~q~pn-~~~ 195 (1710)
T KOG1070|consen 120 LLGVISKINGNDL---KISVKGGLNGYVLNTHLSDEMLAAGEVLDTAVVSIEDHGAILDVGLDEITGFIEKSQFPN-LGA 195 (1710)
T ss_pred eeeeeeeccccce---eEEccCcccccccccccCHhHhhhhhhhccccccccccccchhcCCccccchhhhccCch-hhh
Confidence 9999998876553 568999999999999999999999999999999999999999999999999999988753 334
Q ss_pred cCCCCcEEEEEEEEEeCCCCEEEEccCccccccccccccccccccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEecc
Q 001115 273 DVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIF 352 (1152)
Q Consensus 273 ~l~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~ 352 (1152)
.+++||.+.|.|++++. + .+++|..+.......+++.+.++++.|.||++|+|.|.+|.++|+.++|+++|+|+++..
T Consensus 196 ~lKvGq~l~~~V~k~~s-~-~v~ks~~~~~~~t~~~t~~~~~~~~~LvpGt~vqa~V~sv~~~Gi~~dil~~ftG~l~~~ 273 (1710)
T KOG1070|consen 196 KLKVGQWLRVSVTKSTS-E-RVVKSTKFVEVLTLNPTSCNGLALNDLVPGTMVQAEVQSVEDHGITLDILNGFTGFLDKK 273 (1710)
T ss_pred hcccCceEEEEEEeccC-c-eEEecccceeeecccchhccccchhhcCCcceEEEEecceecCcEEEEecccccceeehh
Confidence 79999999999999876 3 888888888888888888889999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhhcCCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCC
Q 001115 353 HLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPST 432 (1152)
Q Consensus 353 ~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~~~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~ 432 (1152)
||.++. .|..||...|.|+ +++.|.+. ++.++.+....+... |+..
T Consensus 274 hl~~~~-------~~~~~~~~l~~vi--~~s~Rv~~-------------------~~f~~ka~ki~~l~~-~v~a----- 319 (1710)
T KOG1070|consen 274 HLPPFL-------RYFENQEKLGKVI--HKSDRVFV-------------------VDFFDKASKILVLKA-GVDA----- 319 (1710)
T ss_pred hCCchh-------hccccHHHhhccc--chhhheee-------------------echhhccceEEEecC-ccce-----
Confidence 997643 3778888888865 23333221 222222222222222 3333
Q ss_pred CCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEccccccccccccccccCCCCEEEEEEEEEeCC
Q 001115 433 PVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSF 512 (1152)
Q Consensus 433 ~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~ 512 (1152)
+++-+.+.- -. ...+++|..++|||+.+-+++.+...+++.+.++.++..+.+++||.++.+.+ .+..+
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 ------IAPSRIEKV---LS-FEIFKIGNKVKCRVIDVLQMDSLALFTLKESAIEGKFSLVSDVSPRGLLKKPV-SVDTE 388 (1710)
T ss_pred ------EccCCcccc---cc-hhhcccCceEEEEEEEEeeccceEEeecchhhccCceEEEeccCCceEEEecc-cCChh
Confidence 333222221 11 13589999999999999999999999999999999999999999999999998 66655
Q ss_pred eEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEEeCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEE
Q 001115 513 GAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGW 592 (1152)
Q Consensus 513 G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~ 592 (1152)
..|++|+.|+..+...+|+.+|..|..|.|||+.+..+++.+|+| .+..++.|.+..|.++.+ ..+|+
T Consensus 389 ---------~~~l~~L~hv~~f~~a~p~~~~~~~~di~~~vl~~~ak~~~vt~~-v~~~sK~pvis~y~~~~~--~t~~~ 456 (1710)
T KOG1070|consen 389 ---------EVGLSPLPHVLGFEYADPSKKISDGKDIGFRVLTCKAKCGSVTLK-VLCVSKLPVISMYADAVK--LTHGM 456 (1710)
T ss_pred ---------hhhccccchhhceeecCCCcccccccceeeEEeeccceeeeeeee-eeEeecCcceEEEeeccc--cCcch
Confidence 669999999999999999999999999999999998889999999 888888888887877766 66777
Q ss_pred EEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC--CCccccccccCC
Q 001115 593 ITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP--TRVSEDDLVKLG 670 (1152)
Q Consensus 593 V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~--~~~~~~~~l~vG 670 (1152)
+.++. .|++|+-+ +|.++.+||.+|-+.++.+.+|++++. ..+....++++|
T Consensus 457 l~~v~------------q~~v~~~e--------------~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nDI~iG 510 (1710)
T KOG1070|consen 457 LSKVP------------QGMVPIYE--------------VGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVNDIEIG 510 (1710)
T ss_pred hhccc------------cCCCCcee--------------cCCcccCccceecccCcEEEEEEehHhhccccccccccccc
Confidence 77665 45666544 444555555555555555555555432 234455679999
Q ss_pred CEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEeEEEEeecccCceeeecchhhccccc
Q 001115 671 SLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQ 750 (1152)
Q Consensus 671 ~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~~vl~~d~~~~~i~lS~K~sl~~~~~ 750 (1152)
++|.|+|.++++.|+.|.+. .+++.|+||..|++|++.+.+...-++..|.++ |||.++.+.+++.||+|++|++-..
T Consensus 511 ~~V~~~I~~vt~~Gv~v~v~-~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~-RVl~~~~~~~~v~l~~K~slv~~~~ 588 (1710)
T KOG1070|consen 511 QLVPGVIRKVTPQGVEVLVT-FGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKL-RVLSVNRDRNRVALTLKKSLVNTQL 588 (1710)
T ss_pred ceeeeEEEEecCCcEEEEEe-cCceeeecChHhhhhcccccccceeeeccccEE-EEEEEEccCCeeEEEechhhhcccC
Confidence 99999999999999999996 367999999999999999998887777777777 8999999999999999999999988
Q ss_pred cCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 751 QLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 751 ~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
++|.+|+++++|+++.|+|+++.++||||+|+|+++||+|.++|++.|+.+++++|.+||+|.++|.++|++++||.|++
T Consensus 589 plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~ 668 (1710)
T KOG1070|consen 589 PLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGL 668 (1710)
T ss_pred CCccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeC
Q 001115 831 KQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLA 910 (1152)
Q Consensus 831 k~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~ 910 (1152)
+++.|+.+...+..+| |..|.+..+.+...+...++|++.+. ++.|.+...++.
T Consensus 669 r~s~~~~a~~~~~~e~-------------------------~~~g~v~s~~~~~~tkd~viVei~~~-~~~~v~~~~~L~ 722 (1710)
T KOG1070|consen 669 RASSCARACVKRSVEN-------------------------FVKGGVKSLKSIDKTKDSVIVEIVDQ-GITGVGVFGELV 722 (1710)
T ss_pred hhhhhHHHHHHHHHHH-------------------------hhccccccceeehhccccEEEEccCc-ceEEEEEEEEEc
Confidence 9998755443333333 33444444444444444455555442 345555444443
Q ss_pred C-------------------CcccCCCEEEEEEEEEECCCCEEEEEEcccchhhhhcccchhhhhhhccccccccccCCC
Q 001115 911 G-------------------ATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVH 971 (1152)
Q Consensus 911 ~-------------------~~~~~G~~v~a~Vl~vd~~~~~v~LSlk~s~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G 971 (1152)
| ..+.+||.+.++|+.++..+..+.+++++.+... +.++..|
T Consensus 723 dg~v~~~~~~~~kl~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~-------------------~~~l~k~ 783 (1710)
T KOG1070|consen 723 DGSVVVNKVLENKLRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTDLPNN-------------------ATKLLKG 783 (1710)
T ss_pred cCceEEccchhhhhhhcchhheeeecceeEEEEEEeehhhhhhhccccccccch-------------------HHHHhcC
Confidence 2 1357899999999999999999999988877653 3468889
Q ss_pred CEEEEEEEEEecCEEEEEEcCCCceEEEEEecccccc-cCCcCCCCCCCEEEEEEEeecCC-----------CCccEEEE
Q 001115 972 QTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQ-KFPQKQFLNGQSVIATVMALPSS-----------STAGRLLL 1039 (1152)
Q Consensus 972 ~~v~g~V~~i~~~~l~V~l~~~~~~~~~~~~s~~~~~-~~~~~~f~~Gq~v~~~V~~~d~~-----------~~~~~l~l 1039 (1152)
....++|+++.+.+.|+++ ..++++++..++..+. +.+.....-||.|.++..+++.. ...+++.+
T Consensus 784 ~~~~~~v~~is~~~~~~a~--~~~~i~~v~~s~~v~s~~~d~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~ 861 (1710)
T KOG1070|consen 784 SYALALVRSISKEGKFVAF--VSNLIALVKVSHLVDSELDDLTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKF 861 (1710)
T ss_pred chhHHHHHhhhhheeheee--cccccceeeccccccccccccceeeeecccceEEEecChhHHHHHHhhcchhhccceeE
Confidence 9999999999999999999 4458899988887643 33444555679999999988741 11111111
Q ss_pred EecccccccccccccccccCCCcCCcEEEEEEEEEeCCeEEEEeCCCeeEEEEeeeccCCccccccccccCCCCCCEEEE
Q 001115 1040 LLKAISETETSSSKRAKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTA 1119 (1152)
Q Consensus 1040 ~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~V~~i~~~~l~V~L~~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~ 1119 (1152)
..........++..+.++++++.+|.++.|.|++|+|+||+|-|+++.+||+|++|++|+|.+ ...|+++|++||.|+|
T Consensus 862 ~~~~~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~e-itDp~~k~~vG~~I~v 940 (1710)
T KOG1070|consen 862 IKVSSNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHE-ITDPLDKFKVGDGIFV 940 (1710)
T ss_pred EEeccccCCCccccccccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccc-cCChhhhcccCCeEEE
Confidence 110111112233456778999999999999999999999999999999999999999999976 4569999999999999
Q ss_pred EEEeee-cCC-----CCCCCceEEEEeecCCcCCCCc
Q 001115 1120 RIIAKS-NKP-----DMKKSFLWELSIKPSMLTGKWF 1150 (1152)
Q Consensus 1120 ~Vl~~~-~~~-----~~~k~~~~~LSlr~s~~~~~~~ 1150 (1152)
||+|.+ .+. .-++..++|||+|||.++.++|
T Consensus 941 rviG~~D~k~lpith~i~k~~v~ElSvkps~les~~~ 977 (1710)
T KOG1070|consen 941 RVIGGHDVKDLPITHLISKEQVLELSVKPSELESDEF 977 (1710)
T ss_pred EEEcCCccccCccccccchhhhhhhccChhhhccccc
Confidence 999984 211 2233579999999999986665
No 3
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-64 Score=585.24 Aligned_cols=491 Identities=23% Similarity=0.286 Sum_probs=439.5
Q ss_pred ccccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecch
Q 001115 314 ISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1152)
Q Consensus 314 ~~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p 393 (1152)
.+...+.||++|.|+|++|.+.+++|++++...|+||+.+++.... ...|++|+.+.+.|+.+......+.||.+.
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 4677889999999999999999999999999999999999987543 237999999999999999888899999876
Q ss_pred hhhc--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEe
Q 001115 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1152)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~ 471 (1152)
.... |......+..|.+++ ++|...-++ |+.|++. +++||+|.|+++..+++++. -.+|.++.++|+.++
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 5443 655567889999999 567777788 9999996 37999999999987776654 578999999999999
Q ss_pred cCCCeEEEEcccccc----ccccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCC
Q 001115 472 HLEGLATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGA 547 (1152)
Q Consensus 472 ~~~~~~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~ 547 (1152)
..++.+.+|++.... ++....++.+++|++|.|+|++++++|+||+|+ |++|++|.+||||.++.+|++.|++||
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 999999999887665 445677899999999999999999999999999 599999999999999999999999999
Q ss_pred EEEEEEEEE--eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCC
Q 001115 548 ELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCE 625 (1152)
Q Consensus 548 ~V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~ 625 (1152)
+|+|+|+++ +++|+.||+|+++.++|..+ .+.+.+|+.+.|+|+++.+|||||++++|++||+|+|||+|.+...
T Consensus 241 ~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i---~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~ 317 (541)
T COG0539 241 EVKVKVISLDEERGRVSLSLKQLEEDPWEGI---EKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNV 317 (541)
T ss_pred EEEEEEEEEccCCCeEEEEehhcccCcHHHH---hhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCC
Confidence 999999999 79999999999998644332 2355789999999999999999999999999999999999998877
Q ss_pred CCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCC
Q 001115 626 PSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEH 703 (1152)
Q Consensus 626 ~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~h 703 (1152)
|++++++||+|.|+|+++|++++||.||||+.. +||.. .+.+++|+.++|.|.+++++|+||.+ +++++|+++..+
T Consensus 318 P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~l--e~gidG~vh~~d 395 (541)
T COG0539 318 PSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVEL--EGGIDGLVHLSD 395 (541)
T ss_pred HHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEcc--CCCccceEEHHh
Confidence 999999999999999999999999999999875 56654 34589999999999999999999999 788999999999
Q ss_pred cCCccccccccccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEEC
Q 001115 704 LADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFL 782 (1152)
Q Consensus 704 lsd~~~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~ 782 (1152)
++|.....+.. .|+.|+.++ .+|.+|++++++.|+.|++..+||+.. ...++.|+.++|+|+++.++|+||+|.
T Consensus 396 ~sw~~~~~~~~--~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~---~~~~~~~~~v~~~v~~i~~~G~~v~l~ 470 (541)
T COG0539 396 LSWDRPGEEAE--KYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEF---SEKYKKGSVVKGKVKSVKDKGAFVELG 470 (541)
T ss_pred cCccccCcHHH--hhccCcEEEEEEEEEecccceeeeehhhhccCchhhh---HhhccCCCeEEEEEEEEccCceEEEec
Confidence 99865443333 899999999 999999999999999999999998753 356899999999999999999999999
Q ss_pred CCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 783 GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 783 ~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
+++.||++.++++.. .|++||.|.|+|+++|+.++++.||+|...
T Consensus 471 ~~v~G~i~~~~~~~~-------~~~~gd~v~a~v~~id~k~~ki~lSik~~~ 515 (541)
T COG0539 471 GGVEGLIRLSELSRD-------VLKVGDEVEAVVVSIDKKNRKILLSIKALE 515 (541)
T ss_pred Cceeeeeecchhhhh-------hccCCCEEEEEEEEEcCCCCEEEEEechhh
Confidence 999999999999864 899999999999999999999999999864
No 4
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-62 Score=567.25 Aligned_cols=484 Identities=25% Similarity=0.333 Sum_probs=424.4
Q ss_pred ccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEeechh
Q 001115 491 FTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKT 568 (1152)
Q Consensus 491 ~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~ 568 (1152)
.....+.||++|+|+|+++.+.+++|+++...+|+||.++++..+.. ..|++|+.+.+.|+.+ ..+.+.||.+++
T Consensus 14 ~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~---~~~~~gd~v~v~v~~~e~~~g~~~lS~~k~ 90 (541)
T COG0539 14 KSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVE---DVVQVGDEVEVLVLRVEDGEGELVLSRRKA 90 (541)
T ss_pred cchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhcccccc---ceecCCCEEEEEEEEEecCCceEEeeHHHH
Confidence 45678999999999999999999999999999999999999875433 3789999999999999 456899999876
Q ss_pred hhhhhhhHhhhhhhc-cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCC
Q 001115 569 LVKSKLAILSSYAEA-TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPAS 647 (1152)
Q Consensus 569 l~~~~~~~~~~~~~~-~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~ 647 (1152)
... ..|..++++ ..|.++.|.|+...+.|++|++ +|++||+|.|+++..++.++. -.+|+++.++|+++|+++
T Consensus 91 ~~~---~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi-~gvr~FlP~S~v~~r~v~d~~--~~~Gk~~~~kiie~d~~~ 164 (541)
T COG0539 91 ERE---RAWEKLEEAFENGEIVEGKITGKVKGGLTVDI-EGVRAFLPGSLVDVRPVRDLD--PLIGKELEFKILELDKKR 164 (541)
T ss_pred HHH---HhHHHHHHHHhcCCeEEEEEEEEecCcEEEEE-CCEEEeccHHHhccccccccc--ccCCceEEEEEEEEcccc
Confidence 543 455555544 4699999999999999999999 569999999999988877764 369999999999999999
Q ss_pred CEEEEEEeeCCC------CccccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCC
Q 001115 648 RRINLSFMMKPT------RVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPG 721 (1152)
Q Consensus 648 ~ri~lS~k~~~~------~~~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G 721 (1152)
+++.+|.+.... +......+++|++|+|+|++++++|+||+| +|++|+||..||||.+..+| .+.+++|
T Consensus 165 n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi---gGvdGLlHiseiS~~rv~~P--~~vvkvG 239 (541)
T COG0539 165 NNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI---GGVDGLLHISEISWKRVDHP--SEVVKVG 239 (541)
T ss_pred CcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEe---cCeeeEEehhhccccccCCH--HHhcccC
Confidence 999999986543 223356899999999999999999999999 67999999999999776554 6789999
Q ss_pred CeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcccc
Q 001115 722 YEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRA 800 (1152)
Q Consensus 722 ~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~ 800 (1152)
|+|+ +|+.+|.+++||.||+|+++.+||..+- ..+++|+.+.|+|+++++||+||++.+|+.||+|.|+|+|.+..
T Consensus 240 d~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~---~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~ 316 (541)
T COG0539 240 DEVKVKVISLDEERGRVSLSLKQLEEDPWEGIE---KKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKN 316 (541)
T ss_pred CEEEEEEEEEccCCCeEEEEehhcccCcHHHHh---hhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccC
Confidence 9999 9999999999999999999999998653 67889999999999999999999999999999999999999988
Q ss_pred CccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEE
Q 001115 801 DLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEG 880 (1152)
Q Consensus 801 ~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g 880 (1152)
.|++++++||.|.|+|++||++++||.||||++.. +||+.. ...|++|+.++|
T Consensus 317 ~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~------------~pw~~~---------------~~~~~~g~~v~g 369 (541)
T COG0539 317 VPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKE------------NPWEEF---------------ADKHPVGDVVEG 369 (541)
T ss_pred CHHHhcccCCEEEEEEEeeCchhceEEeeehhhhc------------Chhhhh---------------hhhcCCCCeEEE
Confidence 89999999999999999999999999999999865 566433 345899999999
Q ss_pred EEEEEecceEEEEecCCCCeEEEEEeEeeCC-------CcccCCCEEEEEEEEEECCCCEEEEEEcccchhhhhcccchh
Q 001115 881 KVHESNDFGVVVSFEEHSDVYGFITHHQLAG-------ATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNR 953 (1152)
Q Consensus 881 ~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~-------~~~~~G~~v~a~Vl~vd~~~~~v~LSlk~s~~~~~~~~~~~~ 953 (1152)
+|.+++++|+|+.+++ +++|++|.++++. ..|+.|+.++|+|+.+|.+++++.|++|+..-+++.
T Consensus 370 ~v~~~t~~g~fv~le~--gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~------ 441 (541)
T COG0539 370 KVKSITDFGAFVELEG--GIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWE------ 441 (541)
T ss_pred EEeeecccceEEccCC--CccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchh------
Confidence 9999999999999986 6999999999973 278999999999999999999999999985444332
Q ss_pred hhhhhccccccccccCCCCEEEEEEEEEecCEEEEEEcCCCceEEEEEecccccccCCcCCCCCCCEEEEEEEeecCCCC
Q 001115 954 QAQKKKRKREASKDLGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSST 1033 (1152)
Q Consensus 954 ~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~~l~V~l~~~~~~~~~~~~s~~~~~~~~~~~f~~Gq~v~~~V~~~d~~~~ 1033 (1152)
.....++.|+.+.|.|..+++.+++|.|+ ++..|+++.+++... .|++||.|.|+|+++|. .
T Consensus 442 ---------~~~~~~~~~~~v~~~v~~i~~~G~~v~l~--~~v~G~i~~~~~~~~-----~~~~gd~v~a~v~~id~--k 503 (541)
T COG0539 442 ---------EFSEKYKKGSVVKGKVKSVKDKGAFVELG--GGVEGLIRLSELSRD-----VLKVGDEVEAVVVSIDK--K 503 (541)
T ss_pred ---------hhHhhccCCCeEEEEEEEEccCceEEEec--Cceeeeeecchhhhh-----hccCCCEEEEEEEEEcC--C
Confidence 22346999999999999999999999995 456899999888532 89999999999999997 6
Q ss_pred ccEEEEEeccc
Q 001115 1034 AGRLLLLLKAI 1044 (1152)
Q Consensus 1034 ~~~l~l~~~~~ 1044 (1152)
+..+.||.++.
T Consensus 504 ~~ki~lSik~~ 514 (541)
T COG0539 504 NRKILLSIKAL 514 (541)
T ss_pred CCEEEEEechh
Confidence 67788887643
No 5
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.1e-58 Score=565.38 Aligned_cols=496 Identities=20% Similarity=0.256 Sum_probs=435.2
Q ss_pred cccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhh
Q 001115 317 DLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLL 396 (1152)
Q Consensus 317 ~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~ 396 (1152)
..+.+|++|.|+|.++.++|++|++++...|++|..|++... ....|++|+.++|+|+.+++..+++.||.++...
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 446899999999999999999999988899999999998532 2346999999999999999988999999987644
Q ss_pred c--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCC
Q 001115 397 H--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLE 474 (1152)
Q Consensus 397 ~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~ 474 (1152)
. |....+.+..|++++ ++|..+.++ |++|+++ +++||+|.+++++....++. +.+|+++.|+|+.++...
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 555556788999999 688889887 9999997 37999999999987655544 569999999999999999
Q ss_pred CeEEEEccccccc----cccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEE
Q 001115 475 GLATGILKASAFE----GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELV 550 (1152)
Q Consensus 475 ~~~~lS~k~~~~~----~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~ 550 (1152)
+.+.||+++.... +|...++++++|++++|+|+++.++|++|+++ |++|+||.++++|.+..+|.+.|++|++|+
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 23345678999999999999999999999998 999999999999998889999999999999
Q ss_pred EEEEEE--eCCeEEEeechhhhhhhhhHhhhh-hhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCC-CCCCC
Q 001115 551 FRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLD-PGCEP 626 (1152)
Q Consensus 551 ~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~-~~~~~ 626 (1152)
|+|+++ +++++.||+|++..++ |..+ +.+.+|+++.|+|+++.++|+||++.+++.||+|.++++|. ...+|
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 VKVLKFDKEKKRVSLGLKQLGEDP----WEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHP 328 (565)
T ss_pred EEEEEEeCCCCeEEEEEEecccCh----hHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCH
Confidence 999999 5789999999877653 3333 35678999999999999999999999999999999999875 34667
Q ss_pred CCCccCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCc
Q 001115 627 SSMYHVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHL 704 (1152)
Q Consensus 627 ~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hl 704 (1152)
...|++||.|+|+|+++|++++++.||+++.. .+|.. .+.+++|+++.|+|..++++|+||++ .+++.|++|..++
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 77899999999999999999999999998753 34442 34688999999999999999999999 6799999999999
Q ss_pred CCccccccccccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECC
Q 001115 705 ADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLG 783 (1152)
Q Consensus 705 sd~~~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~ 783 (1152)
++... ...+.+.|++|+.++ +|+.+|.++++|.||+|++..+||... .+++++|+++.|+|.++.++|+||++.+
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 87432 123457899999999 899999999999999999998888643 4678999999999999999999999999
Q ss_pred CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 784 RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 784 ~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
++.||+|.+++++.++.++.+.|++||.|+|+|+++|++++|+.||+|....
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 9999999999999999999999999999999999999999999999998643
No 6
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=1.1e-57 Score=565.07 Aligned_cols=490 Identities=18% Similarity=0.269 Sum_probs=415.0
Q ss_pred CCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEc
Q 001115 402 PSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGIL 481 (1152)
Q Consensus 402 ~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~ 481 (1152)
...+..|++++ ++|.++++. ++||+++.+ .+|+|+.+++.. .+++|++++|.|++.+.. + +.||.
T Consensus 316 ~~~~~~G~iV~-G~Vv~i~~~-~v~VdiG~K---~eGiI~~~E~~~--------~~kvGd~i~~~V~~~~~~-~-~~LS~ 380 (863)
T PRK12269 316 FEAPEPGSVRM-GTVVQVNAG-TVFVDIGGK---SEGRVPVEEFEA--------PPKAGDGVRVYVERVTPY-G-PELSK 380 (863)
T ss_pred cccCCCCCEEE-EEEEEEECC-EEEEEeCCC---ceEEeEHHHhcc--------CCCCCCEEEEEEEEEcCC-c-eEEEe
Confidence 45788999999 689999988 899999864 489999988742 379999999999999864 4 77887
Q ss_pred cccc-cccccccccccCCCCEEEEEEEEEe--CCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE-e
Q 001115 482 KASA-FEGLVFTHSDVKPGMVVKGKVIAVD--SFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-K 557 (1152)
Q Consensus 482 k~~~-~~~~~~~~~~l~~G~iv~g~V~~v~--~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v-~ 557 (1152)
+... ...|....+.++.|++|+|+|++++ +.|++|+++.+++||||.+|++.....++. ..+|++++|+|+.+ .
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 7553 2335555677899999999999985 469999998789999999998653333232 35899999999987 2
Q ss_pred ------CCeEEEeechhhhhhhhhH-hhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCc
Q 001115 558 ------SKRITVTHKKTLVKSKLAI-LSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMY 630 (1152)
Q Consensus 558 ------~~~i~LS~K~~l~~~~~~~-~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f 630 (1152)
++++.||+|+.+....... -..++++++|+++.|+|.++.++|+||++ +|++||+|.|+++|.++.+|.+.|
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 2589999998776533222 22355667899999999999999999999 799999999999999998999999
Q ss_pred cCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCcc
Q 001115 631 HVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHL 708 (1152)
Q Consensus 631 ~vGq~v~vrV~~vd~~~~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~ 708 (1152)
++||+++|+|+++|++++++.||+|+.. .+|.. .+.+++|++++|+|++++++|+||++ .+++.|++|.+++||..
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 9999999999999999999999999753 45544 34699999999999999999999999 77999999998888732
Q ss_pred ccccccccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEE
Q 001115 709 EHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTG 787 (1152)
Q Consensus 709 ~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~G 787 (1152)
. ...+.+.|++||+++ +|+.+|.+++++.||+|+...+||+.+ .+++++|++++|+|++++++|+||++.+|++|
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 K-TSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEI---EARYPVGARFTRRIVKVTNAGAFIEMEEGIDG 691 (863)
T ss_pred c-cCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHH---HHhCCCCCEEEEEEEEEecceEEEEeCCCcEE
Confidence 1 112356799999999 999999999999999999999999764 25688999999999999999999999999999
Q ss_pred EEeccCCCCcccc-CccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHHHhhcCcCCCccc
Q 001115 788 FAPRSKAVDGQRA-DLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSEL 866 (1152)
Q Consensus 788 lv~~s~ls~~~~~-~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~ 866 (1152)
|+|.++++|.... .+...|++||.|+|+|+++|++++|+.||+|+... +||+..
T Consensus 692 lIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~------------dpw~~~------------- 746 (863)
T PRK12269 692 FLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSD------------NPWQVF------------- 746 (863)
T ss_pred EEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEeccccc------------ChHHHH-------------
Confidence 9999999996654 44568999999999999999999999999998743 355332
Q ss_pred ccccCcccccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCCC----------cccCCCEEEEEEEEEECCCCEEEE
Q 001115 867 KWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGA----------TVESGSVIQAAILDVAKAERLVDL 936 (1152)
Q Consensus 867 ~~~~~~~vG~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~~----------~~~~G~~v~a~Vl~vd~~~~~v~L 936 (1152)
...|++|++++|+|.+++++|+||+|.+ ++.|++|.+++++. .|++||.|+|+|+++|.+++++.|
T Consensus 747 --~~~~~vG~iV~GkV~~v~~~GvFVeL~~--gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~L 822 (863)
T PRK12269 747 --ANAYGVGSTVEGEVSSVTDFGIFVRVPG--GVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAF 822 (863)
T ss_pred --HhhCCCCCEEEEEEEEEecCeEEEEcCC--CeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEE
Confidence 4568899999999999999999999986 69999999999741 389999999999999999999999
Q ss_pred EEcccchh
Q 001115 937 SLKTVFID 944 (1152)
Q Consensus 937 Slk~s~~~ 944 (1152)
|+|++...
T Consensus 823 Slk~~~~~ 830 (863)
T PRK12269 823 SVRDYQRK 830 (863)
T ss_pred EEechhhH
Confidence 99987654
No 7
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1e-57 Score=560.80 Aligned_cols=495 Identities=22% Similarity=0.298 Sum_probs=427.1
Q ss_pred CCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEcc
Q 001115 403 SHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILK 482 (1152)
Q Consensus 403 ~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k 482 (1152)
..+..|++++ ++|.+++++ |++|+++.+ ..||+|.+++++.. ....|++|++++|+|+.++..++.+.+|++
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 4578999999 689999988 999999743 58999999998532 223599999999999999999999999998
Q ss_pred ccccc-cccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCC
Q 001115 483 ASAFE-GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSK 559 (1152)
Q Consensus 483 ~~~~~-~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~ 559 (1152)
+.... .|....+.++.|++|+|+|.++.++|++|+++ |++||||.+|+++....++. +.+|++++|+|+.+ +++
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 76443 34444567889999999999999999999998 89999999999986554443 56999999999999 678
Q ss_pred eEEEeechhhhhhhhhHh-hhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEE
Q 001115 560 RITVTHKKTLVKSKLAIL-SSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKC 638 (1152)
Q Consensus 560 ~i~LS~K~~l~~~~~~~~-~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~v 638 (1152)
++.||+|+++.......| ..+.++++|+++.|+|+++.++|+||++. |+.||+|.++++|.+..+|.+.|++||+|+|
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 999999998754433333 23567789999999999999999999995 9999999999999988899999999999999
Q ss_pred EEEEEecCCCEEEEEEeeCC-CCcccc-ccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCcccccccccc
Q 001115 639 RIMSSIPASRRINLSFMMKP-TRVSED-DLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKS 716 (1152)
Q Consensus 639 rV~~vd~~~~ri~lS~k~~~-~~~~~~-~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~ 716 (1152)
+|+++|++++++.||++... .+|... ..+++|++++|+|.+++++|++|++ ..++.|++|..+++|... ......
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 99999999999999999753 466543 4789999999999999999999999 779999999999986431 112245
Q ss_pred ccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCC
Q 001115 717 VIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAV 795 (1152)
Q Consensus 717 ~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls 795 (1152)
.|++|+.++ +|+.+|.+++++.||+|+++.+||..+ ..++++|+.+.|+|.+++++|+||++.++++||+|.++++
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 899999999999999999998888653 3567899999999999999999999988999999999999
Q ss_pred Cccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCccc
Q 001115 796 DGQR-ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFII 874 (1152)
Q Consensus 796 ~~~~-~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~v 874 (1152)
|.+. .++.+.|++||.|.|+|+++|++++|+.||+|+... +||. .+...+++
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 8776 788899999999999999999999999999998743 2332 22456889
Q ss_pred ccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCC-------CcccCCCEEEEEEEEEECCCCEEEEEEcccchh
Q 001115 875 GSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG-------ATVESGSVIQAAILDVAKAERLVDLSLKTVFID 944 (1152)
Q Consensus 875 G~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~-------~~~~~G~~v~a~Vl~vd~~~~~v~LSlk~s~~~ 944 (1152)
|++|.|+|.++.++|+||++.+ ++.|+||.+++++ ..|++||.|+|+|+.++.+++++.||+|++...
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 9999999999999999999975 7999999999964 368999999999999999999999999987654
No 8
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=6.9e-58 Score=566.97 Aligned_cols=493 Identities=20% Similarity=0.248 Sum_probs=420.5
Q ss_pred cccccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecc
Q 001115 313 GISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLN 392 (1152)
Q Consensus 313 ~~~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~ 392 (1152)
..++..+.+|++|.|+|.+|.+++++|++++..+|+|+..++.. .+++|++|.|.|+.+++. . +.||..
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 34577889999999999999999999999999999999999832 368999999999998864 3 788876
Q ss_pred hhh--hcCCCCCCCCCCCCeEEceEEEEEe--CCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEE
Q 001115 393 PYL--LHNRAPPSHVKVGDIYDQSKVVRVD--RGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRIL 468 (1152)
Q Consensus 393 p~~--~~~~~~~~~~~~G~iv~~~~V~~v~--~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi 468 (1152)
... ..|+...+++..|++++ ++|.+++ .+ |++|+++. +++||+|.|+++....+++. ..+|+++++.|+
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 443 22444557889999999 6788774 35 89999963 35899999998754444333 358999999999
Q ss_pred EEec-----CCCeEEEEcccccccc----ccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCC
Q 001115 469 GFRH-----LEGLATGILKASAFEG----LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKP 539 (1152)
Q Consensus 469 ~~~~-----~~~~~~lS~k~~~~~~----~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~ 539 (1152)
.++. .++.+.+|.++...+. ....++++++|++|+|+|.++.++|+||+++ |++||||.+|++|.+..+|
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 3468999987654322 1223568999999999999999999999995 8999999999999888899
Q ss_pred CCccccCCEEEEEEEEE--eCCeEEEeechhhhhhhhhHhhhh-hhccCCceEEEEEEEEecCeEEEEEcCCeEEEEecc
Q 001115 540 GKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRS 616 (1152)
Q Consensus 540 ~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~s 616 (1152)
.+.|++|++++|+|+.+ +++++.||+|+.+.++ |..+ +.+.+|+++.|+|+++.++|+||++.+|+.||+|+|
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 REFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDP----WLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHIS 609 (863)
T ss_pred HHhccCCCEEEEEEEEEecCCCeEEEEEeccccch----hhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHH
Confidence 88899999999999999 5789999999876543 3333 346789999999999999999999999999999999
Q ss_pred ccCC-CCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCC
Q 001115 617 ELGL-DPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKG 693 (1152)
Q Consensus 617 el~~-~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~ 693 (1152)
+++| ....+|.+.|++||+|+|+|+++|++++|+.||+++.. ++|.. .+.+++|++++|+|++++++|+||++ .+
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 9998 56778999999999999999999999999999999754 56765 35789999999999999999999999 78
Q ss_pred ceEEEEeCCCcCCccccccccccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEE
Q 001115 694 YSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNI 772 (1152)
Q Consensus 694 ~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i 772 (1152)
+++|+||..++|+.... ......|++||.|+ +|+.+|++++++.||+|+...+||..+ .+++++|+.+.|+|.++
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 99999999999874421 12235799999999 999999999999999999999998753 24578999999999999
Q ss_pred ecceEEEEECCCeEEEEeccCCCCccccCcc---ccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 773 IETGCFVRFLGRLTGFAPRSKAVDGQRADLS---KTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 773 ~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~---~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
+++|+||++.++++||+|.++++|++..++. ..|++||.|.|+|+++|+++++|.||+|+..
T Consensus 764 ~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~~~ 828 (863)
T PRK12269 764 TDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQ 828 (863)
T ss_pred ecCeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEechh
Confidence 9999999999999999999999998765443 4599999999999999999999999999764
No 9
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=1.5e-57 Score=554.73 Aligned_cols=490 Identities=22% Similarity=0.296 Sum_probs=426.2
Q ss_pred cccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhh
Q 001115 317 DLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLL 396 (1152)
Q Consensus 317 ~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~ 396 (1152)
..+.||++|.|+|.++.++|++|++++..+|+++..+++... ..|++||.+.|+|+.+++..+++.||.++...
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 357899999999999999999999999999999999997532 56999999999999999888899999986543
Q ss_pred c--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCC
Q 001115 397 H--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLE 474 (1152)
Q Consensus 397 ~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~ 474 (1152)
. |.....++..|++++ ++|.++.++ |++|+++ +++||+|.++++.....+. .+.+|++++|+|+.++...
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 443346788999999 689999888 9999997 3699999999875432322 3679999999999999999
Q ss_pred CeEEEEcccccccc----ccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEE
Q 001115 475 GLATGILKASAFEG----LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELV 550 (1152)
Q Consensus 475 ~~~~lS~k~~~~~~----~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~ 550 (1152)
+.+.+|+++..... +...++++++|++++|+|.++.++|++|+++ +++|++|.+|++|.+..+|...|++|++++
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 99999998764332 3344678999999999999999999999996 799999999999988888888899999999
Q ss_pred EEEEEE--eCCeEEEeechhhhhhhhhHhhhh-hhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCC-CCCCC
Q 001115 551 FRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLD-PGCEP 626 (1152)
Q Consensus 551 ~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~-~~~~~ 626 (1152)
|+|+++ +++++.||+|+...+ +|..+ +.+.+|+++.|+|+++.++|+||++.+++.||+|.+++++. ...+|
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 34443 35679999999999999999999999999999999999875 34566
Q ss_pred CCCccCCCEEEEEEEEEecCCCEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCc
Q 001115 627 SSMYHVGQVVKCRIMSSIPASRRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHL 704 (1152)
Q Consensus 627 ~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hl 704 (1152)
.+.|++||.++|+|+++|++++++.||+++.. .+|.. .+.+++|++++|+|++++++|+||++ +++++|++|..++
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 67799999999999999999999999998753 34433 34688999999999999999999999 6799999999999
Q ss_pred CCccccccccccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECC
Q 001115 705 ADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLG 783 (1152)
Q Consensus 705 sd~~~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~ 783 (1152)
+|.... ......|++|+.+. +++.+|.++++|.||+|++..+||... .+++++|+.+.|+|.+++++|+||++.+
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 SWDKDG-READHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKF---AAKYKVGSVVKGKVTEIKDFGAFVELPG 468 (516)
T ss_pred cCcccC-CCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhh---hhccCcceEEEEEEEEEecceEEEEcCC
Confidence 975321 12346899999999 999999999999999999998888543 3668999999999999999999999999
Q ss_pred CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 784 RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 784 ~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
++.||+|.++++|.+..++.+.|++||.|+|+|+++|.+++|+.||+|
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 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=1.6e-56 Score=545.87 Aligned_cols=496 Identities=20% Similarity=0.256 Sum_probs=423.0
Q ss_pred cccCCCCCCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChhhcccccccccCCCCCccCCCCEEEEEEEEEecCCc
Q 001115 126 ITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKK 205 (1152)
Q Consensus 126 l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~~~~~~~~~l~~~f~vGq~v~~~V~~~~~~~~ 205 (1152)
|....+.+|+++.|+|.+|++++++|+++++..|++|.+|+++. .+.|++||.+.|.|.++++..+
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 3579999999999998876543
Q ss_pred ccceeEEEEecchHHHhcCCC--ccccCCCCEEEEEEEEEecCeEEEEeCCCceeeeecCCCCCCC--CCCcCCCCcEEE
Q 001115 206 EIGKRKIWLSLRLSLLYKGLS--LETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAEN--SGIDVKPGLLLQ 281 (1152)
Q Consensus 206 ~~~~~~i~LS~~p~~vn~~l~--~~~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~--~~~~l~~G~~~~ 281 (1152)
++.||..+....+.|. ..++.+|+++.|.|.++.++||+||+| +++||||.+++... ......+|+.+.
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 7999999877665555 456789999999999999999999998 89999999987521 233578999999
Q ss_pred EEEEEEeCCCCEEEEccCccccccccccccccccccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCC
Q 001115 282 GVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTT 361 (1152)
Q Consensus 282 ~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~ 361 (1152)
|.|+.++..++.+.||..+. +..+.. ......++.+.+|+.+.|+|.++.++|++|++++ ++|++|..++++... .
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 FKIIKLDQKRNNIVVSRRAY-LEEERS-QAREELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRV-K 225 (516)
T ss_pred EEEEEEECCCCcEEEEHHHH-HHHHHH-HHHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCC-C
Confidence 99999999989999996322 111111 1122346789999999999999999999999964 999999999998654 4
Q ss_pred CCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhhc-CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceee
Q 001115 362 NWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLH-NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYV 440 (1152)
Q Consensus 362 ~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~~-~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv 440 (1152)
++.+.|++|+.+.|+|+++|+.++++.||++....+ |......+++|++++ ++|+++.+. |+||+++. ++.||+
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 333335688999999 789999887 99999974 469999
Q ss_pred eecccchH-HHhhhccccCCCCEEEEEEEEEecCCCeEEEEccccccccccccccccCCCCEEEEEEEEEeCCeEEEEeC
Q 001115 441 TISDVAEE-EVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFP 519 (1152)
Q Consensus 441 ~~s~~~~~-~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~ 519 (1152)
|+++++|. ...++.+.|++|+.++|+|+++++.++.+.||+++...++|....+++.+|++++|+|+++.++|+||+++
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 23444456999999999999999999999999998777777666678999999999999999999999999
Q ss_pred CCeEEEEeCCccccccc-cCCCCccccCCEEEEEEEEE--eCCeEEEeechhhhhhhhhHhhhh-hhccCCceEEEEEEE
Q 001115 520 GGVKALCPLPHMSEFEI-VKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSY-AEATDRLITHGWITK 595 (1152)
Q Consensus 520 ~~v~g~vp~~hls~~~~-~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~-~~~~~G~~~~G~V~~ 595 (1152)
++++|+||.+|++|... .++...|++|+.|+|+|+++ ++++|.||+|++..++ |..+ +++.+|+++.|+|++
T Consensus 381 ~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p----~~~~~~~~~~G~~v~g~V~~ 456 (516)
T TIGR00717 381 GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENP----WEKFAAKYKVGSVVKGKVTE 456 (516)
T ss_pred CCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCc----hhhhhhccCcceEEEEEEEE
Confidence 99999999999998643 45667899999999999999 5789999999876543 3333 456789999999999
Q ss_pred EecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 596 IEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 596 i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
+.++|+||++.+++.||+|.+++++.+..++.+.|++||.++++|+++|++++++.||+|
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 999999999999999999999999988888999999999999999999999999999985
No 11
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=1.6e-49 Score=475.14 Aligned_cols=401 Identities=20% Similarity=0.256 Sum_probs=346.1
Q ss_pred ccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEEeCCeEEEeechhhhhhhh
Q 001115 495 DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKL 574 (1152)
Q Consensus 495 ~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~LS~K~~l~~~~~ 574 (1152)
.+.+|++|+|+|+++++.|++|+++.+.+|+||..|+++.. ....|++|++|+|+|+.++.+.+.||.+....
T Consensus 31 ~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~---~~~~~~~G~~i~~~Vi~~~~~~~~lS~~~~~~---- 103 (491)
T PRK13806 31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD---GELTVAVGDEVELYVVSVNGQEIRLSKALSGQ---- 103 (491)
T ss_pred cCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc---ccccccCCCEEEEEEEEEcCCEEEEEhHHhhh----
Confidence 48899999999999999999999998999999999987532 23458999999999999966679999764321
Q ss_pred hHhhhh-hhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 575 AILSSY-AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 575 ~~~~~~-~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
..|..+ +.+..|+++.|+|.++.++|++|++ +|++||+|.|++++.+..++.. .+|++++|+|+++|++++++.||
T Consensus 104 ~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i-~g~~~flP~s~~~~~~~~~~~~--~vG~~i~~~V~~id~~~~~v~lS 180 (491)
T PRK13806 104 GGAAMLEEAYENGVPVEGKVTGTCKGGFNVEV-LGRRAFCPVSQIDLRYVEDPES--YVGQTFQFLITRVEENGRNIVVS 180 (491)
T ss_pred hhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEE-CCEEEEEEHHHhccccCCChHH--cCCCeEEEEEEEEECCCCeEEEE
Confidence 233333 3346899999999999999999998 5899999999999887777765 39999999999999999999999
Q ss_pred EeeCCC-----Ccc-ccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEe-E
Q 001115 654 FMMKPT-----RVS-EDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-Q 726 (1152)
Q Consensus 654 ~k~~~~-----~~~-~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~-~ 726 (1152)
++.... .+. ....+++|++++|+|+++.++|++|++ .+++.|+||..+++|.+... +.+.|++||.++ +
T Consensus 181 rk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l--~~gv~g~v~~sels~~~~~~--~~~~~~vGd~i~vk 256 (491)
T PRK13806 181 RRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVEL--APGVEGMVHISELSWSRVQK--ADEAVSVGDTVRVK 256 (491)
T ss_pred eehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEc--CCCcEEEEEHHHCCCccccC--hhHhcCCCCEEEEE
Confidence 986532 111 134689999999999999999999999 77899999999999865433 356799999999 9
Q ss_pred EEEeeccc----CceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCC-ccccC
Q 001115 727 LLVLDNES----SNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD-GQRAD 801 (1152)
Q Consensus 727 vl~~d~~~----~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~-~~~~~ 801 (1152)
|+.+|.++ +++.||+|++..+||..+ .+++++|+.+.|+|++++++|+||++.+++.||+|.++++| .++.+
T Consensus 257 Vl~id~~~~~~~~ri~lS~K~~~~~p~~~~---~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~ 333 (491)
T PRK13806 257 VLGIERAKKGKGLRISLSIKQAGGDPWDTV---GDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNK 333 (491)
T ss_pred EEEEecccCCcceEEEEEehhhhcccchhh---hccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCC
Confidence 99999876 469999999999998754 46789999999999999999999999989999999999998 56788
Q ss_pred ccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEEE
Q 001115 802 LSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGK 881 (1152)
Q Consensus 802 ~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g~ 881 (1152)
|.+.|++||.|.|+|+++|++++|+.||+|+... +||+.. ...|.+|++|+|+
T Consensus 334 ~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~------------~p~~~~---------------~~~~~vG~~v~G~ 386 (491)
T PRK13806 334 PEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEG------------DPWADV---------------AERFAPGTTVTGT 386 (491)
T ss_pred HHHcCCCCCEEEEEEEEEEccCCEEEEEEeeccc------------ChhHHh---------------hhhCCCCCEEEEE
Confidence 8899999999999999999999999999998743 455332 4678999999999
Q ss_pred EEEEecceEEEEecCCCCeEEEEEeEeeCC-------CcccCCCEEEEEEEEEECCCCEEEEEEccc
Q 001115 882 VHESNDFGVVVSFEEHSDVYGFITHHQLAG-------ATVESGSVIQAAILDVAKAERLVDLSLKTV 941 (1152)
Q Consensus 882 V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~-------~~~~~G~~v~a~Vl~vd~~~~~v~LSlk~s 941 (1152)
|++++++|+||++.+ ++.|+||.+++++ ..|++||+|+|+|+.+|.+++++.||+|..
T Consensus 387 V~~i~~~G~FV~l~~--gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~ 451 (491)
T PRK13806 387 VEKRAQFGLFVNLAP--GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGA 451 (491)
T ss_pred EEEEecCceEEEcCC--CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence 999999999999975 7999999999974 368999999999999999999999999954
No 12
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=7.8e-50 Score=477.92 Aligned_cols=411 Identities=20% Similarity=0.288 Sum_probs=356.2
Q ss_pred CCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEccc
Q 001115 404 HVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKA 483 (1152)
Q Consensus 404 ~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~ 483 (1152)
.+..|++++ ++|.+++++ |++|+++.+ ..||||.+++.+... ...+++|++++|+|++++. +.+.||.+.
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---VDGVVDRAELLDADG---ELTVAVGDEVELYVVSVNG--QEIRLSKAL 100 (491)
T ss_pred cCCCCCEEE-EEEEEEECC-EEEEEECCC---cEEEEEHHHhcCccc---cccccCCCEEEEEEEEEcC--CEEEEEhHH
Confidence 488999999 689999998 999999753 489999999864321 1348999999999999884 468888664
Q ss_pred cccccccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeE
Q 001115 484 SAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRI 561 (1152)
Q Consensus 484 ~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i 561 (1152)
.....|....+.+..|++++|+|+++.+.|++|++. |+.||+|.+|+++....+|.. + +|++++|+|+.+ +++++
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 433455555778899999999999999999999998 899999999999876666654 3 999999999999 56799
Q ss_pred EEeechhhhhhhhhHhhh-hhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEE
Q 001115 562 TVTHKKTLVKSKLAILSS-YAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRI 640 (1152)
Q Consensus 562 ~LS~K~~l~~~~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV 640 (1152)
.||+|+.+.......|.. ++.+++|+++.|+|+++.++|+||++++++.||+|.++++|.+..+|.+.|++||.++|+|
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 999998776544344444 3457899999999999999999999988999999999999998889999999999999999
Q ss_pred EEEecCC----CEEEEEEeeCC-CCccc-cccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCcccccccc
Q 001115 641 MSSIPAS----RRINLSFMMKP-TRVSE-DDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVM 714 (1152)
Q Consensus 641 ~~vd~~~----~ri~lS~k~~~-~~~~~-~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~ 714 (1152)
+++|+++ +|+.||+|+.. ++|.. .+.+++|++++|+|++++++|+||++ .++++|++|..+|++... ....
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 9999976 47999999763 45654 45799999999999999999999999 779999999999887321 1233
Q ss_pred ccccCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccC
Q 001115 715 KSVIKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSK 793 (1152)
Q Consensus 715 ~~~lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ 793 (1152)
.+.+++||.++ +|+.+|.+++++.||+|++..+||..+. +++++|+.++|+|+++++||+||++.+|++||||.++
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 EDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVA---ERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASV 411 (491)
T ss_pred HHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhh---hhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHH
Confidence 56899999999 9999999999999999999999997643 5788999999999999999999999999999999999
Q ss_pred CCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 794 AVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 794 ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|.+..++.+.|++||.|.|+|+++|++++|+.||+++.
T Consensus 412 ~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~ 451 (491)
T PRK13806 412 ISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGA 451 (491)
T ss_pred cCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence 9999888999999999999999999999999999999965
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.1e-44 Score=420.99 Aligned_cols=328 Identities=22% Similarity=0.267 Sum_probs=292.5
Q ss_pred ccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEeechhhh
Q 001115 493 HSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLV 570 (1152)
Q Consensus 493 ~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~l~ 570 (1152)
+..+++|++|+|+|++++++|++|+|+.+++|+||..|+++....+|+..|++|++|+|+|+.+ +.+++.||+|++..
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 4568999999999999999999999998999999999999988889999999999999999999 46799999998764
Q ss_pred hhhhhHhhhhhhcc-CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCE
Q 001115 571 KSKLAILSSYAEAT-DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRR 649 (1152)
Q Consensus 571 ~~~~~~~~~~~~~~-~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~r 649 (1152)
. ..|..++++. .|+++.|+|+++.++|+||++ |++||+|.|++++.+..++.. .+||+|+|+|+++|+++++
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 3 4677787775 799999999999999999999 699999999999887767654 5999999999999999999
Q ss_pred EEEEEeeCCC-----Cc-cccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCe
Q 001115 650 INLSFMMKPT-----RV-SEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYE 723 (1152)
Q Consensus 650 i~lS~k~~~~-----~~-~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~ 723 (1152)
+.||+|.... ++ .....+++|++++|+|++++++|+||+| ++++|+||..+|+|..... +.+.|++||.
T Consensus 183 ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl---ggv~Glv~~Sels~~~v~~--~~~~~kvGd~ 257 (486)
T PRK07899 183 VVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL---GGVDGLVHVSELSWKHIDH--PSEVVEVGQE 257 (486)
T ss_pred EEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHCCCcccCC--HHHhcCCCCE
Confidence 9999985321 11 2235789999999999999999999999 5799999999999865333 3467999999
Q ss_pred Ee-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCc
Q 001115 724 FD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADL 802 (1152)
Q Consensus 724 v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~ 802 (1152)
|+ +|+.+|+++++|.||+|++..+||..+ .+.+++|+++.|+|++++++|+||++.+++.||+|.+++++.++.++
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 999999999999999999999999653 24577899999999999999999999989999999999999888889
Q ss_pred cccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 803 SKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 803 ~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
...|++||.|.|+|+++|.+++|+.||+|+...
T Consensus 335 ~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~ 367 (486)
T PRK07899 335 EQVVQVGDEVFVKVIDIDLERRRISLSLKQANE 367 (486)
T ss_pred cceeCCCCEEEEEEEEEECCCCEEEEEEEEccc
Confidence 999999999999999999999999999998754
No 14
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.4e-42 Score=406.22 Aligned_cols=334 Identities=24% Similarity=0.308 Sum_probs=294.8
Q ss_pred cccccccccCCCCEEEEEEEEEeCCeEEEEe-CCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEe
Q 001115 488 GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQF-PGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVT 564 (1152)
Q Consensus 488 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i-~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS 564 (1152)
+.+.+++++++|++++|+|++++++|++|++ +++++|+||..|+++....+|...|++|++|+|+|+.+ +++++.||
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 3445778899999999999999999999999 77999999999999988889999999999999999999 56689999
Q ss_pred echhhhhhhhhHhhhhhhc-cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEE
Q 001115 565 HKKTLVKSKLAILSSYAEA-TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSS 643 (1152)
Q Consensus 565 ~K~~l~~~~~~~~~~~~~~-~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~v 643 (1152)
+|+.... +.|..+.++ ++|+++.|+|+++.++|+||+| +|++||+|.+++++.+..++.. + +||+++|+|+++
T Consensus 87 ~k~~~~~---~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~~~~~~-~-vG~~v~~~Vl~~ 160 (390)
T PRK06676 87 KRRLEAE---KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-F-KGKTLEVKIIEL 160 (390)
T ss_pred HHHhhhh---hhHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccCCChHH-c-CCCEEEEEEEEE
Confidence 9986432 456665443 6899999999999999999999 6889999999999887777764 3 999999999999
Q ss_pred ecCCCEEEEEEeeCCC-----Cc-cccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccc
Q 001115 644 IPASRRINLSFMMKPT-----RV-SEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSV 717 (1152)
Q Consensus 644 d~~~~ri~lS~k~~~~-----~~-~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~ 717 (1152)
|++++++.||++.... .+ .....+++|++++|+|.+++++|+||.+ +++.|+||..++++.+.. .+.+.
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---GGVDGLVHISELSHERVE--KPSEV 235 (390)
T ss_pred ECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe---CCeEEEEEHHHcCccccC--CHHHh
Confidence 9999999999986422 11 1235689999999999999999999999 579999999999985432 23567
Q ss_pred cCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCC
Q 001115 718 IKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD 796 (1152)
Q Consensus 718 lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~ 796 (1152)
+++|+.++ +|+.+|.+++++.||+|+.+.+||..+ ++++++|+.+.|+|++++++|+||++.+++.||+|.+++++
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 99999999 999999999999999999998888654 46799999999999999999999999999999999999999
Q ss_pred ccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 797 GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 797 ~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
.+..++...|++||.|.|+|+++|++++|+.||+++...
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 888888889999999999999999999999999998754
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.9e-40 Score=388.53 Aligned_cols=329 Identities=23% Similarity=0.265 Sum_probs=287.7
Q ss_pred cccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchh
Q 001115 315 SIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPY 394 (1152)
Q Consensus 315 ~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~ 394 (1152)
++..+.+|++|.|+|.+|.++|++|+++..+.|+||..|+++... .++.+.|++|+.|+|+|+.+++..+++.||+++.
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 356789999999999999999999999889999999999998554 3577889999999999999999889999999976
Q ss_pred hhc--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEec
Q 001115 395 LLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRH 472 (1152)
Q Consensus 395 ~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~ 472 (1152)
... |....+.+..|++++ ++|.++.++ |++|+++ ++||+|.|++++.++.++.. .+|+.++|+|+.++.
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 433334567899999 689999987 9999994 58999999999876655543 599999999999999
Q ss_pred CCCeEEEEcccccc----ccccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCE
Q 001115 473 LEGLATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAE 548 (1152)
Q Consensus 473 ~~~~~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~ 548 (1152)
..+.+.||++.... ..+...+.++++|++++|+|++++++|+||+++ +++||||.+|++|.+..+|.+.|++|++
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 234445678999999999999999999999996 7999999999999888899889999999
Q ss_pred EEEEEEEE--eCCeEEEeechhhhhhhhhHhhhhh-hccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCC
Q 001115 549 LVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYA-EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCE 625 (1152)
Q Consensus 549 V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~-~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~ 625 (1152)
|+|+|+.+ ++++|.||+|+...++ |..+. ...+|+++.|+|+++.++|+||++.+|+.||+|++++++.+..+
T Consensus 258 V~vkVl~iD~e~~rI~LSlK~~~~dP----w~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~ 333 (486)
T PRK07899 258 VTVEVLDVDMDRERVSLSLKATQEDP----WQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEV 333 (486)
T ss_pred EEEEEEEEECCCCEEEEEEeeccccc----hhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccC
Confidence 99999999 5789999999887653 44444 35679999999999999999999998999999999999888888
Q ss_pred CCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 626 PSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 626 ~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+.+.|++||.|+|+|+++|++++|+.||+|+..
T Consensus 334 ~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~ 366 (486)
T PRK07899 334 PEQVVQVGDEVFVKVIDIDLERRRISLSLKQAN 366 (486)
T ss_pred ccceeCCCCEEEEEEEEEECCCCEEEEEEEEcc
Confidence 888999999999999999999999999999753
No 16
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=1.4e-38 Score=393.48 Aligned_cols=333 Identities=23% Similarity=0.275 Sum_probs=294.7
Q ss_pred ccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEeec
Q 001115 489 LVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHK 566 (1152)
Q Consensus 489 ~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K 566 (1152)
|....+.+++|++++|+|.+++++|++|+++++.+|++|..|+++....+|.+.|++|++|+|+|+.+ +.+++.||+|
T Consensus 293 ~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k 372 (647)
T PRK00087 293 MNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKK 372 (647)
T ss_pred HHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEee
Confidence 44567789999999999999999999999998999999999999988889999999999999999999 5789999999
Q ss_pred hhhhhhhhhHhhhhhh-ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEec
Q 001115 567 KTLVKSKLAILSSYAE-ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIP 645 (1152)
Q Consensus 567 ~~l~~~~~~~~~~~~~-~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~ 645 (1152)
+.... ..|..+.+ +.+|+++.|+|+++.++|+||+++ +++||+|.+++++.+..+++. .+|++++|+|+++|+
T Consensus 373 ~~~~~---~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d~~~--~vG~~v~v~Vl~vd~ 446 (647)
T PRK00087 373 EADRE---KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLSE--YKGQELEVKIIEFNR 446 (647)
T ss_pred hhcch---hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCCHHH--hCCCEEEEEEEEEEc
Confidence 87543 33555544 468999999999999999999995 699999999999887777754 399999999999999
Q ss_pred CCCE-EEEEEeeCCC-----C-ccccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCcccccccccccc
Q 001115 646 ASRR-INLSFMMKPT-----R-VSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVI 718 (1152)
Q Consensus 646 ~~~r-i~lS~k~~~~-----~-~~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~l 718 (1152)
++++ +.+|++.... + ....+++++|+++.|+|.++.++|+||++ ++++|+||..+++|.+.. ...+.|
T Consensus 447 e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l---~gv~Gll~~sels~~~~~--~~~~~~ 521 (647)
T PRK00087 447 KRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVE--KPSDVL 521 (647)
T ss_pred CCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE---CCEEEEEEHHHcCccccC--CHHHhc
Confidence 9998 9999987531 1 12234688999999999999999999999 689999999999986543 235679
Q ss_pred CCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCc
Q 001115 719 KPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG 797 (1152)
Q Consensus 719 k~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~ 797 (1152)
++|+.++ +|+.+|++++++.||+|+.+.+||..+ .+++++|+.+.|.|++++++|+||++.+++.||+|.+++++.
T Consensus 522 ~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~---~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~ 598 (647)
T PRK00087 522 KVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENV---EEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK 598 (647)
T ss_pred CCCCEEEEEEEEEECCCCEEEEEeeccccChhhhh---hhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc
Confidence 9999999 999999999999999999999998764 356789999999999999999999999999999999999999
Q ss_pred cccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 798 QRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 798 ~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
+..++...|++||.|+|+|+++|++++|+.||+|....
T Consensus 599 ~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~ 636 (647)
T PRK00087 599 RIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEE 636 (647)
T ss_pred ccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence 99999999999999999999999999999999998743
No 17
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.8e-38 Score=369.74 Aligned_cols=331 Identities=22% Similarity=0.317 Sum_probs=288.0
Q ss_pred cccccCCCcEEEEEEEEEeCCeEEEEe-CCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecch
Q 001115 315 SIDLLVPGMMVSTRVQSILENGVMLSF-LTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1152)
Q Consensus 315 ~~~~l~pG~~V~g~V~~v~~~Gl~v~~-~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p 393 (1152)
++..+.+|++|.|+|.++.++|++|++ ++.++|++|..|+++... .++...|++|+.++|+|+.++...+++.||+++
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 567789999999999999999999999 778999999999987644 356778999999999999999988899999997
Q ss_pred hhhc--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEe
Q 001115 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1152)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~ 471 (1152)
.... |......+..|+++. ++|.++.++ |++|+++ ++.||+|.+++++....++.. + +|+.++|+|++++
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 433345678999999 689999887 9999995 259999999999876555543 4 9999999999999
Q ss_pred cCCCeEEEEccccccc----cccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCC
Q 001115 472 HLEGLATGILKASAFE----GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGA 547 (1152)
Q Consensus 472 ~~~~~~~lS~k~~~~~----~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~ 547 (1152)
..++.+.+|++..... .+...+.++++|++++|+|+++.++|+||+++ +++|+||.+|++|....+|.+.|++|+
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 9999999999875432 33445678999999999999999999999996 799999999999987788888899999
Q ss_pred EEEEEEEEE--eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCC
Q 001115 548 ELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCE 625 (1152)
Q Consensus 548 ~V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~ 625 (1152)
.|+|+|+.+ +++++.||+|+.+.+++.. .++++++|+++.|+|+++.++|+||++.+|+.||+|.|++++.+..+
T Consensus 241 ~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~---~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~ 317 (390)
T PRK06676 241 EVEVKVLSIDWETERISLSLKDTLPGPWEG---VEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIAT 317 (390)
T ss_pred EEEEEEEEEeCCCCEEEEEEeecccCcccc---chhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCC
Confidence 999999999 5789999999887654322 23457889999999999999999999999999999999999888778
Q ss_pred CCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 626 PSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 626 ~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+.+.|++||.|+|+|+++|++++++.||+++..
T Consensus 318 ~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~ 350 (390)
T PRK06676 318 PSEVLEEGQEVKVKVLEVNEEEKRISLSIKALE 350 (390)
T ss_pred hhhccCCCCEEEEEEEEEECCCCEEEEEEEecc
Confidence 888999999999999999999999999999754
No 18
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=2.7e-36 Score=373.13 Aligned_cols=332 Identities=24% Similarity=0.300 Sum_probs=289.9
Q ss_pred ccccccCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecch
Q 001115 314 ISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393 (1152)
Q Consensus 314 ~~~~~l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p 393 (1152)
.+++.+.+|++|.|+|.++.++|++|++++...|++|..++++... .++.+.|++|+.++|+|+.++..++++.||+++
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 4678899999999999999999999999999999999999997543 457788999999999999999888999999987
Q ss_pred hhhc--CCCCCCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEe
Q 001115 394 YLLH--NRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFR 471 (1152)
Q Consensus 394 ~~~~--~~~~~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~ 471 (1152)
.... |....+.+..|+++. ++|.++.++ |++++++. +.||+|.+++++....++.+ | +|+.++|+|+.++
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 6432 333345678999999 678888887 99999973 69999999999876666543 4 9999999999999
Q ss_pred cCCCe-EEEEcccccc----ccccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccC
Q 001115 472 HLEGL-ATGILKASAF----EGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVG 546 (1152)
Q Consensus 472 ~~~~~-~~lS~k~~~~----~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG 546 (1152)
..++. +.+|++.... .++...++++++|+++.|+|.++.++|+||++ ++++|++|.++++|.+..+|.+.|++|
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 9999987642 23345567899999999999999999999999 699999999999998888888899999
Q ss_pred CEEEEEEEEE--eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCC
Q 001115 547 AELVFRVLGV--KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGC 624 (1152)
Q Consensus 547 ~~V~~rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~ 624 (1152)
+.|+|+|+++ +++++.||+|+.+.+++... .+++++|+++.|+|+++.++|+||++.+++.||+|.+++++.+..
T Consensus 525 d~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~---~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~ 601 (647)
T PRK00087 525 DEIKVYILDIDKENKKLSLSLKKLLPDPWENV---EEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID 601 (647)
T ss_pred CEEEEEEEEEECCCCEEEEEeeccccChhhhh---hhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccC
Confidence 9999999999 57899999999887644322 245678999999999999999999999999999999999998888
Q ss_pred CCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 625 EPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 625 ~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
++.+.|++||.|+|+|+++|++++++.+|++...
T Consensus 602 ~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~ 635 (647)
T PRK00087 602 KPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 635 (647)
T ss_pred CHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 8888999999999999999999999999998753
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.1e-32 Score=311.16 Aligned_cols=237 Identities=22% Similarity=0.288 Sum_probs=213.9
Q ss_pred ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC--CC
Q 001115 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP--TR 660 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~--~~ 660 (1152)
+++|+++.|+|+++.++|+||+|+++..||+|.+++++.++.++.+.|++||+++|+|+++|++++++.||+|... ..
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~ 108 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRA 108 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhH
Confidence 6789999999999999999999988899999999999998889999999999999999999999999999999753 34
Q ss_pred ccccccc-cCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEe-EEEEeecccCcee
Q 001115 661 VSEDDLV-KLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVLDNESSNLL 738 (1152)
Q Consensus 661 ~~~~~~l-~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~-~vl~~d~~~~~i~ 738 (1152)
|.....+ ..|++|+|+|+.+.++|++|++ ++++||||.+|+|+... . ...+|+.++ +|+.+|++++++.
T Consensus 109 w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l---~Gv~gfip~s~ls~~~~-----~-~~~vG~~i~~kVl~id~~~~~i~ 179 (318)
T PRK07400 109 WERVRQLQKEDATVRSEVFATNRGGALVRI---EGLRGFIPGSHISTRKP-----K-EELVGEELPLKFLEVDEERNRLV 179 (318)
T ss_pred HHHHHHhccCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHcCccCC-----c-cccCCCEEEEEEEEEEcccCEEE
Confidence 4443334 4689999999999999999999 69999999999998532 1 234999999 9999999999999
Q ss_pred eecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEE
Q 001115 739 LSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILD 818 (1152)
Q Consensus 739 lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~ 818 (1152)
||+|+.+.+. .+.++++|+++.|+|+++++||+||++ +++.||+|.++++|.+..++.+.|++||.|+|+|++
T Consensus 180 lS~K~~~~~~------~~~~~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~ 252 (318)
T PRK07400 180 LSHRRALVER------KMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIID 252 (318)
T ss_pred EEhhHhhhhh------hhccCCCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEE
Confidence 9999888653 257899999999999999999999998 689999999999999999999999999999999999
Q ss_pred EeCCCCeEEEEeecccc
Q 001115 819 VNSETGRITLSLKQSCC 835 (1152)
Q Consensus 819 vd~e~~ri~LSlk~~~~ 835 (1152)
+|.+++|+.||+|+...
T Consensus 253 iD~e~~rI~LS~K~l~~ 269 (318)
T PRK07400 253 LDAERGRISLSTKQLEP 269 (318)
T ss_pred EeCCCCEEEEEEecccc
Confidence 99999999999999854
No 20
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=3.2e-30 Score=291.05 Aligned_cols=243 Identities=19% Similarity=0.303 Sum_probs=213.6
Q ss_pred ccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEeechhhhhh
Q 001115 495 DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKTLVKS 572 (1152)
Q Consensus 495 ~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~l~~~ 572 (1152)
.+++|++|+|+|+++.++|++|+|+++.+||||.+++++....+|...|++|++++|+|+++ +.+++.||+|+....
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 568999999986432
Q ss_pred hhhHhhhhhhcc-CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 573 KLAILSSYAEAT-DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 573 ~~~~~~~~~~~~-~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
..|..+.+++ .|.++.|+|+++.++|+||++ +|++||+|.|++++.. +.+. .+|+.+.|+|+++|++++++.
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 4577776666 589999999999999999999 7999999999999863 3333 499999999999999999999
Q ss_pred EEEeeCCCCccccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEe-EEEEe
Q 001115 652 LSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFD-QLLVL 730 (1152)
Q Consensus 652 lS~k~~~~~~~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~-~vl~~ 730 (1152)
||+|+... .....++++|+++.|+|++++++|+||++ +++.|+||...+++.+.. .+.+.|++||.++ +++.+
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---GGVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDL 253 (318)
T ss_pred EEhhHhhh-hhhhccCCCCCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEE
Confidence 99986532 22356799999999999999999999999 579999999999886532 3457899999999 99999
Q ss_pred ecccCceeeecchhhcccccc
Q 001115 731 DNESSNLLLSAKYSLINSAQQ 751 (1152)
Q Consensus 731 d~~~~~i~lS~K~sl~~~~~~ 751 (1152)
|.+++++.||+|+...+||+.
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
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.44 E-value=3.5e-13 Score=149.46 Aligned_cols=126 Identities=20% Similarity=0.187 Sum_probs=105.1
Q ss_pred ccCC-CCCEEEEEEEEEecceEEEEEC--CCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 757 SHIH-PNSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 757 ~~~~-~G~~v~G~V~~i~~~GvfV~~~--~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++++ +|+++.|.|++|.+||+||++. +|+.||+|.|+++|.++.++.+.+++||.|.|+|++||+++++|.||+|+.
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 3566 7999999999999999999995 799999999999999999999999999999999999999999999999998
Q ss_pred ccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEEEEEEEec-ceEEEE-ec---CCCCeEEEEEeEe
Q 001115 834 CCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESND-FGVVVS-FE---EHSDVYGFITHHQ 908 (1152)
Q Consensus 834 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~-~g~~v~-l~---~~~~v~G~i~~s~ 908 (1152)
.. ++|+.. ...|+.|++|+++|..+.+ +|++++ +- ......++.|.++
T Consensus 92 ~~------------~pw~~~---------------~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~ 144 (319)
T PTZ00248 92 SP------------EDIEAC---------------EEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALD 144 (319)
T ss_pred cc------------chHHHH---------------HHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHH
Confidence 65 466443 4578999999999999955 898664 00 0013456666665
Q ss_pred e
Q 001115 909 L 909 (1152)
Q Consensus 909 l 909 (1152)
.
T Consensus 145 a 145 (319)
T PTZ00248 145 A 145 (319)
T ss_pred H
Confidence 4
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=1.6e-13 Score=127.64 Aligned_cols=77 Identities=30% Similarity=0.486 Sum_probs=73.5
Q ss_pred cCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 758 HIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
.+++|++++|.|+.|++||+||+|.++-+||+|+|++.+.|++|..+++.+||.|.|+|+++|. ++++.||+|....
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 9999999998744
No 23
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.41 E-value=2.8e-11 Score=127.85 Aligned_cols=214 Identities=17% Similarity=0.159 Sum_probs=163.1
Q ss_pred ccCCCEEEEEEEEEeCCcEEEEEeeCC-ceEEEEeCCCcCCccccccccccccCCCCeEeEEEEeecccCceeeecchhh
Q 001115 667 VKLGSLVSGVVDVVTPNAVVVYVIAKG-YSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSL 745 (1152)
Q Consensus 667 l~vG~iv~g~V~~v~~~g~~V~l~~~~-~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~~vl~~d~~~~~i~lS~K~sl 745 (1152)
..+|++.+..|.+.++.|+|+.= ++ +-.-++|....- ...+.+||.++..+..|.+.+ +++|.+.
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~--~~~~~~ilL~k~~~~---------~~e~evGdev~vFiY~D~~~r-l~aTt~~-- 68 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDA--GEDGTTILLPKSEPE---------EDELEVGDEVTVFIYVDSEDR-LIATTRE-- 68 (287)
T ss_pred ccccceEEEEEEEeeceeEEEec--CCCceEEeccccCCc---------CCccccCcEEEEEEEECCCCc-eeheeec--
Confidence 57899999999999999999976 22 224444333221 235889999998888887754 6666542
Q ss_pred ccccccCCCccccCCCCCEEEEEEEEEe-cceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCC
Q 001115 746 INSAQQLPSDASHIHPNSVVHGYVCNII-ETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETG 824 (1152)
Q Consensus 746 ~~~~~~~~~~~~~~~~G~~v~G~V~~i~-~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ 824 (1152)
-.+.+|.--.+.|..+. +.|+||++.=.-+-++|.++++... +--+++|+.+.|+ +.+|.+ +
T Consensus 69 -----------p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~wpq~Gd~l~v~-l~~Dkk-~ 131 (287)
T COG2996 69 -----------PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SLWPQKGDKLLVY-LYVDKK-G 131 (287)
T ss_pred -----------ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc----ccCCCCCCEEEEE-EEEccC-C
Confidence 13678999999999998 8999999865578899999886421 2237899999998 557864 4
Q ss_pred eEEEEeeccccCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcc---cccEEEEEEEEEecceEEEEecCCCCeE
Q 001115 825 RITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFI---IGSVIEGKVHESNDFGVVVSFEEHSDVY 901 (1152)
Q Consensus 825 ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~---vG~~v~g~V~~i~~~g~~v~l~~~~~v~ 901 (1152)
||.-.++.... ++.+ ..... -++.|.|+|....+.|.|+-+++ +..
T Consensus 132 Ri~g~~a~~~~-----------------l~~l------------~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~--~~~ 180 (287)
T COG2996 132 RIWGTLAIEKI-----------------LENL------------ATPAYNNLKNQEVDATVYRLLESGTFVITEN--GYL 180 (287)
T ss_pred cEEEEecchhH-----------------HHhc------------CCccchhhhcCeeeeEEEEEeccceEEEEcC--CeE
Confidence 99888764421 0111 11222 39999999999999999988854 799
Q ss_pred EEEEeEeeCCCcccCCCEEEEEEEEEECCCCEEEEEEcccchh
Q 001115 902 GFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFID 944 (1152)
Q Consensus 902 G~i~~s~l~~~~~~~G~~v~a~Vl~vd~~~~~v~LSlk~s~~~ 944 (1152)
|+||.+++. ..++.|+.++++|+++.. ++.++||++|-..+
T Consensus 181 GfIh~sEr~-~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E 221 (287)
T COG2996 181 GFIHKSERF-AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHE 221 (287)
T ss_pred EEEcchhhc-ccccCCceEEEEEEEEcc-CCeeecccccccHH
Confidence 999999986 678999999999999976 89999999996544
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=99.39 E-value=9.4e-13 Score=116.66 Aligned_cols=71 Identities=25% Similarity=0.386 Sum_probs=66.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCc---cccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADL---SKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~---~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
+++|+.+.|+|++++++|+||++.++++||+|.++++|.++.++ .+.|++||.|.|+|+++|++++|+.||
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 47899999999999999999999999999999999999887765 589999999999999999999999886
No 25
>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=99.38 E-value=1.5e-12 Score=115.31 Aligned_cols=70 Identities=47% Similarity=0.783 Sum_probs=64.2
Q ss_pred ccCCCCEEEEEEEEEecCeEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEEeCCCCEEEEccCc
Q 001115 229 TVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDP 300 (1152)
Q Consensus 229 ~l~~g~~l~~~V~svedhG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~~~~v~ls~~~ 300 (1152)
||.+|++++|+|+|||||||+||||+.+++||||+++++.. ..+++||.+.|.|++++.+++.+.||+.+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 58899999999999999999999999999999999998643 37999999999999999999999999743
No 26
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=3.5e-12 Score=112.87 Aligned_cols=71 Identities=23% Similarity=0.287 Sum_probs=65.8
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEC-CCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 758 HIHPNSVVHGYVCNIIETGCFVRFL-GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~GvfV~~~-~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
++++|++++|+|++|.++|+||+|. ++++||+|.++++|. ..|++||.+.|+|+++|++++++.||+|+..
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 4789999999999999999999995 699999999999875 6899999999999999999999999999763
No 27
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.34 E-value=5.9e-13 Score=147.64 Aligned_cols=144 Identities=18% Similarity=0.270 Sum_probs=117.7
Q ss_pred cccC-CCCEEEEEEEEEeCCeEEEEeC--CCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCCeEEEeechh
Q 001115 494 SDVK-PGMVVKGKVIAVDSFGAIVQFP--GGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSKRITVTHKKT 568 (1152)
Q Consensus 494 ~~l~-~G~iv~g~V~~v~~~G~~V~i~--~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~~i~LS~K~~ 568 (1152)
+.++ +|++|.|+|++|.++|+||+|. ++++|+||.+++||.+..+|.+.+++|+++.|+||.+ ++++|.||+|+.
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 4566 7999999999999999999996 6899999999999999999999999999999999999 688999999988
Q ss_pred hhhhhhhHhhhh-hhccCCceEEEEEEEEe-cCeEEEE------EcCCeEEEEeccccCCCCCCCCCCCcc---CCCEEE
Q 001115 569 LVKSKLAILSSY-AEATDRLITHGWITKIE-KHGCFVR------FYNGVQGFAPRSELGLDPGCEPSSMYH---VGQVVK 637 (1152)
Q Consensus 569 l~~~~~~~~~~~-~~~~~G~~~~G~V~~i~-~~G~~V~------~~~gv~Gflp~sel~~~~~~~~~~~f~---vGq~v~ 637 (1152)
..++ |..+ +.+..|++++|+|.++. .+|++++ .....++|.|..+++...+.++.+.|. +++.++
T Consensus 92 ~~~p----w~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~ 167 (319)
T PTZ00248 92 SPED----IEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDIPEEVK 167 (319)
T ss_pred ccch----HHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHH
Confidence 7763 3333 34568999999999996 4999998 456788999998886554555554444 555544
Q ss_pred EEEE
Q 001115 638 CRIM 641 (1152)
Q Consensus 638 vrV~ 641 (1152)
..++
T Consensus 168 ~~l~ 171 (319)
T PTZ00248 168 ESLL 171 (319)
T ss_pred HHHH
Confidence 4443
No 28
>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=99.33 E-value=2.9e-12 Score=120.28 Aligned_cols=90 Identities=40% Similarity=0.590 Sum_probs=72.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChhhccc----------ccccccCCCCCccCCCCEEEEEEEEE
Q 001115 131 ISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNE----------IEANEDNLLPTIFHVGQLVSCIVLQL 200 (1152)
Q Consensus 131 l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~----------~~~~~~~~l~~~f~vGq~v~~~V~~~ 200 (1152)
|++||+|+|+|.+|.+.++.|+||++++|+++++++++.+.... ..+.+...+.+.|++||.|+|.|+++
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 57899999999999999999999999999999999998641110 01111336778999999999999998
Q ss_pred ecCCcccceeEEEEecchHHHh
Q 001115 201 DDDKKEIGKRKIWLSLRLSLLY 222 (1152)
Q Consensus 201 ~~~~~~~~~~~i~LS~~p~~vn 222 (1152)
++.++ ++++|.||++|+++|
T Consensus 81 d~~~~--~~~~i~LSlr~~~vn 100 (100)
T cd05693 81 DKSKS--GKKRIELSLEPELVN 100 (100)
T ss_pred cCCcC--CCcEEEEEecHHHCC
Confidence 76532 246999999999987
No 29
>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=99.32 E-value=4.2e-12 Score=115.64 Aligned_cols=79 Identities=47% Similarity=0.685 Sum_probs=75.1
Q ss_pred CCCccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 752 LPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 752 ~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
++..++++++|+++.|+|+++.++|+||++.+++.||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.|||
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 5567889999999999999999999999999999999999999999888999999999999999999999999999986
No 30
>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=99.31 E-value=6.4e-12 Score=111.16 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=66.4
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcc--ccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ--RADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~--~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
|+.+.|+|+++.++|+||++.++++|++|.++++|.. ..+|.+.|++||.|.|+|+++|++++|+.||++
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 788999999999999999999999999999986
No 31
>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=99.30 E-value=7.9e-12 Score=110.79 Aligned_cols=70 Identities=16% Similarity=0.338 Sum_probs=64.9
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCC---CCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEP---SSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~---~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
++|+++.|+|+++.++|+||++.++++||+|.+++++.+..+| .+.|++||.++|+|+++|++++++.||
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 6799999999999999999999999999999999999876554 478999999999999999999999886
No 32
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.30 E-value=1.7e-12 Score=120.89 Aligned_cols=75 Identities=25% Similarity=0.234 Sum_probs=71.2
Q ss_pred ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+++|+++.|+|++|++||+||+|++|-.||+|+||+...++.+..+++++||.|+|+|+++|. ++++.||++...
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~ 77 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLE 77 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhh
Confidence 468999999999999999999999999999999999999999999999999999999999998 999999998653
No 33
>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=99.29 E-value=1.8e-11 Score=108.84 Aligned_cols=73 Identities=37% Similarity=0.625 Sum_probs=70.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
+++|+++.|+|.++.++|+||++.++++||+|.+++++.+..++...|.+||+|.|+|+++|.+++++.||+|
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 6789999999999999999999999999999999999998999999999999999999999999999999985
No 34
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.28 E-value=5.5e-10 Score=118.23 Aligned_cols=212 Identities=22% Similarity=0.239 Sum_probs=160.8
Q ss_pred CCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEcccc
Q 001115 405 VKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKAS 484 (1152)
Q Consensus 405 ~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~ 484 (1152)
..+|++.. ..|.+.... |+|++=+... -.=++|.++..+ ....+|+.+.+-|.- ..++.+.+|++..
T Consensus 3 ~~iG~~~~-l~V~~~~~~-g~fL~~~~~~--~~ilL~k~~~~~-------~e~evGdev~vFiY~--D~~~rl~aTt~~p 69 (287)
T COG2996 3 IKIGQINS-LEVVEFSDF-GYFLDAGEDG--TTILLPKSEPEE-------DELEVGDEVTVFIYV--DSEDRLIATTREP 69 (287)
T ss_pred ccccceEE-EEEEEeece-eEEEecCCCc--eEEeccccCCcC-------CccccCcEEEEEEEE--CCCCceeheeecc
Confidence 45788887 577777765 9999976432 145667665432 248899999988853 4566777776654
Q ss_pred ccccccccccccCCCCEEEEEEEEEe-CCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEEeCCeEEE
Q 001115 485 AFEGLVFTHSDVKPGMVVKGKVIAVD-SFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITV 563 (1152)
Q Consensus 485 ~~~~~~~~~~~l~~G~iv~g~V~~v~-~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~L 563 (1152)
.+..|+.-.++|+.+. +-|+||+.+-.-+-+||.+|+...+... .++|+++-|++.--.++||.-
T Consensus 70 ----------~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~w----pq~Gd~l~v~l~~Dkk~Ri~g 135 (287)
T COG2996 70 ----------KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLW----PQKGDKLLVYLYVDKKGRIWG 135 (287)
T ss_pred ----------eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccC----CCCCCEEEEEEEEccCCcEEE
Confidence 3678999999999998 7899999987788999998886432222 479999999974446778888
Q ss_pred eechhhhhhhhhHhhhhhhccC---CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEE
Q 001115 564 THKKTLVKSKLAILSSYAEATD---RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRI 640 (1152)
Q Consensus 564 S~K~~l~~~~~~~~~~~~~~~~---G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV 640 (1152)
+++..-. ...-...+.. ++.++|+|.++...|.||=..++..||+|.||.... .+.|+.+++||
T Consensus 136 ~~a~~~~-----l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~--------prlG~~l~~rV 202 (287)
T COG2996 136 TLAIEKI-----LENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE--------PRLGERLTARV 202 (287)
T ss_pred EecchhH-----HHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc--------ccCCceEEEEE
Confidence 8763221 1111123333 999999999999999999999999999999998643 57999999999
Q ss_pred EEEecCCCEEEEEEeeC
Q 001115 641 MSSIPASRRINLSFMMK 657 (1152)
Q Consensus 641 ~~vd~~~~ri~lS~k~~ 657 (1152)
+.+.+ +++|.||+++-
T Consensus 203 i~~re-Dg~lnLSl~p~ 218 (287)
T COG2996 203 IGVRE-DGKLNLSLRPR 218 (287)
T ss_pred EEEcc-CCeeecccccc
Confidence 99987 99999999864
No 35
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.28 E-value=1.1e-11 Score=112.76 Aligned_cols=79 Identities=27% Similarity=0.515 Sum_probs=73.9
Q ss_pred HhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 576 ILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 576 ~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
++..+.++++|+++.|+|+++.++|+||++.+++.||+|.+++++.+..++.+.|++||+++|+|+++|++++++.||+
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 3556778899999999999999999999999999999999999988888899999999999999999999999999985
No 36
>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=1.9e-11 Score=107.51 Aligned_cols=70 Identities=30% Similarity=0.558 Sum_probs=67.0
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
|+++.|+|.++.++|+||+|++++.||+|.+++++.+..++.+.|++||.+.|+|+++|++++++.||+|
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 37
>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=3.1e-11 Score=106.83 Aligned_cols=70 Identities=19% Similarity=0.290 Sum_probs=65.5
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCC--CCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDP--GCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~--~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
|+++.|+|+++.++|+||++.++++||+|.+++++.. ..++.+.|++||.++|+|+++|++++++.||++
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 7889999999999999999999999999999998753 667888999999999999999999999999985
No 38
>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=99.23 E-value=3.6e-11 Score=106.92 Aligned_cols=73 Identities=36% Similarity=0.577 Sum_probs=68.9
Q ss_pred ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
.+.|+++.|+|+++.++|+||++.+++.||+|.+++++....++...|++||+++|+|+++|++++++.||+|
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 4679999999999999999999988999999999999887778889999999999999999999999999975
No 39
>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=99.22 E-value=3.5e-11 Score=105.79 Aligned_cols=70 Identities=44% Similarity=0.725 Sum_probs=66.2
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
|+++.|+|+++.++|+||+|++++.||+|.++++.++..++.+.|++||.++|+|+++|++++++.||++
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 7889999999999999999999999999999998877778888999999999999999999999999985
No 40
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.19 E-value=6.8e-11 Score=104.12 Aligned_cols=69 Identities=23% Similarity=0.334 Sum_probs=64.3
Q ss_pred CceEE-EEEEEE-ecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 586 RLITH-GWITKI-EKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 586 G~~~~-G~V~~i-~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
|+++. |+|+++ .++|+||++.+|++||+|.|++++.+...+.+.|++||.++|+|+++|++++++.||+
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 67887 999998 6999999999999999999999988777788899999999999999999999999995
No 41
>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=99.19 E-value=6.5e-11 Score=103.77 Aligned_cols=69 Identities=26% Similarity=0.473 Sum_probs=65.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
|+++.|+|+++.++|+||++.++++||+|.++++|.+..++.+.|++||.+.|+|+++|++++++.||+
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 789999999999999999999999999999999998888888899999999999999999999999985
No 42
>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=99.18 E-value=6.1e-11 Score=103.63 Aligned_cols=68 Identities=31% Similarity=0.503 Sum_probs=65.2
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
|+.+.|+|+++.++|+||+|.++++||+|.+++++.+..++.+.|++||.|.|+|+++|++++|+.||
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 78999999999999999999999999999999999989999999999999999999999999999875
No 43
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.17 E-value=7.2e-11 Score=104.24 Aligned_cols=71 Identities=25% Similarity=0.342 Sum_probs=66.5
Q ss_pred CCCCCEEEEEEEEEec-ceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 759 IHPNSVVHGYVCNIIE-TGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~-~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
+++|+++.|.|.++.+ +|+||++.++.+|++|.++++|.+..++.+.|++||.|+|+|+++|. +|+.||++
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 4689999999999986 89999999999999999999999999998999999999999999984 89999985
No 44
>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=99.17 E-value=1.8e-10 Score=102.21 Aligned_cols=73 Identities=22% Similarity=0.339 Sum_probs=68.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
+++|+++.|.|+.++++|+||++.++++|++|.++++|.+..++.+.|++||.|+|+|+++|.+++++.||++
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 4689999999999999999999999999999999999988888888999999999999999999999999974
No 45
>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=99.16 E-value=1e-10 Score=102.47 Aligned_cols=69 Identities=28% Similarity=0.512 Sum_probs=65.0
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
|+++.|+|+++.++|+||++.++++||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
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 788999999999999999999999999999999988777788899999999999999999999999985
No 46
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.15 E-value=1.5e-10 Score=101.96 Aligned_cols=69 Identities=22% Similarity=0.323 Sum_probs=65.2
Q ss_pred CCEEE-EEEEEE-ecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 762 NSVVH-GYVCNI-IETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 762 G~~v~-G~V~~i-~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
|+++. |.|+++ .++|+||++.++++||+|.+++++.+..++.+.|++||.+.|+|+++|++++++.||+
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 6999999999999999999999998888888999999999999999999999999986
No 47
>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=99.12 E-value=1.7e-10 Score=100.80 Aligned_cols=68 Identities=29% Similarity=0.407 Sum_probs=64.4
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
|+++.|+|+++.++|+||+|.+++.||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||
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 67899999999999999999999999999999998888888899999999999999999999999876
No 48
>PRK08582 hypothetical protein; Provisional
Probab=99.11 E-value=3.6e-10 Score=112.45 Aligned_cols=75 Identities=31% Similarity=0.454 Sum_probs=71.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
+++|+++.|+|++|+++|+||++.++++||+|.++++|.++.++.+.|++||.|.|+|+++|. .++|.||+++..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~ 77 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAK 77 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 678999999999999999999999999999999999999999999999999999999999997 489999999874
No 49
>PRK07252 hypothetical protein; Provisional
Probab=99.11 E-value=3.9e-10 Score=109.22 Aligned_cols=76 Identities=24% Similarity=0.319 Sum_probs=71.9
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
++|+++.|+|.+|+++|+||++.++++||+|.+++++.+..++...|++||.|.|+|+++|.+.+++.||++....
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 5799999999999999999999999999999999999888888889999999999999999999999999998743
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=99.09 E-value=4.6e-10 Score=100.33 Aligned_cols=73 Identities=26% Similarity=0.364 Sum_probs=68.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEC--CCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeec
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQ 832 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~--~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~ 832 (1152)
+.|+.+.|.|.++.++|+||++. +++.||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.||+++
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 47999999999999999999996 46999999999999999999999999999999999999999999999874
No 51
>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=99.08 E-value=6.8e-10 Score=98.45 Aligned_cols=72 Identities=19% Similarity=0.173 Sum_probs=67.2
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
++|+++.|+|+++.++|+||++.++++||+|.+++++++..++.+.|++||.++|+|+++|++++++.||++
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 579999999999999999999999999999999998877667778899999999999999999999999974
No 52
>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=99.08 E-value=3.4e-10 Score=100.00 Aligned_cols=70 Identities=24% Similarity=0.348 Sum_probs=65.3
Q ss_pred cCCceEEEEEEEEec-CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 584 TDRLITHGWITKIEK-HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~-~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
++|+++.|+|+++.+ +|+||++.++.+|++|+|++++++..++.+.|++||.++|+|+++|. +++.||++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 579999999999986 89999999999999999999999888888899999999999999985 89999985
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=99.08 E-value=5.5e-10 Score=100.07 Aligned_cols=74 Identities=32% Similarity=0.558 Sum_probs=69.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECC-CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~-~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|+.+.|+|.+++++|+||++.+ +++|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.|++|++
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 369999999999999999999985 89999999999998888888999999999999999999999999999875
No 54
>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=99.07 E-value=3.9e-10 Score=98.78 Aligned_cols=68 Identities=29% Similarity=0.423 Sum_probs=63.1
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD-GQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~-~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
|+.+.|.|.+++++|+||++.+++.||+|.++++| ....++.+.|++||.|.|+|+++|.+++|+.|+
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 78899999999999999999999999999999996 567788889999999999999999999998874
No 55
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.06 E-value=2.5e-10 Score=107.23 Aligned_cols=75 Identities=28% Similarity=0.454 Sum_probs=68.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccc-------------------cCccccccCCCEEEEEEEEE
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQR-------------------ADLSKTYYVGQSVRSNILDV 819 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~-------------------~~~~~~f~~Gq~V~v~Vl~v 819 (1152)
+++|+++.|.|.++.++|+||.++++++|++|.++++|.+. .++.+.|++||.|+|+|+++
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 46899999999999999999999999999999999998663 34778899999999999999
Q ss_pred eCC---CCeEEEEeecc
Q 001115 820 NSE---TGRITLSLKQS 833 (1152)
Q Consensus 820 d~e---~~ri~LSlk~~ 833 (1152)
|.+ ++|+.||++.+
T Consensus 81 d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 81 DKSKSGKKRIELSLEPE 97 (100)
T ss_pred cCCcCCCcEEEEEecHH
Confidence 987 78999999865
No 56
>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=99.06 E-value=8.2e-10 Score=97.89 Aligned_cols=70 Identities=26% Similarity=0.406 Sum_probs=64.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECC-CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~-~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
..|+.+.|.|.++++||+||++.+ +.+||+|.++++|..+.++.+.|++||.|.|+|+++|.++ |+.||+
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 3799999999999988899999999999999999999876 999886
No 57
>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=99.04 E-value=9.3e-10 Score=97.48 Aligned_cols=72 Identities=25% Similarity=0.433 Sum_probs=68.5
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
|+++.|+|..+.++|+||++.++++|++|.+++++.+..++.+.|++||.+.|+|+++|.+++++.||++..
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 58
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.04 E-value=9.1e-10 Score=95.44 Aligned_cols=66 Identities=23% Similarity=0.404 Sum_probs=59.4
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
|+++.|+|+++.++|+||++.+++.||+|.++++..... .+.|++|+.++|+|+++|++++++.||
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 788999999999999999998899999999999754333 567999999999999999999998886
No 59
>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=99.03 E-value=1.1e-09 Score=97.78 Aligned_cols=73 Identities=16% Similarity=0.172 Sum_probs=67.6
Q ss_pred cCCceEEEEEEEEecCeEEEEEc--CCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 584 TDRLITHGWITKIEKHGCFVRFY--NGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~--~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
+.|+++.|+|+++.++|+||++. +++.||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||+++
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 36999999999999999999996 36999999999999888888899999999999999999999999999863
No 60
>PRK07252 hypothetical protein; Provisional
Probab=99.03 E-value=1.2e-09 Score=105.71 Aligned_cols=74 Identities=23% Similarity=0.193 Sum_probs=69.8
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
++|+++.|+|+++.++|+||++.+++.||+|.+++++.+..++.+.|++||.|+|+|+++|++++++.||++..
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 46999999999999999999999999999999999988888888899999999999999999999999999865
No 61
>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=99.03 E-value=7.6e-10 Score=96.96 Aligned_cols=68 Identities=26% Similarity=0.433 Sum_probs=62.5
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCC-CCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGL-DPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~-~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
|+++.|+|+++.++|+||++.+++.||+|.++++| ....++.+.|++||.++|+|+++|++++++.||
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 67899999999999999999999999999999986 456677788999999999999999999999875
No 62
>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=9.2e-10 Score=95.42 Aligned_cols=66 Identities=29% Similarity=0.384 Sum_probs=60.1
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
|+.+.|.|.++.++|+||++.++++||+|.++++..... .+.|++||.|.|+|+++|++++|+.||
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 789999999999999999998899999999999765443 678999999999999999999998876
No 63
>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=1.1e-09 Score=96.77 Aligned_cols=71 Identities=27% Similarity=0.407 Sum_probs=63.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCc-cccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG-QRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~-~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
+++|+.+.|.|.+++++|+||++.+++.||+|.++++|. ...++...|++||.|.|+|.++|.+++++.|+
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 468999999999999999999999899999999999874 44467788999999999999999999998764
No 64
>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=1.7e-09 Score=96.92 Aligned_cols=73 Identities=21% Similarity=0.407 Sum_probs=68.1
Q ss_pred CCceEEEEEEEEecCeEEEEEcC-CeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 585 DRLITHGWITKIEKHGCFVRFYN-GVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~-gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
+|+++.|+|+++.++|+||++.+ ++.|++|.+++++.+..++.+.|++||.++|+|+++|++++++.+|++++
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 58999999999999999999975 79999999999988777888899999999999999999999999999865
No 65
>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=99.01 E-value=7.3e-10 Score=95.13 Aligned_cols=72 Identities=26% Similarity=0.412 Sum_probs=65.2
Q ss_pred CCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEeEEEEeecccCceeeecc
Q 001115 670 GSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAK 742 (1152)
Q Consensus 670 G~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~~vl~~d~~~~~i~lS~K 742 (1152)
|++|+|+|.++++++++|++. +.+++|+||.+||||+..+++.+++++++||++..+++++...+.|++|.|
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 249999999999999888999999999999999878888888788999876
No 66
>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=99.00 E-value=1.9e-09 Score=95.56 Aligned_cols=71 Identities=28% Similarity=0.455 Sum_probs=67.2
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
|+++.|+|+++.++|+||++.+++.||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 68899999999999999999999999999999998877788889999999999999999999999999975
No 67
>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=99.00 E-value=1.6e-09 Score=95.17 Aligned_cols=70 Identities=24% Similarity=0.336 Sum_probs=66.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
|+++.|+|.++.++|+||++.++.+|++|.+++++.+..++.+.|++||.+.|+|+++|++++++.||++
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 7899999999999999999988999999999999999999999999999999999999988899999975
No 68
>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=98.99 E-value=2.2e-09 Score=94.38 Aligned_cols=70 Identities=20% Similarity=0.218 Sum_probs=66.1
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
|+++.|+|.++.++|+||++.++..|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||++
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 7889999999999999999988999999999999888888999999999999999999998999999974
No 69
>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=2.1e-09 Score=93.59 Aligned_cols=67 Identities=30% Similarity=0.370 Sum_probs=60.5
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
|+++.|+|+++.++|++|+| +|++||+|.+++++.+..++.. .+||.++|+|+++|++++++.||++
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 68899999999999999999 8999999999998776655554 4999999999999999999999974
No 70
>PRK08582 hypothetical protein; Provisional
Probab=98.98 E-value=2.5e-09 Score=106.50 Aligned_cols=75 Identities=21% Similarity=0.257 Sum_probs=69.9
Q ss_pred ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+++|+++.|+|++++++|+||+|.+++.||+|++++++.++.++.+.|++||.|+|+|+++|. +++|.||+++..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~ 77 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAK 77 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 467999999999999999999999999999999999988888888999999999999999997 599999999754
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=98.96 E-value=2.9e-09 Score=94.34 Aligned_cols=70 Identities=21% Similarity=0.320 Sum_probs=63.3
Q ss_pred cCCceEEEEEEEEecCeEEEEEcC-CeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYN-GVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~-gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
..|+++.|.|+++.++|+||++.+ +..||+|++++++.+..++.+.|++||.++|+|+++|.++ ++.||+
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 369999999999999999999943 2699999999999888888889999999999999999976 898886
No 72
>PRK08059 general stress protein 13; Validated
Probab=98.95 E-value=3.2e-09 Score=103.94 Aligned_cols=80 Identities=30% Similarity=0.417 Sum_probs=74.7
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 756 ASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
++++++|+.+.|.|.+++++|+||++.+++.|++|.+++++.+..++...|++||.|.|+|.++|.+++++.||++....
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 45688999999999999999999999999999999999999888888889999999999999999999999999998743
No 73
>PRK05807 hypothetical protein; Provisional
Probab=98.95 E-value=3.9e-09 Score=104.76 Aligned_cols=74 Identities=27% Similarity=0.466 Sum_probs=69.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
+++|+++.|.|..|+++|+||++ ++..||+|.+++++.++.++...|++||.|.|+|+++|. ++++.||++...
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 57899999999999999999999 678999999999999999999999999999999999998 799999999864
No 74
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.93 E-value=3.7e-09 Score=93.44 Aligned_cols=70 Identities=27% Similarity=0.477 Sum_probs=62.9
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCC-CCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLD-PGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~-~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
.+|+.+.|+|+++.++|+||++.+++.||+|.+++.+. ...++...|++||.++|+|+++|++++++.++
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 47999999999999999999999999999999999864 44466678999999999999999999998764
No 75
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.93 E-value=3.9e-09 Score=91.89 Aligned_cols=67 Identities=27% Similarity=0.477 Sum_probs=61.2
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
|+.+.|.|.++.++|+||+| +++.||+|.+++++.+..++.. .+||.+.|+|+++|.+++++.||.|
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 8899999999999877777654 4899999999999999999999964
No 76
>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=98.92 E-value=4.2e-09 Score=91.92 Aligned_cols=69 Identities=30% Similarity=0.518 Sum_probs=65.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
|+.+.|.|.+++++|+||++.++..||+|.+++++.+..++.+.|++||.|.|+|.++|. ++++.||+|
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 789999999999999999999999999999999998888888899999999999999998 899999975
No 77
>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=98.92 E-value=4.2e-09 Score=91.91 Aligned_cols=69 Identities=23% Similarity=0.384 Sum_probs=64.5
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
|+++.|+|+++.++|+||++.++..||+|.+++++.+..++.+.|++||.++|+|+++|+ ++++.||++
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 678999999999999999999899999999999988777888889999999999999999 899999975
No 78
>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=98.89 E-value=4.4e-09 Score=91.57 Aligned_cols=68 Identities=31% Similarity=0.440 Sum_probs=63.8
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
|+.+.|+|.+++++|+||++.++..|++|.+++++.+..++...|++||.|.|+|+++|.+++++.||
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 67899999999999999999999999999999998888888888999999999999999999998875
No 79
>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=98.88 E-value=9.4e-09 Score=92.65 Aligned_cols=71 Identities=31% Similarity=0.523 Sum_probs=65.4
Q ss_pred CCEEEEEEEEEecceEEEEEC---CCeEEEEeccCCCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 762 NSVVHGYVCNIIETGCFVRFL---GRLTGFAPRSKAVDGQR-ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~---~~l~Glv~~s~ls~~~~-~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
|+.+.|.|.+++++|+||++. ++..||+|.++++|.+. .++...|++||.|+|+|+++| ++++.+|+|+..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~ 75 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVD 75 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecc
Confidence 678999999999999999997 47999999999999875 888889999999999999999 799999999864
No 80
>PRK08059 general stress protein 13; Validated
Probab=98.88 E-value=8.7e-09 Score=100.90 Aligned_cols=77 Identities=23% Similarity=0.271 Sum_probs=71.5
Q ss_pred hhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 581 AEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 581 ~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
+++++|+++.|+|+++.++|+||++.+++.||+|.++++..+..++.+.|++||.++|+|+++|++++++.+|++..
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence 44678999999999999999999999999999999999888777778889999999999999999999999999875
No 81
>PHA02945 interferon resistance protein; Provisional
Probab=98.87 E-value=9.7e-09 Score=90.62 Aligned_cols=72 Identities=17% Similarity=0.305 Sum_probs=66.5
Q ss_pred CCCCEEEEEEEEEecceEEEEE--CCCeEEEEeccCC--CCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRF--LGRLTGFAPRSKA--VDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~--~~~l~Glv~~s~l--s~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
.+|+.+.|+|.. .++|+||.+ ++|+.||+|.|+. +...+++ .+++ +||+|.|+|+++|+.++.|-||||...
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 479999999999 999999998 5899999999955 8888888 8888 999999999999999999999999764
No 82
>PRK05807 hypothetical protein; Provisional
Probab=98.86 E-value=1.3e-08 Score=101.18 Aligned_cols=73 Identities=22% Similarity=0.241 Sum_probs=68.3
Q ss_pred ccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 583 ATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
+++|+++.|+|+.+.++|+||++ ++..||+|++++++.++.++.+.|++||.|+|+|+++|+ ++++.||+++.
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~ 75 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQA 75 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEec
Confidence 46799999999999999999999 789999999999988888888899999999999999998 79999999875
No 83
>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=1.6e-08 Score=91.08 Aligned_cols=70 Identities=30% Similarity=0.459 Sum_probs=63.8
Q ss_pred CceEEEEEEEEecCeEEEEEc---CCeEEEEeccccCCCCC-CCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 586 RLITHGWITKIEKHGCFVRFY---NGVQGFAPRSELGLDPG-CEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~---~gv~Gflp~sel~~~~~-~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
|+++.|.|+++.++|+||++. ++..||+|.+++++.+. .++...|++||.++|+|+++| ++++.+|++..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~ 74 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDV 74 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEec
Confidence 678999999999999999997 47999999999988775 788889999999999999999 79999999864
No 84
>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=98.83 E-value=8.8e-09 Score=89.64 Aligned_cols=68 Identities=25% Similarity=0.376 Sum_probs=63.0
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
|+++.|+|+++.++|+||++.++..||+|.+++++.+..++...|++||.++|+|+++|++++++.||
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 67899999999999999999999999999999988777778888999999999999999999999876
No 85
>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=98.82 E-value=1.3e-08 Score=88.75 Aligned_cols=68 Identities=29% Similarity=0.381 Sum_probs=63.0
Q ss_pred CceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
|+++.|+|+++.++|+||++.++..||+|.+++++.+..++.+.|++||.++|+|+++|+ ++++.+|+
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 678999999999999999999899999999999988777777889999999999999999 89999884
No 86
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.82 E-value=1.7e-08 Score=88.45 Aligned_cols=71 Identities=37% Similarity=0.528 Sum_probs=66.5
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
+|+.+.|.|.+++++|+||++.+++.|++|.+++++.+..++...|++||.|.|+|.+++.+++++.||++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 69999999999999999999998999999999999887777778899999999999999999999999974
No 87
>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=98.81 E-value=1.7e-08 Score=88.03 Aligned_cols=68 Identities=28% Similarity=0.468 Sum_probs=63.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
|+.+.|.|.++.++|+||++.++..||+|.+++++.+..++.+.|++||.|.|+|.++|+ ++++.||+
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 678999999999999999999899999999999998888888899999999999999998 88998874
No 88
>PHA02945 interferon resistance protein; Provisional
Probab=98.80 E-value=2.2e-08 Score=88.46 Aligned_cols=71 Identities=10% Similarity=0.069 Sum_probs=63.6
Q ss_pred cCCceEEEEEEEEecCeEEEEEc--CCeEEEEecccc--CCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 584 TDRLITHGWITKIEKHGCFVRFY--NGVQGFAPRSEL--GLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~--~gv~Gflp~sel--~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
.+|+++.|+|.. .++|+||.+. +|++||+|+|++ +...+.+ .+++ +||++.|+|+.+|+.++.|.||+|.-
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 469999999999 9999999984 699999999966 7666667 7888 99999999999999999999999863
No 89
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.79 E-value=2.4e-08 Score=87.54 Aligned_cols=71 Identities=34% Similarity=0.461 Sum_probs=65.2
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
+|+++.|+|.++.++|+||++.+++.||+|.+++...+..++...|++||.++|+|+++|+.++++.+|++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 59999999999999999999988999999999998776666667899999999999999999999999974
No 90
>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=98.78 E-value=2.1e-08 Score=87.35 Aligned_cols=68 Identities=25% Similarity=0.428 Sum_probs=62.8
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
+|+++.|+|+++.++|+||++. ++.||+|.+++++.+..++.+.|++||.++|+|+++|++++++.||
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 4889999999999999999995 7999999999988777788888999999999999999999999876
No 91
>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=2.5e-08 Score=86.81 Aligned_cols=68 Identities=29% Similarity=0.405 Sum_probs=63.3
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
+|+.+.|.|..+.++|+||++. ++.|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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 4899999999999999999985 7999999999998888888889999999999999999999998875
No 92
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.76 E-value=2e-08 Score=125.02 Aligned_cols=78 Identities=18% Similarity=0.229 Sum_probs=72.0
Q ss_pred ccCCCCCEEE-EEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 757 SHIHPNSVVH-GYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 757 ~~~~~G~~v~-G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
.+.++|+++. |.|++|++||+||++.++++||+|+|+++|.++.++.+.|++||.|.|+|+++|. ++||.||+|+...
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 3567999996 6999999999999999999999999999999999999999999999999999997 7899999998643
No 93
>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=98.74 E-value=3.1e-08 Score=90.80 Aligned_cols=74 Identities=16% Similarity=0.161 Sum_probs=66.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCC----ccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVD----GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~----~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
.++|+.+.|.|.++.++|+||++.++++|++|.+++++ ....+..+.|++||.+.|+|+++|++ +++.||++..
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~ 81 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSL 81 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCcc
Confidence 36899999999999999999999999999999999985 34456677899999999999999876 9999999875
No 94
>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=98.72 E-value=3.8e-08 Score=86.47 Aligned_cols=61 Identities=41% Similarity=0.737 Sum_probs=56.6
Q ss_pred CcEEEEEEEEEeCCeEEEEeCCCeeEEEEeeeccCCc-cccccccccCCCCCCEEEEEEEeeec
Q 001115 1064 GSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDK-SNVVENLFSNFKIGQTVTARIIAKSN 1126 (1152)
Q Consensus 1064 G~~v~~~V~~i~~~~l~V~L~~~~~G~v~~te~~D~~-~~~~~~p~~~f~~g~~V~~~Vl~~~~ 1126 (1152)
|++|+|+|+++.+.+++|+|+.+..|++|++|++++| .. .+|.+.|++||.|+|+|++++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~--~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDG--KNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccc--cChhHhCCCCCEEEEEEEEEeC
Confidence 7899999999999999999999999999999999987 33 5788899999999999999994
No 95
>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=7.4e-08 Score=88.39 Aligned_cols=75 Identities=17% Similarity=0.150 Sum_probs=65.7
Q ss_pred cCCCCCEEEEEEEEEecc--eEEEEECCCeEEEEeccCCCC---ccccCccccccCCCEEEEEEEEEeCCCCeEEEEeec
Q 001115 758 HIHPNSVVHGYVCNIIET--GCFVRFLGRLTGFAPRSKAVD---GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQ 832 (1152)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~--GvfV~~~~~l~Glv~~s~ls~---~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~ 832 (1152)
.++.|+++.|.|++|.++ |+||++.++..||+|.++++| ..+.++.+.|++||.|.|+|+......+.-.|+...
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 457899999999999997 999999999999999999998 567788889999999999999988776666666543
No 96
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.66 E-value=2.2e-08 Score=105.93 Aligned_cols=75 Identities=27% Similarity=0.393 Sum_probs=71.8
Q ss_pred CCCEEEEEEEEEecceEEEEE--CCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 761 PNSVVHGYVCNIIETGCFVRF--LGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~--~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
+|+.|-|+|++|.+||+||.+ ++|+.||+|.|+++...+.+..+++++||.|.|+|++||++++.+-||||..+.
T Consensus 11 eGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 699999999999999999998 689999999999999999999999999999999999999999999999998754
No 97
>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=98.66 E-value=1.2e-07 Score=86.10 Aligned_cols=70 Identities=19% Similarity=0.335 Sum_probs=61.5
Q ss_pred CCCEEEEEEEEEecceEEEEECC-CeEEEEeccCCCCcccc-----------CccccccCCCEEEEEEEEEeCCCCeEEE
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVNSETGRITL 828 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~-~l~Glv~~s~ls~~~~~-----------~~~~~f~~Gq~V~v~Vl~vd~e~~ri~L 828 (1152)
+|+.+.|+|.+++++|+||++.+ +++|++|.+++++.+.. ++...|++||.|+|+|.++|.+++++.+
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 38899999999999999999987 89999999999865321 3457899999999999999999999998
Q ss_pred Ee
Q 001115 829 SL 830 (1152)
Q Consensus 829 Sl 830 (1152)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 86
No 98
>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=98.65 E-value=7e-08 Score=88.49 Aligned_cols=73 Identities=15% Similarity=0.123 Sum_probs=64.7
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCC----CCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGL----DPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~----~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
++|+++.|+|+.+.++|++|++.++..|++|.+++++ ....++.+.|++||.++|+|+++|++ +++.||++..
T Consensus 5 ~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~ 81 (86)
T cd05789 5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSL 81 (86)
T ss_pred CCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCcc
Confidence 5799999999999999999999999999999999985 23345566799999999999999986 9999999864
No 99
>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=98.63 E-value=1.1e-07 Score=87.19 Aligned_cols=73 Identities=18% Similarity=0.160 Sum_probs=63.7
Q ss_pred ccCCceEEEEEEEEecC--eEEEEEcCCeEEEEeccccCC---CCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 583 ATDRLITHGWITKIEKH--GCFVRFYNGVQGFAPRSELGL---DPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~--G~~V~~~~gv~Gflp~sel~~---~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
+..|+++.|+|+++.++ ||||++.+|.+||||.++++| ..+.++.+.+++||.|.|+|+..........|+..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 45799999999999997 999999989999999999988 55667778899999999999998776666666654
No 100
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.62 E-value=1e-07 Score=104.90 Aligned_cols=76 Identities=26% Similarity=0.359 Sum_probs=71.0
Q ss_pred CCCCEEEEEEEEEecceEEEEECC--CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecccc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLG--RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC 835 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~--~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~ 835 (1152)
++|+.+.|.|.++.++|+||++.. ++.||+|.+++++.+..++.+.|++||.|.|+|+++|.+++++.||++....
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 579999999999999999999964 8999999999999888899999999999999999999999999999997653
No 101
>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=98.62 E-value=1.2e-07 Score=83.37 Aligned_cols=63 Identities=14% Similarity=0.206 Sum_probs=58.2
Q ss_pred CCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcc--ccCccccccCCCEEEEEEEEEeCCCC
Q 001115 762 NSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ--RADLSKTYYVGQSVRSNILDVNSETG 824 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~--~~~~~~~f~~Gq~V~v~Vl~vd~e~~ 824 (1152)
|+++.|.|..+.++|+||++.++++|++|.+++++.+ ..++.+.|++||.|.|+|+++|.++.
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 102
>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=98.62 E-value=2.1e-07 Score=83.36 Aligned_cols=71 Identities=24% Similarity=0.337 Sum_probs=62.6
Q ss_pred hHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 575 AILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 575 ~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
+.+..+++++.|+.+.|+|+++.++|+||++.++..||+|.+++. ..|++||.++++|.++ .+++++.+|+
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 334456678899999999999999999999999999999999863 3589999999999999 8899999885
No 103
>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=98.62 E-value=2.7e-07 Score=82.64 Aligned_cols=67 Identities=25% Similarity=0.442 Sum_probs=61.2
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 755 DASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 755 ~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
.+++++.|+.+.|.|.+++++|+||++.++..||+|.+++. ..|+.||.++++|.++ .+++|+.+++
T Consensus 10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 45778999999999999999999999999999999999863 4699999999999999 8899999885
No 104
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.61 E-value=6.3e-08 Score=118.26 Aligned_cols=71 Identities=21% Similarity=0.324 Sum_probs=65.7
Q ss_pred cCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCC----CccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 758 HIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAV----DGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 758 ~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls----~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
+.++|+++.|.|++|++||+||++.+|++||+|+|+++ |.++.++.+.|++||.|.|+|+++|. ++|+.|+
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 7898876
No 105
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.60 E-value=1.1e-07 Score=118.72 Aligned_cols=81 Identities=25% Similarity=0.279 Sum_probs=72.9
Q ss_pred hccCCceEE-EEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC-CC
Q 001115 582 EATDRLITH-GWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK-PT 659 (1152)
Q Consensus 582 ~~~~G~~~~-G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~-~~ 659 (1152)
+.++|+++. |+|+++.+||+||++.+|++||+|+|+|++.++.++.+.|++||.|+|+|+++|+ ++|+.||+|.. .+
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 446899995 6999999999999999999999999999999888999999999999999999997 79999999974 34
Q ss_pred Cccc
Q 001115 660 RVSE 663 (1152)
Q Consensus 660 ~~~~ 663 (1152)
+|..
T Consensus 829 Pw~~ 832 (891)
T PLN00207 829 ANSE 832 (891)
T ss_pred chhh
Confidence 6654
No 106
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.58 E-value=6.5e-08 Score=116.99 Aligned_cols=82 Identities=23% Similarity=0.379 Sum_probs=77.8
Q ss_pred CccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 754 SDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 754 ~~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
.++.++++|+.+.|+|+|++++|+||.+.=+.+|++|+|.+++.|+.+|.+.+++||.|+|+|+++|..++||.|||+..
T Consensus 651 ~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~ 730 (780)
T COG2183 651 ESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD 730 (780)
T ss_pred hhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeecc
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cc
Q 001115 834 CC 835 (1152)
Q Consensus 834 ~~ 835 (1152)
..
T Consensus 731 ~~ 732 (780)
T COG2183 731 EE 732 (780)
T ss_pred CC
Confidence 54
No 107
>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=98.58 E-value=1.3e-07 Score=80.95 Aligned_cols=64 Identities=34% Similarity=0.551 Sum_probs=58.7
Q ss_pred EEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 590 HGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 590 ~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
.|+|+++.++|+||++.++..||+|.+++++....++.+.|++||.++|+|+++|++++++.||
T Consensus 2 ~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred EEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 6899999999999999989999999999987766677788999999999999999999988875
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=98.57 E-value=1.3e-07 Score=81.04 Aligned_cols=65 Identities=35% Similarity=0.527 Sum_probs=59.9
Q ss_pred EEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 765 VHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 765 v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
+.|+|.++.++|+||++.++..|++|.+++++.+..++.+.|++||.|.|+|+++|++++++.||
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 46999999999999999989999999999998877788889999999999999999988888775
No 109
>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=98.57 E-value=2.5e-07 Score=83.97 Aligned_cols=73 Identities=16% Similarity=0.235 Sum_probs=68.0
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|+.+.|+|.++.+.+++|++..+..|++|.++++.....++.+.|++|+.+.|+|+++|.+ +++.||++..
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 579999999999999999999999999999999999877778888999999999999999987 8999999864
No 110
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.57 E-value=2e-07 Score=102.67 Aligned_cols=74 Identities=23% Similarity=0.341 Sum_probs=68.9
Q ss_pred cCCceEEEEEEEEecCeEEEEEcC--CeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYN--GVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~--gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
.+|+++.|+|+++.++|+||++.+ |+.||+|.|++++.+..++.+.|++||.+.|+|+++|++++++.||++..
T Consensus 7 ~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v 82 (262)
T PRK03987 7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 469999999999999999999974 89999999999988888888899999999999999999999999999854
No 111
>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=98.56 E-value=3.2e-07 Score=83.37 Aligned_cols=69 Identities=26% Similarity=0.372 Sum_probs=60.3
Q ss_pred CceEEEEEEEEecCeEEEEEcC-CeEEEEeccccCCCCC-----------CCCCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFYN-GVQGFAPRSELGLDPG-----------CEPSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~~-gv~Gflp~sel~~~~~-----------~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
|+++.|+|+++.++|+||++.+ +++||+|.+++.+... ..+...|++||.|+|+|+++|++++++.++
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~~ 81 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDFE 81 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEEE
Confidence 7899999999999999999987 8999999999975431 134467999999999999999999999988
Q ss_pred E
Q 001115 654 F 654 (1152)
Q Consensus 654 ~ 654 (1152)
+
T Consensus 82 l 82 (83)
T cd04471 82 L 82 (83)
T ss_pred E
Confidence 5
No 112
>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=98.56 E-value=2.5e-07 Score=113.10 Aligned_cols=98 Identities=15% Similarity=0.176 Sum_probs=75.5
Q ss_pred EE-eCCeEEEeechhhh-hhhhhHhhhhh---hccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccC----CCCCCC
Q 001115 555 GV-KSKRITVTHKKTLV-KSKLAILSSYA---EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELG----LDPGCE 625 (1152)
Q Consensus 555 ~v-~~~~i~LS~K~~l~-~~~~~~~~~~~---~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~----~~~~~~ 625 (1152)
.+ +.+.+.++-..... +.....+..+. ..++|+++.|+|+++.+||+||++.+|++||+|+|+++ +.++.+
T Consensus 612 di~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~ 691 (719)
T TIGR02696 612 SIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN 691 (719)
T ss_pred EEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCC
Confidence 44 56777776643211 11112222222 25689999999999999999999999999999999995 467889
Q ss_pred CCCCccCCCEEEEEEEEEecCCCEEEEE
Q 001115 626 PSSMYHVGQVVKCRIMSSIPASRRINLS 653 (1152)
Q Consensus 626 ~~~~f~vGq~v~vrV~~vd~~~~ri~lS 653 (1152)
+.+.|++||.|+|+|+++|+ ++|+.|+
T Consensus 692 ~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 692 VEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred HHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 99999999999999999995 7888875
No 113
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.54 E-value=5.7e-08 Score=102.83 Aligned_cols=73 Identities=23% Similarity=0.328 Sum_probs=68.1
Q ss_pred CCceEEEEEEEEecCeEEEEE--cCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 585 DRLITHGWITKIEKHGCFVRF--YNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~--~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
.|+++.|+|..|.++|+||.| |+|++||+|+||++...+.+..++.++||.+-|+|+++||.++.+.||+|.-
T Consensus 11 eGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV 85 (269)
T COG1093 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRV 85 (269)
T ss_pred CCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhC
Confidence 699999999999999999998 5799999999999877777888999999999999999999999999999864
No 114
>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=98.53 E-value=3.1e-07 Score=83.45 Aligned_cols=72 Identities=13% Similarity=0.006 Sum_probs=66.1
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
++|+++.|+|+++.+.|++|+++.+..|++|.++++.....++.+.|++|+.+.|+|+++|.+ +++.||++.
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 479999999999999999999999999999999998766667778899999999999999986 899999975
No 115
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.48 E-value=4e-07 Score=114.14 Aligned_cols=76 Identities=25% Similarity=0.418 Sum_probs=71.9
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
.+.++|+++.|.|+++.+||+||++.++.+||+|+++++|.++.++.+.|++||.|+|+|+++|.+ +|+.||+|..
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 9999999853
No 116
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.40 E-value=1.2e-06 Score=92.71 Aligned_cols=94 Identities=18% Similarity=0.331 Sum_probs=76.1
Q ss_pred EEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEecceEEEEEC----------CCeEEEEeccCCCC
Q 001115 727 LLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFL----------GRLTGFAPRSKAVD 796 (1152)
Q Consensus 727 vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV~~~----------~~l~Glv~~s~ls~ 796 (1152)
.+.+|.++++|.+ +||... ....++|+++.|.|+++.++|+||++. .++.|++|.+++++
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 4455666555555 233321 235679999999999999999999984 37999999999999
Q ss_pred ccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 797 GQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 797 ~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
....++.+.|++||.|.|+|++++ +++.||++..
T Consensus 110 ~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~ 143 (189)
T PRK09521 110 GYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGK 143 (189)
T ss_pred hhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecC
Confidence 888888889999999999999998 7899999864
No 117
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.40 E-value=1.1e-06 Score=110.10 Aligned_cols=74 Identities=24% Similarity=0.290 Sum_probs=70.0
Q ss_pred hccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 582 EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
+.++|+++.|+|+++.++|+||+++++..||+|+|++++.++.++.+.|++||.|+|+|+++|++ +++.||+|.
T Consensus 618 ~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~ 691 (693)
T PRK11824 618 EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKA 691 (693)
T ss_pred cCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEe
Confidence 45789999999999999999999999999999999999998989999999999999999999987 999999974
No 118
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.38 E-value=5.2e-07 Score=109.34 Aligned_cols=80 Identities=24% Similarity=0.358 Sum_probs=75.5
Q ss_pred hhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 579 SYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 579 ~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+++++++|+++.|+|+++.++|+||++.-...|++|+|+++..++.+|.+.+++||.|+|+|+++|..++||.||++...
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 46678999999999999999999999988888999999999999999999999999999999999999999999998654
No 119
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.37 E-value=8.2e-07 Score=105.36 Aligned_cols=122 Identities=20% Similarity=0.221 Sum_probs=90.3
Q ss_pred EEEeCCccccccccCCCCccccCCEEEEEEEEEeCC-eEEEeechhhhhhhhh--Hhhhhhhcc--CCceEEEEEEEEec
Q 001115 524 ALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSK-RITVTHKKTLVKSKLA--ILSSYAEAT--DRLITHGWITKIEK 598 (1152)
Q Consensus 524 g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~~~-~i~LS~K~~l~~~~~~--~~~~~~~~~--~G~~~~G~V~~i~~ 598 (1152)
+.|+.++.. ..+| .+++|+.+++.|...+-+ ....+.|+.+...... .-.-|+.++ .|+++.|+|.++.+
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 566654432 2244 578999999999776433 3344455544432211 011244454 79999999999999
Q ss_pred CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCC--EEEEEEeeC
Q 001115 599 HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR--RINLSFMMK 657 (1152)
Q Consensus 599 ~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~--ri~lS~k~~ 657 (1152)
+|+||++ +++.||||.+++. |.+.|++|+.++|.|+++|++++ ++.||+..+
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 7999999999985 66789999999999999999877 899999754
No 120
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.36 E-value=2.8e-06 Score=89.89 Aligned_cols=102 Identities=15% Similarity=0.236 Sum_probs=80.0
Q ss_pred CccccCCEEEEEEEEE---e--CCeEEEeechhhhhhhhhHhhh-hhhccCCceEEEEEEEEecCeEEEEEc--------
Q 001115 541 KKFKVGAELVFRVLGV---K--SKRITVTHKKTLVKSKLAILSS-YAEATDRLITHGWITKIEKHGCFVRFY-------- 606 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v---~--~~~i~LS~K~~l~~~~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~-------- 606 (1152)
-.|..+..+.+.++.. + +++|.|. +|.. ....++|+++.|+|+++.++|+||++.
T Consensus 25 Gty~~~~~i~as~~G~~~id~~~~~Isv~-----------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~ 93 (189)
T PRK09521 25 GTYEDNGEVYASVVGKVFIDDINRKISVI-----------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERE 93 (189)
T ss_pred CEEeeCCEEEEEeeEEEEEcCCCCEEEEe-----------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccc
Confidence 3566677788877776 2 3345442 1222 223468999999999999999999985
Q ss_pred --CCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 607 --NGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 607 --~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
.++.||+|.+++++....++.+.|++||.|+|+|+++| +++.||++.
T Consensus 94 l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 94 LATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred cCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 36889999999988776677888999999999999998 789999974
No 121
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.30 E-value=9.4e-07 Score=104.88 Aligned_cols=119 Identities=16% Similarity=0.254 Sum_probs=93.1
Q ss_pred ceeeeecccchHHHhhhccccCCCCEEEEEEEEEecCCCeEEEEccccccccc-----cccccccC--CCCEEEEEEEEE
Q 001115 437 PAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGL-----VFTHSDVK--PGMVVKGKVIAV 509 (1152)
Q Consensus 437 ~Gfv~~s~~~~~~~~~~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~~~~~~-----~~~~~~l~--~G~iv~g~V~~v 509 (1152)
.++++.++.... ...+++|+.+.+.|...+ .++....+.++..+..+ ...++.++ .|++|+|+|.++
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 TKEISLEEARKI-----DPDAEVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRV 145 (470)
T ss_pred cceeeHHHHhhh-----CccccCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEE
Confidence 467776665322 234899999999999877 55655555555544332 35567776 999999999999
Q ss_pred eCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE--eCC--eEEEeechh
Q 001115 510 DSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV--KSK--RITVTHKKT 568 (1152)
Q Consensus 510 ~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~~--~i~LS~K~~ 568 (1152)
+++|++|+++ +++||+|.++++ |...|++|+.|+|+|+.+ +++ +|.||++..
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 899999998874 778999999999999999 344 899999743
No 122
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.28 E-value=8e-06 Score=89.22 Aligned_cols=73 Identities=16% Similarity=0.186 Sum_probs=65.1
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCC----CCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPG----CEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~----~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
++|+++.|.|+++.++|++|++..+..|+||.+++++.++ .++.+.|++||.|+|+|+++|++ +.+.||++..
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~LS~k~~ 138 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVLTLKGK 138 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEEEEcCC
Confidence 5799999999999999999999889999999999988765 67778899999999999999975 4599999743
No 123
>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=98.27 E-value=3.9e-06 Score=79.11 Aligned_cols=71 Identities=28% Similarity=0.448 Sum_probs=60.4
Q ss_pred CEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccC-----------ccccccCCCEEEEEEEEEeCCC-----CeE
Q 001115 763 SVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRAD-----------LSKTYYVGQSVRSNILDVNSET-----GRI 826 (1152)
Q Consensus 763 ~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~-----------~~~~f~~Gq~V~v~Vl~vd~e~-----~ri 826 (1152)
+++.|.|..+.++|+||++. ++.|++|.+++++.+... +...|++||.|.++|.++|.+. .++
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 499999999998765432 3467999999999999999764 589
Q ss_pred EEEeeccc
Q 001115 827 TLSLKQSC 834 (1152)
Q Consensus 827 ~LSlk~~~ 834 (1152)
.||+++..
T Consensus 80 ~ls~k~~~ 87 (99)
T cd04460 80 GLTMRQPG 87 (99)
T ss_pred EEEEecCC
Confidence 99999764
No 124
>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=98.26 E-value=3.5e-06 Score=73.27 Aligned_cols=62 Identities=31% Similarity=0.470 Sum_probs=53.0
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE-e---CCeEEEee
Q 001115 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-K---SKRITVTH 565 (1152)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v-~---~~~i~LS~ 565 (1152)
+.|++|+|+|.+++++|++|+++ +++|++|.++++ |.+.|++|+++++.|+.+ + ..+|.||+
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 499999998876 345789999999999999 2 23678774
No 125
>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=3.2e-06 Score=105.81 Aligned_cols=70 Identities=24% Similarity=0.335 Sum_probs=64.4
Q ss_pred hccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEE
Q 001115 582 EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINL 652 (1152)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~l 652 (1152)
..++|+++.|+|+++.++|+||+++++..||+|+|++++.++.++.+.|++||.|+|+|+++|+ ++++.|
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 3468999999999999999999999999999999999998888999999999999999999998 677643
No 126
>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=98.24 E-value=4.7e-06 Score=72.50 Aligned_cols=63 Identities=19% Similarity=0.411 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCC--CeEEEE
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSET--GRITLS 829 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~--~ri~LS 829 (1152)
+.|+.+.|+|.++.++|+||++. +.+|++|.++++. .+.|++|+.|.+.|.+++.++ ..+.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 36999999999999999999994 5999999999863 457899999999999999654 357776
No 127
>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=98.21 E-value=2.1e-06 Score=107.40 Aligned_cols=71 Identities=23% Similarity=0.423 Sum_probs=65.8
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEE
Q 001115 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITL 828 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~L 828 (1152)
.+.++|+++.|.|+++.+||+||++.++++||+|+|+++|.++.++.+.|++||.|.|+|+++|. ++|+.|
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 45789999999999999999999999999999999999999999999999999999999999997 677653
No 128
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.09 E-value=4.5e-06 Score=99.75 Aligned_cols=76 Identities=24% Similarity=0.440 Sum_probs=71.3
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
.++.+|+++.|.|+.+.+||+||+|.++-.|++|+|++++..+.+.++.+++||.|.|+|+.+|. .+|+.||++..
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 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence 67889999999999999999999999999999999999999999999999999999999999995 68999998753
No 129
>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=98.08 E-value=1.3e-05 Score=75.60 Aligned_cols=71 Identities=24% Similarity=0.315 Sum_probs=59.3
Q ss_pred ceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCC-----------CCCCccCCCEEEEEEEEEecCC-----CEE
Q 001115 587 LITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCE-----------PSSMYHVGQVVKCRIMSSIPAS-----RRI 650 (1152)
Q Consensus 587 ~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~-----------~~~~f~vGq~v~vrV~~vd~~~-----~ri 650 (1152)
+++.|+|+.+.++|+||++. ++.||+|.+++..++... +...|++||.++++|.++|.+. .++
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 36789999999999999996 699999999997654322 3467999999999999999874 489
Q ss_pred EEEEeeCC
Q 001115 651 NLSFMMKP 658 (1152)
Q Consensus 651 ~lS~k~~~ 658 (1152)
.||++...
T Consensus 80 ~ls~k~~~ 87 (99)
T cd04460 80 GLTMRQPG 87 (99)
T ss_pred EEEEecCC
Confidence 99998754
No 130
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.98 E-value=1.5e-05 Score=95.53 Aligned_cols=99 Identities=17% Similarity=0.230 Sum_probs=78.4
Q ss_pred eCCeEEEeechhhhhh-hhhHhhh-hhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCC
Q 001115 557 KSKRITVTHKKTLVKS-KLAILSS-YAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQ 634 (1152)
Q Consensus 557 ~~~~i~LS~K~~l~~~-~~~~~~~-~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq 634 (1152)
+.+.+.++....-... ....+.. ..++.+|+++.|+|+++.+||+||+|++|-.|++|+|++++.++...++.+++||
T Consensus 589 ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd 668 (692)
T COG1185 589 DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGD 668 (692)
T ss_pred CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCc
Confidence 5666666554321111 1122222 2456789999999999999999999999999999999999988888889999999
Q ss_pred EEEEEEEEEecCCCEEEEEEee
Q 001115 635 VVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 635 ~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
.+.|+|+++|+ ++|+.||++.
T Consensus 669 ~v~Vkv~~iD~-~Gri~ls~~~ 689 (692)
T COG1185 669 EVKVKVIEIDK-QGRIRLSIKA 689 (692)
T ss_pred eEEEEEeeecc-cCCccceehh
Confidence 99999999996 6899999864
No 131
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.96 E-value=2.2e-05 Score=85.75 Aligned_cols=73 Identities=22% Similarity=0.327 Sum_probs=65.9
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccc----cCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQR----ADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~----~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|++|.|.|.+++++|+||++...+.|++|.+++++.++ .++...|++||.|.|+|++++.++ ++.||++..
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~-~~~LS~k~~ 138 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTR-DVVLTLKGK 138 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCC-cEEEEEcCC
Confidence 6899999999999999999999889999999999999876 678888999999999999998654 599998753
No 132
>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=2.2e-05 Score=89.69 Aligned_cols=109 Identities=16% Similarity=0.337 Sum_probs=79.0
Q ss_pred CccccCCEEEEEEEEEe-CCeEEEeechhhhhh-----hhhHhhhhhhccCCceEEEEEEEEecCe-EEEEEcCCeEEEE
Q 001115 541 KKFKVGAELVFRVLGVK-SKRITVTHKKTLVKS-----KLAILSSYAEATDRLITHGWITKIEKHG-CFVRFYNGVQGFA 613 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v~-~~~i~LS~K~~l~~~-----~~~~~~~~~~~~~G~~~~G~V~~i~~~G-~~V~~~~gv~Gfl 613 (1152)
..+++|+.+++.+...+ .+....+.|+.+... +..++..|.+ +.|+++.|+|.++.+.| +||++ +++.|||
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 46899999998874433 333344444433211 1122222322 48999999999999987 69999 7999999
Q ss_pred eccccCCCCCCCCCCCccCCCEEEEEEEEEecCC--CEEEEEEeeC
Q 001115 614 PRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPAS--RRINLSFMMK 657 (1152)
Q Consensus 614 p~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~--~ri~lS~k~~ 657 (1152)
|.+++. |.+.|++|+.++|.|++++... ..+.||.+..
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 999986 4457999999999999999653 5799998754
No 133
>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=97.91 E-value=4.4e-05 Score=80.11 Aligned_cols=72 Identities=31% Similarity=0.481 Sum_probs=61.9
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcccc-C----------ccccccCCCEEEEEEEEEe-----CCCC
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRA-D----------LSKTYYVGQSVRSNILDVN-----SETG 824 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~-~----------~~~~f~~Gq~V~v~Vl~vd-----~e~~ 824 (1152)
.|+++.|.|++++++|+||++ +.++|++|.+++.+.+.. + ....|+.|+.|+++|.++| ++..
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 599999999999999999998 569999999998754322 2 2367999999999999998 6678
Q ss_pred eEEEEeecc
Q 001115 825 RITLSLKQS 833 (1152)
Q Consensus 825 ri~LSlk~~ 833 (1152)
++.+|||+.
T Consensus 160 ~I~lt~k~~ 168 (179)
T TIGR00448 160 KIGLTMRQP 168 (179)
T ss_pred eEEEEeccC
Confidence 999999986
No 134
>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=97.88 E-value=2.2e-05 Score=89.76 Aligned_cols=108 Identities=19% Similarity=0.309 Sum_probs=80.8
Q ss_pred hccccCCCCEEEEEEEEEecCCCeEEEEcccccc-----cccccccccc--CCCCEEEEEEEEEeCCe-EEEEeCCCeEE
Q 001115 453 LEKKYKEGSCVRVRILGFRHLEGLATGILKASAF-----EGLVFTHSDV--KPGMVVKGKVIAVDSFG-AIVQFPGGVKA 524 (1152)
Q Consensus 453 ~~~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~~~-----~~~~~~~~~l--~~G~iv~g~V~~v~~~G-~~V~i~~~v~g 524 (1152)
+...+++|+.+++.|... .+++.+..+.++... ..+...++.+ +.|++|+|+|.++.+.| ++|+++ +++|
T Consensus 80 ~d~~~~vGD~I~~~I~~~-~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea 157 (341)
T TIGR01953 80 IDPDVQIGDEVKKEIPPE-NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG-KTEG 157 (341)
T ss_pred hccccccCCEEEEEeccc-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEE
Confidence 345699999999988543 344544444554321 1233445556 59999999999999988 699996 8999
Q ss_pred EEeCCccccccccCCCCccccCCEEEEEEEEEe----CCeEEEeechh
Q 001115 525 LCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVK----SKRITVTHKKT 568 (1152)
Q Consensus 525 ~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~----~~~i~LS~K~~ 568 (1152)
++|.+++. |.+.|++|+.++|.|+.++ ..++.||++..
T Consensus 158 ~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 158 ILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred EecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 99998775 5567999999999999992 34799999854
No 135
>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=97.87 E-value=5e-05 Score=65.70 Aligned_cols=62 Identities=18% Similarity=0.328 Sum_probs=56.0
Q ss_pred ccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCC---------CcccCCCEE-EEEEEEEECCCCEEEEEEc
Q 001115 875 GSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG---------ATVESGSVI-QAAILDVAKAERLVDLSLK 939 (1152)
Q Consensus 875 G~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~---------~~~~~G~~v-~a~Vl~vd~~~~~v~LSlk 939 (1152)
|++|+|+|.+.++++++|++++. ++.|+++..|++| ..+++||++ .+.|+ +...+.+.||.|
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 GKLVDARVLKKTLNGLEVAILPE-EIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCC-CcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 78999999999999999999985 8999999999997 368999999 89999 778888888865
No 136
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.86 E-value=3e-05 Score=89.16 Aligned_cols=109 Identities=16% Similarity=0.239 Sum_probs=79.3
Q ss_pred CccccCCEEEEEEEEEe-CCeEEEeechhhhhhhhh--Hhhhhhhc--cCCceEEEEEEEEecCeEEEEEcCCeEEEEec
Q 001115 541 KKFKVGAELVFRVLGVK-SKRITVTHKKTLVKSKLA--ILSSYAEA--TDRLITHGWITKIEKHGCFVRFYNGVQGFAPR 615 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v~-~~~i~LS~K~~l~~~~~~--~~~~~~~~--~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~ 615 (1152)
...++|+.++..+...+ .+....+.|+.+...-.. --.-|+++ +.|+++.|+|.++.++|+||++ +++.||||.
T Consensus 85 ~~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~ 163 (362)
T PRK12327 85 PAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPP 163 (362)
T ss_pred ccccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecH
Confidence 35789999998875442 334444555554432111 01124444 6899999999999999999999 679999998
Q ss_pred cccCCCCCCCCCCCccCCCEEEEEEEEEecCCC--EEEEEEee
Q 001115 616 SELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR--RINLSFMM 656 (1152)
Q Consensus 616 sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~--ri~lS~k~ 656 (1152)
+++. |.+.|++|+.++|.|++++...+ .+.||+..
T Consensus 164 ~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 164 AEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred HHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 8874 45679999999999999996654 58888743
No 137
>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=97.85 E-value=6.3e-05 Score=78.94 Aligned_cols=73 Identities=23% Similarity=0.312 Sum_probs=62.0
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCC-----------CCCCCccCCCEEEEEEEEEe-----cCCC
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGC-----------EPSSMYHVGQVVKCRIMSSI-----PASR 648 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~-----------~~~~~f~vGq~v~vrV~~vd-----~~~~ 648 (1152)
.|+++.|+|++++++|+||++ +.+.|++|.+++..++.. +....|++|+.|++||+++| ++..
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 599999999999999999999 679999999998644321 23357999999999999998 6778
Q ss_pred EEEEEEeeCC
Q 001115 649 RINLSFMMKP 658 (1152)
Q Consensus 649 ri~lS~k~~~ 658 (1152)
++.+|+|+..
T Consensus 160 ~I~lt~k~~~ 169 (179)
T TIGR00448 160 KIGLTMRQPL 169 (179)
T ss_pred eEEEEeccCc
Confidence 9999999763
No 138
>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=97.79 E-value=8.3e-05 Score=68.88 Aligned_cols=77 Identities=25% Similarity=0.436 Sum_probs=62.9
Q ss_pred cCCcEEEEEEEEEeCCeEEEEe--------CCCeeEEEEeeeccCCccccccccccCCCCCCEEEEEEEeeecCCCCCCC
Q 001115 1062 DVGSLVQAEITEIKPLELRLKF--------GIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKS 1133 (1152)
Q Consensus 1062 ~~G~~v~~~V~~i~~~~l~V~L--------~~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~~~~~~~k~ 1133 (1152)
++|++|-|+|+++...+..+++ +....|.+|++|+.+.+.+. ....+.|++||.|+|+|++... ...
T Consensus 5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~-~~~~~~f~~GDiV~AkVis~~~---~~~- 79 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDK-VEMYKCFRPGDIVRAKVISLGD---ASS- 79 (92)
T ss_pred CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccch-HHHHhhcCCCCEEEEEEEEcCC---CCC-
Confidence 7899999999999999999999 88889999999998876431 1234689999999999999873 122
Q ss_pred ceEEEEeecCCc
Q 001115 1134 FLWELSIKPSML 1145 (1152)
Q Consensus 1134 ~~~~LSlr~s~~ 1145 (1152)
+.||++...+
T Consensus 80 --~~Lst~~~~l 89 (92)
T cd05791 80 --YYLSTAENEL 89 (92)
T ss_pred --cEEEecCCCC
Confidence 8899986543
No 139
>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=97.73 E-value=8.7e-05 Score=94.39 Aligned_cols=74 Identities=19% Similarity=0.346 Sum_probs=63.9
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEECC-CeEEEEeccCCCCccc-----------cCccccccCCCEEEEEEEEEeCCCC
Q 001115 757 SHIHPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQR-----------ADLSKTYYVGQSVRSNILDVNSETG 824 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~-~l~Glv~~s~ls~~~~-----------~~~~~~f~~Gq~V~v~Vl~vd~e~~ 824 (1152)
-.-++|+.+.|.|.+|+++|+||++.+ ++.||+|.+++.+.+. .+....|++||.|.|+|.++|.+++
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 344679999999999999999999987 8999999999986432 2334679999999999999999999
Q ss_pred eEEEEe
Q 001115 825 RITLSL 830 (1152)
Q Consensus 825 ri~LSl 830 (1152)
++.+++
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 999886
No 140
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.65 E-value=4.4e-05 Score=88.09 Aligned_cols=76 Identities=22% Similarity=0.276 Sum_probs=68.7
Q ss_pred hccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 582 EATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 582 ~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
++..|.++.++|+.+.++|+||+||++-.|++|+|+++-+++.+|++.+.+||.+.++-++.|+..+...+|.+..
T Consensus 665 ~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 665 DLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALL 740 (760)
T ss_pred ceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhhhhc
Confidence 3456899999999999999999999999999999999999999999999999999999999999877777766543
No 141
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.65 E-value=4.8e-05 Score=87.85 Aligned_cols=73 Identities=19% Similarity=0.244 Sum_probs=67.0
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
.++..|-+++|+|+++.+||+||+|+++..||+|.++++...+.+|++.+.+||.|.++.+..|+..+...++
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ 736 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSS 736 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehh
Confidence 4677899999999999999999999999999999999999999999999999999999999999866655554
No 142
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=97.64 E-value=0.00015 Score=92.29 Aligned_cols=71 Identities=21% Similarity=0.297 Sum_probs=61.9
Q ss_pred cCCceEEEEEEEEecCeEEEEEcC-CeEEEEeccccCCCCC-----------CCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYN-GVQGFAPRSELGLDPG-----------CEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~-gv~Gflp~sel~~~~~-----------~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
+.|+++.|+|+++.++|+||++.+ +++|++|.+++..+.. ......|++||.|+|+|+++|..++++.
T Consensus 626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~ 705 (709)
T TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKID 705 (709)
T ss_pred cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 469999999999999999999987 7999999999974321 2334579999999999999999999999
Q ss_pred EEE
Q 001115 652 LSF 654 (1152)
Q Consensus 652 lS~ 654 (1152)
+++
T Consensus 706 ~~l 708 (709)
T TIGR02063 706 FEL 708 (709)
T ss_pred EEE
Confidence 886
No 143
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.60 E-value=7e-05 Score=86.17 Aligned_cols=104 Identities=19% Similarity=0.297 Sum_probs=79.6
Q ss_pred cccCCCCEEEEEEEEEecCCCeEEEEccccccc-----ccccccccc--CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEe
Q 001115 455 KKYKEGSCVRVRILGFRHLEGLATGILKASAFE-----GLVFTHSDV--KPGMVVKGKVIAVDSFGAIVQFPGGVKALCP 527 (1152)
Q Consensus 455 ~~~~vG~~v~~rVi~~~~~~~~~~lS~k~~~~~-----~~~~~~~~l--~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp 527 (1152)
...++|+.+...+.-.+ +++....+.++.+.. .....++.+ +.|++|+|+|.++.++|++|+++ +++|++|
T Consensus 85 ~~~~vGD~i~~~I~~~~-fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP 162 (362)
T PRK12327 85 PAYELGDVIEIEVTPKD-FGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVLP 162 (362)
T ss_pred ccccCCCEEEEecCcCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEec
Confidence 45899999999887543 445444455544332 133456677 89999999999999999999997 6999999
Q ss_pred CCccccccccCCCCccccCCEEEEEEEEE--eC--CeEEEeec
Q 001115 528 LPHMSEFEIVKPGKKFKVGAELVFRVLGV--KS--KRITVTHK 566 (1152)
Q Consensus 528 ~~hls~~~~~~~~~~~kvG~~V~~rVl~v--~~--~~i~LS~K 566 (1152)
..++. |...|++|+.++|.|+.+ +. .+|.||+-
T Consensus 163 ~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 163 PAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred HHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 86653 567899999999999999 22 36888875
No 144
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.56 E-value=0.00022 Score=72.77 Aligned_cols=73 Identities=23% Similarity=0.321 Sum_probs=59.8
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCC-----------CCCCCCccCCCEEEEEEEEEecCC-----C
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPG-----------CEPSSMYHVGQVVKCRIMSSIPAS-----R 648 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~-----------~~~~~~f~vGq~v~vrV~~vd~~~-----~ 648 (1152)
.|+++.|.|+.+.++|+||.+ +.+.||+|.+++.+... ......|.+|+.|++||+.++... .
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 68999999999965421 112236899999999999998655 5
Q ss_pred EEEEEEeeCC
Q 001115 649 RINLSFMMKP 658 (1152)
Q Consensus 649 ri~lS~k~~~ 658 (1152)
++.+++++..
T Consensus 160 ~I~lTmrq~~ 169 (183)
T COG1095 160 KIGLTMRQPG 169 (183)
T ss_pred eEEEEecccc
Confidence 7889998764
No 145
>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=97.53 E-value=0.00022 Score=66.12 Aligned_cols=71 Identities=15% Similarity=0.170 Sum_probs=61.0
Q ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEeCCcccccccc--CCCCccccCCEEEEEEEEE-eCCeEEEee
Q 001115 497 KPGMVVKGKVIAVDSFGAIVQF--------PGGVKALCPLPHMSEFEIV--KPGKKFKVGAELVFRVLGV-KSKRITVTH 565 (1152)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i--------~~~v~g~vp~~hls~~~~~--~~~~~~kvG~~V~~rVl~v-~~~~i~LS~ 565 (1152)
++|++|-|+|+++....+.|+| ...+.|+++.+++...... ++.+.|++||-|+|+|+++ +.+.+.||.
T Consensus 5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Lst 84 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLST 84 (92)
T ss_pred CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEEe
Confidence 7899999999999999999999 7788999998877654433 4567899999999999999 667899998
Q ss_pred ch
Q 001115 566 KK 567 (1152)
Q Consensus 566 K~ 567 (1152)
+.
T Consensus 85 ~~ 86 (92)
T cd05791 85 AE 86 (92)
T ss_pred cC
Confidence 64
No 146
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.50 E-value=0.0003 Score=71.84 Aligned_cols=73 Identities=32% Similarity=0.541 Sum_probs=60.1
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccc----------cC-ccccccCCCEEEEEEEEEeCCC-----C
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQR----------AD-LSKTYYVGQSVRSNILDVNSET-----G 824 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~----------~~-~~~~f~~Gq~V~v~Vl~vd~e~-----~ 824 (1152)
.|+++.|.|.++.++|+||++ +-++||+|.+++.+.+. .+ -...|.+|+.|+++|..+.... -
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 499999999999999999998 47999999999997632 22 2237899999999999887544 5
Q ss_pred eEEEEeeccc
Q 001115 825 RITLSLKQSC 834 (1152)
Q Consensus 825 ri~LSlk~~~ 834 (1152)
++.++|++.-
T Consensus 160 ~I~lTmrq~~ 169 (183)
T COG1095 160 KIGLTMRQPG 169 (183)
T ss_pred eEEEEecccc
Confidence 7899999873
No 147
>PRK11642 exoribonuclease R; Provisional
Probab=97.48 E-value=0.00032 Score=89.40 Aligned_cols=73 Identities=25% Similarity=0.370 Sum_probs=63.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECC-CeEEEEeccCCCCcc-cc----------CccccccCCCEEEEEEEEEeCCCCeEE
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLG-RLTGFAPRSKAVDGQ-RA----------DLSKTYYVGQSVRSNILDVNSETGRIT 827 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~-~l~Glv~~s~ls~~~-~~----------~~~~~f~~Gq~V~v~Vl~vd~e~~ri~ 827 (1152)
++|+.+.|.|++|+++|+||++.+ +++||+|.+++.+.+ .- +....|++||.|.|+|.++|.++++|.
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 689999999999999999999976 499999999998642 11 224679999999999999999999999
Q ss_pred EEeec
Q 001115 828 LSLKQ 832 (1152)
Q Consensus 828 LSlk~ 832 (1152)
+++-.
T Consensus 722 f~l~~ 726 (813)
T PRK11642 722 FSLIS 726 (813)
T ss_pred EEEec
Confidence 99853
No 148
>PRK11642 exoribonuclease R; Provisional
Probab=97.46 E-value=0.00038 Score=88.82 Aligned_cols=72 Identities=24% Similarity=0.350 Sum_probs=62.3
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCC-eEEEEeccccCCCCC-----------CCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNG-VQGFAPRSELGLDPG-----------CEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~g-v~Gflp~sel~~~~~-----------~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
+.|+++.|+|++++++|+||++.+. ++||+|.+++.++.. ......|++||.|+|+|.++|.++++|.
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 5799999999999999999999764 999999999975421 1234579999999999999999999999
Q ss_pred EEEe
Q 001115 652 LSFM 655 (1152)
Q Consensus 652 lS~k 655 (1152)
+++-
T Consensus 722 f~l~ 725 (813)
T PRK11642 722 FSLI 725 (813)
T ss_pred EEEe
Confidence 9984
No 149
>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=97.45 E-value=0.00039 Score=87.46 Aligned_cols=72 Identities=24% Similarity=0.337 Sum_probs=62.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEC-CCeEEEEeccCCCCcc-c----------cCccccccCCCEEEEEEEEEeCCCCeE
Q 001115 759 IHPNSVVHGYVCNIIETGCFVRFL-GRLTGFAPRSKAVDGQ-R----------ADLSKTYYVGQSVRSNILDVNSETGRI 826 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~GvfV~~~-~~l~Glv~~s~ls~~~-~----------~~~~~~f~~Gq~V~v~Vl~vd~e~~ri 826 (1152)
-+.|+.+.|.|.+++++|+||++. .+++||+|.+++.+.+ . .+....|++||.|+|+|.++|.+++++
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I 649 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSI 649 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence 357999999999999999999997 7899999999998753 1 223467999999999999999999999
Q ss_pred EEEe
Q 001115 827 TLSL 830 (1152)
Q Consensus 827 ~LSl 830 (1152)
.+++
T Consensus 650 ~f~l 653 (654)
T TIGR00358 650 IFEL 653 (654)
T ss_pred EEEE
Confidence 8875
No 150
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.41 E-value=0.00066 Score=71.90 Aligned_cols=73 Identities=29% Similarity=0.447 Sum_probs=61.1
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcccc-----------CccccccCCCEEEEEEEEEeCCCC-----
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVNSETG----- 824 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~-----------~~~~~f~~Gq~V~v~Vl~vd~e~~----- 824 (1152)
.|+++.|.|.++.++|+||++. .+.|+++.+++.+++.. +....|+.|+.|+++|.+++.+.+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~ 159 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS 159 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence 6999999999999999999985 59999999999865322 234578999999999999996543
Q ss_pred eEEEEeeccc
Q 001115 825 RITLSLKQSC 834 (1152)
Q Consensus 825 ri~LSlk~~~ 834 (1152)
++.+|+++..
T Consensus 160 ~I~ls~~~~~ 169 (187)
T PRK08563 160 KIGLTMRQPG 169 (187)
T ss_pred EEEEEecCCC
Confidence 8899998763
No 151
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.40 E-value=0.00068 Score=71.78 Aligned_cols=73 Identities=26% Similarity=0.350 Sum_probs=60.7
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCC-----------CCCCCccCCCEEEEEEEEEecCCC-----
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGC-----------EPSSMYHVGQVVKCRIMSSIPASR----- 648 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~-----------~~~~~f~vGq~v~vrV~~vd~~~~----- 648 (1152)
.|+++.|.|+++.++|+||++. .+.||+|.+++..++.. +....|++|+.|+++|+++|..++
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~ 159 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS 159 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence 5999999999999999999995 69999999999654321 234568999999999999997653
Q ss_pred EEEEEEeeCC
Q 001115 649 RINLSFMMKP 658 (1152)
Q Consensus 649 ri~lS~k~~~ 658 (1152)
++.+|++...
T Consensus 160 ~I~ls~~~~~ 169 (187)
T PRK08563 160 KIGLTMRQPG 169 (187)
T ss_pred EEEEEecCCC
Confidence 7889998753
No 152
>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=97.39 E-value=0.00052 Score=86.29 Aligned_cols=71 Identities=25% Similarity=0.383 Sum_probs=61.7
Q ss_pred cCCceEEEEEEEEecCeEEEEEc-CCeEEEEeccccCCCC-----------CCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFY-NGVQGFAPRSELGLDP-----------GCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~-~gv~Gflp~sel~~~~-----------~~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
+.|+.+.|+|+++.++|+||++. .+++||+|.+++.++. ..+....|++||.|+|+|.++|++++++.
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 6899999999997642 12334579999999999999999999999
Q ss_pred EEE
Q 001115 652 LSF 654 (1152)
Q Consensus 652 lS~ 654 (1152)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 875
No 153
>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=97.26 E-value=0.0011 Score=59.61 Aligned_cols=62 Identities=26% Similarity=0.506 Sum_probs=40.7
Q ss_pred cCCcEEEEEEEEEeCCeEEEEe------------------CCCeeEEEEeeeccCCccccccccccCCCCCCEEEEEEEe
Q 001115 1062 DVGSLVQAEITEIKPLELRLKF------------------GIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIA 1123 (1152)
Q Consensus 1062 ~~G~~v~~~V~~i~~~~l~V~L------------------~~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~ 1123 (1152)
++|++|.|+|++|++.+..+.+ +....|.++..|+...+.+ .-...+.|++||+|+|+||+
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~D-kv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKD-KVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS-----GGGT--SSSEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccc-hhhHHhccCCCCEEEEEEee
Confidence 5799999999999999966554 3345799999999887654 22345789999999999997
Q ss_pred e
Q 001115 1124 K 1124 (1152)
Q Consensus 1124 ~ 1124 (1152)
.
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 3
No 154
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.11 E-value=0.0013 Score=58.00 Aligned_cols=69 Identities=14% Similarity=0.246 Sum_probs=61.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEC-CCeEEEEe-ccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEe
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFL-GRLTGFAP-RSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSL 830 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~-~~l~Glv~-~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSl 830 (1152)
.+|+.+. .|+.+.+.|++|.+. .++.|++. .++++..+....++.+ +|.++.|+|+++|.+++-|-||.
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 4688888 789999999999983 35999998 9999988888888888 99999999999999999998873
No 155
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.03 E-value=0.0012 Score=58.12 Aligned_cols=69 Identities=12% Similarity=0.213 Sum_probs=59.6
Q ss_pred cCCceEEEEEEEEecCeEEEEEcC-CeEEEEe-ccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYN-GVQGFAP-RSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSF 654 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~-gv~Gflp-~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~ 654 (1152)
.+|+.+. .|..+.+.|+||.+.+ +++|++. .++++.+++...+..+ +|.+..++|+.+|++++-|.||.
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 3589998 8889999999999853 6999888 9999877666677777 99999999999999999999884
No 156
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.97 E-value=0.0047 Score=56.73 Aligned_cols=64 Identities=16% Similarity=0.252 Sum_probs=48.6
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCC-----------CCCccCCCEEEEEEEEEecCCCE
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEP-----------SSMYHVGQVVKCRIMSSIPASRR 649 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~-----------~~~f~vGq~v~vrV~~vd~~~~r 649 (1152)
.|+++.|.|+++.+.|+||++ +.+++|++.+.+......+| ...+..|+.|++||+.+..+.+.
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 388999999999999999999 78999999988843221121 23477888888888887665433
No 157
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.94 E-value=0.0039 Score=73.23 Aligned_cols=143 Identities=18% Similarity=0.293 Sum_probs=97.7
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 755 DASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 755 ~~~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
+++++..|..++|.|.++..||+||++...+.||+|.++++. ...|.+|+.+.+.+..+-++++.+.+.....+
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~------~~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG------DPDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccCC------CCCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 578999999999999999999999999999999999999875 13688999999999999998888776655443
Q ss_pred cCCCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEE--EEEEEEEecce--EEEEecCCCCeEEEEEeEeeC
Q 001115 835 CSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVI--EGKVHESNDFG--VVVSFEEHSDVYGFITHHQLA 910 (1152)
Q Consensus 835 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v--~g~V~~i~~~g--~~v~l~~~~~v~G~i~~s~l~ 910 (1152)
..... .+- .++.. ....-+.+ .+|+.| +|.|+.|+.++ -++.+.+. +|.+...-+-
T Consensus 190 ~Y~~~-----~~~------ke~~r-----~~i~~id~-~ig~tV~I~GeV~qikqT~GPTVFtltDe---tg~i~aAAFe 249 (715)
T COG1107 190 RYREV-----QVE------KELPR-----TLIDDLDE-MIGKTVRIEGEVTQIKQTSGPTVFTLTDE---TGAIWAAAFE 249 (715)
T ss_pred cchhh-----hhh------hhccc-----ccHHHHHh-hcCceEEEEEEEEEEEEcCCCEEEEEecC---CCceehhhhc
Confidence 11100 000 00000 00011233 678765 68999998764 34466653 4665544332
Q ss_pred C------CcccCCCEEEEE
Q 001115 911 G------ATVESGSVIQAA 923 (1152)
Q Consensus 911 ~------~~~~~G~~v~a~ 923 (1152)
. -..++|+.|++.
T Consensus 250 ~aGvRAyP~IevGdiV~Vi 268 (715)
T COG1107 250 EAGVRAYPEIEVGDIVEVI 268 (715)
T ss_pred cCCcccCCCCCCCceEEEE
Confidence 1 257889988654
No 158
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.91 E-value=0.0018 Score=74.03 Aligned_cols=109 Identities=18% Similarity=0.221 Sum_probs=76.5
Q ss_pred CccccCCEEEEEEEEEe-CCeEEEeechhhhhhh--hhHhhhhhhc--cCCceEEEEEEEEec-CeEEEEEcCCeEEEEe
Q 001115 541 KKFKVGAELVFRVLGVK-SKRITVTHKKTLVKSK--LAILSSYAEA--TDRLITHGWITKIEK-HGCFVRFYNGVQGFAP 614 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v~-~~~i~LS~K~~l~~~~--~~~~~~~~~~--~~G~~~~G~V~~i~~-~G~~V~~~~gv~Gflp 614 (1152)
..+++|+.+...+---+ .+...-+.|+.+...- ..--.-|+++ +.|+++.|+|.++.. .++||++ ++..|+||
T Consensus 89 ~~~~vGd~i~~~i~~~~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~LP 167 (374)
T PRK12328 89 PSVEIGDELTYELSLENMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVLP 167 (374)
T ss_pred CCCCCCCEEEEecChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEeC
Confidence 35889999987653222 3333444555442210 0001123343 369999999999986 4599999 68999999
Q ss_pred ccccCCCCCCCCCCCccCCCEEEEEEEEEecCCC---EEEEEEee
Q 001115 615 RSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASR---RINLSFMM 656 (1152)
Q Consensus 615 ~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~---ri~lS~k~ 656 (1152)
.++.. |.+.|++|+.++|.|.+++...+ .+.||+..
T Consensus 168 ~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~ 206 (374)
T PRK12328 168 MKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTS 206 (374)
T ss_pred HHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence 98874 56789999999999999998766 78888853
No 159
>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=96.67 E-value=0.0088 Score=54.95 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=46.6
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCC-----------CCccccCCEEEEEEEEE
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKP-----------GKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~-----------~~~~kvG~~V~~rVl~v 556 (1152)
.|+++.|+|+++++.|++|+++ .+++|++..++.+....+| ...++.|+.|++||..+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v 69 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGT 69 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEE
Confidence 4899999999999999999997 7888888877765322222 24468999999999988
No 160
>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=96.62 E-value=0.0024 Score=52.90 Aligned_cols=60 Identities=18% Similarity=0.256 Sum_probs=50.4
Q ss_pred CCEEEEEEEEEecCEEEEEEcCCCceEEEEEeccccccc-CCcCCCCCCCEEEEEEEeecC
Q 001115 971 HQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQK-FPQKQFLNGQSVIATVMALPS 1030 (1152)
Q Consensus 971 G~~v~g~V~~i~~~~l~V~l~~~~~~~~~~~~s~~~~~~-~~~~~f~~Gq~v~~~V~~~d~ 1030 (1152)
++..++.|+++.+++++|+|...+++.++--.+++|+.. ...++|++||.+.+++.....
T Consensus 1 ~S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred CCccchhhhhhhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCcc
Confidence 467789999999999999998777776776678998654 478899999999999988763
No 161
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.52 E-value=0.0096 Score=50.67 Aligned_cols=61 Identities=28% Similarity=0.341 Sum_probs=37.2
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEEeCCeEEEeec
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHK 566 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v~~~~i~LS~K 566 (1152)
.|++.+.+|.+++++|+|++.+++-+-++|..++. ..+++|++|.+.|..-..+++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYLDKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEECCCCCEEEecC
Confidence 48899999999999999999988899999987653 35789999999986656778888875
No 162
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.44 E-value=0.013 Score=69.11 Aligned_cols=147 Identities=18% Similarity=0.258 Sum_probs=100.2
Q ss_pred hhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 578 SSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 578 ~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
-+++++..|..++|+|.++.+||+||++...+.|++|.++++.. ..|.+|+.+-+++..+-+.++.+.+-....
T Consensus 115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~ 188 (715)
T COG1107 115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGL 188 (715)
T ss_pred cchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCC
Confidence 35778889999999999999999999999999999999999742 247899999999999999878777665433
Q ss_pred CC----------Cc---cccccccCCCE--EEEEEEEEeCC-c-EEEEEeeCCceEEEEeCCCcCCccccccccccccCC
Q 001115 658 PT----------RV---SEDDLVKLGSL--VSGVVDVVTPN-A-VVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKP 720 (1152)
Q Consensus 658 ~~----------~~---~~~~~l~vG~i--v~g~V~~v~~~-g-~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~ 720 (1152)
.. +- ....+ .+|+. |+|.|+.+... | -+..| -.-+|++|..-+..--. ...-.+++
T Consensus 189 ~~Y~~~~~~ke~~r~~i~~id~-~ig~tV~I~GeV~qikqT~GPTVFtl---tDetg~i~aAAFe~aGv---RAyP~Iev 261 (715)
T COG1107 189 DRYREVQVEKELPRTLIDDLDE-MIGKTVRIEGEVTQIKQTSGPTVFTL---TDETGAIWAAAFEEAGV---RAYPEIEV 261 (715)
T ss_pred ccchhhhhhhhcccccHHHHHh-hcCceEEEEEEEEEEEEcCCCEEEEE---ecCCCceehhhhccCCc---ccCCCCCC
Confidence 21 00 00112 57876 47889887433 3 34455 23456666655543110 01125789
Q ss_pred CCeEeEEEEeecccCce
Q 001115 721 GYEFDQLLVLDNESSNL 737 (1152)
Q Consensus 721 G~~v~~vl~~d~~~~~i 737 (1152)
|+.++.+=.++...+++
T Consensus 262 GdiV~ViG~V~~r~g~l 278 (715)
T COG1107 262 GDIVEVIGEVTRRDGRL 278 (715)
T ss_pred CceEEEEEEEeecCCcE
Confidence 99988444455544544
No 163
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.43 E-value=0.015 Score=59.72 Aligned_cols=77 Identities=23% Similarity=0.343 Sum_probs=59.3
Q ss_pred ccCCCcCCcEEEEEEEEEeCCeEEEEeC----------CCeeEEEEeeeccCCccccccccccCCCCCCEEEEEEEeeec
Q 001115 1057 KKSSYDVGSLVQAEITEIKPLELRLKFG----------IGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSN 1126 (1152)
Q Consensus 1057 ~~~~~~~G~~v~~~V~~i~~~~l~V~L~----------~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~~ 1126 (1152)
+..-.+.|++|-|+|++++....+|++- +...|-+|++++.|.|-. +-...|++||+|+|+|++.-.
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~---~~~d~f~~GDivrA~Vis~~~ 134 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE---KLSDAFRIGDIVRARVISTGD 134 (188)
T ss_pred CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc---ccccccccccEEEEEEEecCC
Confidence 3556788999999999999988877753 234678999999999865 222589999999999999741
Q ss_pred CCCCCCCceEEEEeecCC
Q 001115 1127 KPDMKKSFLWELSIKPSM 1144 (1152)
Q Consensus 1127 ~~~~~k~~~~~LSlr~s~ 1144 (1152)
-+.||.+-.+
T Consensus 135 --------~~~Lst~~~d 144 (188)
T COG1096 135 --------PIQLSTKGND 144 (188)
T ss_pred --------CeEEEecCCc
Confidence 1677766443
No 164
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.39 E-value=0.0022 Score=68.21 Aligned_cols=75 Identities=24% Similarity=0.336 Sum_probs=70.4
Q ss_pred CCCCEEEEEEEEEecceEEEEE--CCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRF--LGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSC 834 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~--~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~ 834 (1152)
.++++|-+-|++|.+.|++|.+ ++++.|++..|+||..++...+...++|..=.|.|+.||.+++-|-||.+...
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCC
Confidence 3689999999999999999998 68999999999999999999999999999999999999999999999998764
No 165
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.32 E-value=0.0047 Score=71.80 Aligned_cols=108 Identities=14% Similarity=0.190 Sum_probs=77.4
Q ss_pred hccccCCCCEEEEEEEEE-ecCCCeEEEEccccccc-----ccccccccc--CCCCEEEEEEEEEeCCeEEEEeC---C-
Q 001115 453 LEKKYKEGSCVRVRILGF-RHLEGLATGILKASAFE-----GLVFTHSDV--KPGMVVKGKVIAVDSFGAIVQFP---G- 520 (1152)
Q Consensus 453 ~~~~~~vG~~v~~rVi~~-~~~~~~~~lS~k~~~~~-----~~~~~~~~l--~~G~iv~g~V~~v~~~G~~V~i~---~- 520 (1152)
+...+++|+.+...|.-. ..++++...+.++.+.. +....++.+ +.|++|+|+|.++...+++|+++ +
T Consensus 99 i~~~~~iGD~v~~~v~~~~~~fgRiAAq~aKQvi~Qkire~ER~~i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~ 178 (449)
T PRK12329 99 VADEAQLGDTVVLDVTPEQEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQ 178 (449)
T ss_pred hCCCCcCCCEEEEecCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCC
Confidence 345699999998777421 23455555555553321 122233344 58999999999999999999993 3
Q ss_pred -CeEEEEeCCccccccccCCCCccccCCEEEEEEEEE-eC----CeEEEeec
Q 001115 521 -GVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-KS----KRITVTHK 566 (1152)
Q Consensus 521 -~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v-~~----~~i~LS~K 566 (1152)
+++|++|..+. -|.+.|++|+.|+|.|..| .. -+|.||+-
T Consensus 179 ~~~EaiLP~~Eq------ip~E~y~~Gdrika~i~~V~~~~~kGpqIilSRt 224 (449)
T PRK12329 179 PEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSRA 224 (449)
T ss_pred cceEEEecHHHc------CCCCcCCCCCEEEEEEEEeecCCCCCCEEEEEcC
Confidence 39999998764 3678999999999999999 32 27888875
No 166
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.29 E-value=0.079 Score=56.80 Aligned_cols=104 Identities=15% Similarity=0.191 Sum_probs=76.1
Q ss_pred CccccCCEEEEEEEEE---eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccc
Q 001115 541 KKFKVGAELVFRVLGV---KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSE 617 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v---~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~se 617 (1152)
..|..|+++...+... ..+.+.+ - |.-..| .-..|+++.|.|..+...+..|++.....|++|.|+
T Consensus 28 Gty~~~~~iyssv~G~~~~~~~~v~V--I--------pl~g~Y-iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~ 96 (239)
T COG1097 28 GTYFEGGKIYSSVVGLLDVKGKLVRV--I--------PLEGRY-IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSD 96 (239)
T ss_pred CcEecCCEEEEEEEeEEEEeCCEEEE--E--------eCCCcc-cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhh
Confidence 3566778888777766 2333221 1 111111 113699999999999999999999888999999999
Q ss_pred cCCCC----CCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 618 LGLDP----GCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 618 l~~~~----~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
+-.+. ..++...|.+|+.|.|+|..+|+ .....|+++.
T Consensus 97 ~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~ 138 (239)
T COG1097 97 FLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKD 138 (239)
T ss_pred hhcccccccccccccccccCCEEEEEEEEccC-CCceEEEeec
Confidence 94333 24667789999999999999997 5778888853
No 167
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.26 E-value=0.015 Score=60.66 Aligned_cols=71 Identities=18% Similarity=0.165 Sum_probs=55.2
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccc------------cCCCCccccCCEEEEEEEEE--e--CCeE
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEI------------VKPGKKFKVGAELVFRVLGV--K--SKRI 561 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~------------~~~~~~~kvG~~V~~rVl~v--~--~~~i 561 (1152)
.|+++.|.|+++++.|++|+++ -++++||.+.|.+... .+-+..++.|+.|++||..+ + .-.+
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~ 159 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFA 159 (176)
T ss_pred CCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEE
Confidence 6999999999999999999997 7889999998874310 11234568999999999998 3 2356
Q ss_pred EEeechhh
Q 001115 562 TVTHKKTL 569 (1152)
Q Consensus 562 ~LS~K~~l 569 (1152)
..|+|+..
T Consensus 160 i~T~~~~~ 167 (176)
T PTZ00162 160 IATINSDY 167 (176)
T ss_pred EEEecCCC
Confidence 66777543
No 168
>PRK05054 exoribonuclease II; Provisional
Probab=96.15 E-value=0.018 Score=72.34 Aligned_cols=69 Identities=20% Similarity=0.231 Sum_probs=56.7
Q ss_pred CCEEEEEEEEEecceEEEEEC-CCeEEEEeccCCCCc---cc--cC-------ccccccCCCEEEEEEEEEeCCCCeEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRFL-GRLTGFAPRSKAVDG---QR--AD-------LSKTYYVGQSVRSNILDVNSETGRITL 828 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~-~~l~Glv~~s~ls~~---~~--~~-------~~~~f~~Gq~V~v~Vl~vd~e~~ri~L 828 (1152)
|+.+.|.|..++++|+||++. .++.||+|.+.+.+. +. .+ -...|+.||.|+|+|.++|.++++|.+
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 459999999999999999995 579999999998652 21 11 124699999999999999999999877
Q ss_pred Ee
Q 001115 829 SL 830 (1152)
Q Consensus 829 Sl 830 (1152)
.+
T Consensus 642 ~~ 643 (644)
T PRK05054 642 RP 643 (644)
T ss_pred EE
Confidence 64
No 169
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.12 E-value=0.045 Score=56.22 Aligned_cols=105 Identities=19% Similarity=0.201 Sum_probs=76.4
Q ss_pred CccccCCEEEEEEEEE---eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcC----------
Q 001115 541 KKFKVGAELVFRVLGV---KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYN---------- 607 (1152)
Q Consensus 541 ~~~kvG~~V~~rVl~v---~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~---------- 607 (1152)
..|..|..|.+-+..+ +.+....+.++... ...-.+.|+++.|.|+++....+.|++.+
T Consensus 25 gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~--------~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~ 96 (188)
T COG1096 25 GTYEEGGEIRAAATGVVRRDDKNRVISVKPGKK--------TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELAT 96 (188)
T ss_pred CeEeECCEEEEeecccEEEcccceEEEeccCCC--------CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCC
Confidence 3455666666666655 45556666654332 12234679999999999999999888752
Q ss_pred CeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 608 GVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 608 gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
-..|-+|.|+++..+..+.++.|++|+.|+++|++.- ..+.||.+.
T Consensus 97 ~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~~~Lst~~ 142 (188)
T COG1096 97 SGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DPIQLSTKG 142 (188)
T ss_pred CceeeEEEEecccccccccccccccccEEEEEEEecC---CCeEEEecC
Confidence 1447899999988888888999999999999999873 357777753
No 170
>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=96.10 E-value=0.015 Score=52.36 Aligned_cols=62 Identities=19% Similarity=0.306 Sum_probs=37.3
Q ss_pred CCCCEEEEEEEEEecceEEEEc------------------CCCcEEEEeccccCChhhcccccccccCCCCCccCCCCEE
Q 001115 132 SAGMKLWGVVAEVNEKDLVICL------------------PGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLV 193 (1152)
Q Consensus 132 ~~G~~vlG~V~~i~~~~l~vsl------------------p~~l~G~v~~~~is~~~~~~~~~~~~~~~l~~~f~vGq~v 193 (1152)
.+|..|+|.|++|++....+++ ...+.|.++..+|-.. +-+...+.+.|++|++|
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~t-------e~Dkv~~~~~FrpGDIV 75 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRAT-------EKDKVKMYDCFRPGDIV 75 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT--------SS----GGGT--SSSEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeeccc-------ccchhhHHhccCCCCEE
Confidence 3699999999999998875554 2356666666666543 11123567899999999
Q ss_pred EEEEEEE
Q 001115 194 SCIVLQL 200 (1152)
Q Consensus 194 ~~~V~~~ 200 (1152)
+|.|+++
T Consensus 76 rA~ViSl 82 (82)
T PF10447_consen 76 RARVISL 82 (82)
T ss_dssp EEEEEEE
T ss_pred EEEEeeC
Confidence 9999974
No 171
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.06 E-value=0.0061 Score=76.62 Aligned_cols=78 Identities=21% Similarity=0.220 Sum_probs=68.5
Q ss_pred ccCCCCCEEEEEEEEEecce---EEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 757 SHIHPNSVVHGYVCNIIETG---CFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~G---vfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
+.+.+|..+.+.|+.++..- +-|.+..|++|++|..++|+..+.+|...+++||+|.|+|+++|.++=-..||++.+
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 44778999999999997654 456789999999999999999999999999999999999999998777777888776
Q ss_pred c
Q 001115 834 C 834 (1152)
Q Consensus 834 ~ 834 (1152)
+
T Consensus 1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred H
Confidence 4
No 172
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=95.94 E-value=0.031 Score=58.36 Aligned_cols=72 Identities=18% Similarity=0.221 Sum_probs=55.7
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCc--ccc----------CccccccCCCEEEEEEEEEeCC--CCeE
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG--QRA----------DLSKTYYVGQSVRSNILDVNSE--TGRI 826 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~--~~~----------~~~~~f~~Gq~V~v~Vl~vd~e--~~ri 826 (1152)
.|+++.|.|++++++|+||++ |-+++|+|.+.|.+. |.. +-...+..|+.|++||..+.-+ .-+.
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~-Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~ 159 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQA-GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFA 159 (176)
T ss_pred CCCEEEEEEEEEecceEEEEe-eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEE
Confidence 599999999999999999998 678899999999743 211 1134588999999999877633 3456
Q ss_pred EEEeecc
Q 001115 827 TLSLKQS 833 (1152)
Q Consensus 827 ~LSlk~~ 833 (1152)
.+||++.
T Consensus 160 i~T~~~~ 166 (176)
T PTZ00162 160 IATINSD 166 (176)
T ss_pred EEEecCC
Confidence 6777765
No 173
>PRK05054 exoribonuclease II; Provisional
Probab=95.91 E-value=0.024 Score=71.29 Aligned_cols=71 Identities=23% Similarity=0.241 Sum_probs=57.0
Q ss_pred cCC--ceEEEEEEEEecCeEEEEEcC-CeEEEEeccccCCC---C--CCC-------CCCCccCCCEEEEEEEEEecCCC
Q 001115 584 TDR--LITHGWITKIEKHGCFVRFYN-GVQGFAPRSELGLD---P--GCE-------PSSMYHVGQVVKCRIMSSIPASR 648 (1152)
Q Consensus 584 ~~G--~~~~G~V~~i~~~G~~V~~~~-gv~Gflp~sel~~~---~--~~~-------~~~~f~vGq~v~vrV~~vd~~~~ 648 (1152)
++| ..+.|.|+.++++|+||++.+ ++.||+|.+.|... + ..+ -...|++||.|+|+|.++|.+++
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 355 499999999999999999964 69999999998432 1 011 01369999999999999999999
Q ss_pred EEEEEE
Q 001115 649 RINLSF 654 (1152)
Q Consensus 649 ri~lS~ 654 (1152)
++.+.+
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 998764
No 174
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=95.91 E-value=0.027 Score=47.99 Aligned_cols=61 Identities=18% Similarity=0.197 Sum_probs=35.6
Q ss_pred CCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcCCccccccccccccCCCCeEeEEEEeecccCceeeecc
Q 001115 669 LGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAK 742 (1152)
Q Consensus 669 vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~~vl~~d~~~~~i~lS~K 742 (1152)
+|++.+.+|.++++.|+|++. .++-+-+||..++. ..+++|++++..+..|.+. ++..|+|
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 589999999999999999987 56688899877653 3588999999888888776 5777765
No 175
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.90 E-value=0.0075 Score=75.85 Aligned_cols=76 Identities=25% Similarity=0.295 Sum_probs=66.6
Q ss_pred ccCCceEEEEEEEEecC--eE-EEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCC
Q 001115 583 ATDRLITHGWITKIEKH--GC-FVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKP 658 (1152)
Q Consensus 583 ~~~G~~~~G~V~~i~~~--G~-~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~ 658 (1152)
+..|.++.++|++++.. +| -|.+.+|+.||+|.++++...+.+|...+++||+|.|+|+++|.++=...|||+.+.
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~sd 1061 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTSD 1061 (1299)
T ss_pred hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhHH
Confidence 45799999999999854 33 568899999999999999888889999999999999999999998878889987653
No 176
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.74 E-value=0.029 Score=64.50 Aligned_cols=70 Identities=14% Similarity=0.302 Sum_probs=58.2
Q ss_pred CCCEEEEEEEEEecC-eEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEEeCCCC---EEEEccCcccccc
Q 001115 232 EGMVLTAYVKSIEDH-GYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRK---VVYLSSDPDTVSK 305 (1152)
Q Consensus 232 ~g~~l~~~V~svedh-G~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~~~---~v~ls~~~~~~~~ 305 (1152)
.|.+++|.|.+++.. ++++|+| +..|+||.++.-+.+ .|.+|+.+.|.|..+..+.+ .+.||.....+..
T Consensus 138 ~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eqip~E--~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v~ 211 (374)
T PRK12328 138 VGKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNRIKGE--KFKVGDVVKAVLKRVKIDKNNGILIELSRTSPKFLE 211 (374)
T ss_pred cCcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHcCCCC--cCCCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHHH
Confidence 699999999999974 5999998 699999999865555 89999999999999987654 7888875555543
No 177
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.74 E-value=0.057 Score=57.84 Aligned_cols=73 Identities=23% Similarity=0.321 Sum_probs=62.5
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCcc----ccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ----RADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~----~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|+.|-|.|..+...+-.|++.....+++|.+++.+.. ..+....|.+|+.|.|+|.++|. .....|++|..
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~ 139 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDE 139 (239)
T ss_pred CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEeecC
Confidence 479999999999999999999999999999999996543 24567789999999999999996 56778887543
No 178
>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=95.64 E-value=0.029 Score=66.35 Aligned_cols=60 Identities=22% Similarity=0.252 Sum_probs=51.5
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEECCCeEEEEeccCCCCc------------cccCccccccCCCEEEEEEEE
Q 001115 759 IHPNSVVHGYVCNIIET--GCFVRFLGRLTGFAPRSKAVDG------------QRADLSKTYYVGQSVRSNILD 818 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~~--GvfV~~~~~l~Glv~~s~ls~~------------~~~~~~~~f~~Gq~V~v~Vl~ 818 (1152)
..+|.++.|.|.++.+. |+||++..+-.||+|.+++.+. ...+..+.+++||.|.|.|..
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 45799999999999998 9999999999999999998653 123445579999999999998
No 179
>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=95.59 E-value=0.028 Score=66.47 Aligned_cols=59 Identities=25% Similarity=0.347 Sum_probs=49.3
Q ss_pred cCCceEEEEEEEEecC--eEEEEEcCCeEEEEeccccCCC------------CCCCCCCCccCCCEEEEEEEE
Q 001115 584 TDRLITHGWITKIEKH--GCFVRFYNGVQGFAPRSELGLD------------PGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~--G~~V~~~~gv~Gflp~sel~~~------------~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.+|.++.|.|.++.++ |+||+++.+-.||+|.+++.+. ...+..+.+++||.+.|+|+.
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 4799999999999998 9999999999999999998542 122344568899999999987
No 180
>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=95.56 E-value=0.067 Score=48.69 Aligned_cols=69 Identities=17% Similarity=0.090 Sum_probs=56.6
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE-eCCeEEEeec
Q 001115 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV-KSKRITVTHK 566 (1152)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v-~~~~i~LS~K 566 (1152)
++|++|=|+|+.+...+..|+|+....|++|..++... ..+....+++|+-|-|||..+ ......||+.
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~ 74 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCV 74 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEe
Confidence 57999999999999999999999888999998776432 233445789999999999988 4556777764
No 181
>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=95.54 E-value=0.083 Score=48.11 Aligned_cols=72 Identities=17% Similarity=0.027 Sum_probs=59.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
++|+.|-|.|..+...+.+|++.....|++|...+... .+.....|.+|+.|.|+|.++|+. ....|++...
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~ 76 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS 76 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence 47999999999999999999998888999999876533 223356799999999999999875 4578888654
No 182
>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=95.32 E-value=0.14 Score=42.12 Aligned_cols=64 Identities=25% Similarity=0.295 Sum_probs=47.2
Q ss_pred ccEEEEEEEEEecceEEE-EecCCCCeEEEEEeEeeCCCcccCCCEEEEEEEEEECCCCEEEEEE
Q 001115 875 GSVIEGKVHESNDFGVVV-SFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSL 938 (1152)
Q Consensus 875 G~~v~g~V~~i~~~g~~v-~l~~~~~v~G~i~~s~l~~~~~~~G~~v~a~Vl~vd~~~~~v~LSl 938 (1152)
|+..+-.|.++.++|-.. .-+.-.++.-.....|+.+.++.+||+++|.|+.+|.-+..+.+|+
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 677888899988887543 2222123434556678888899999999999999998877777764
No 183
>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=95.16 E-value=0.062 Score=67.46 Aligned_cols=68 Identities=19% Similarity=0.240 Sum_probs=55.2
Q ss_pred CCEEEEEEEEEecceEEEEE-CCCeEEEEeccCCCC--c-c--ccCc-------cccccCCCEEEEEEEEEeCCCCeEEE
Q 001115 762 NSVVHGYVCNIIETGCFVRF-LGRLTGFAPRSKAVD--G-Q--RADL-------SKTYYVGQSVRSNILDVNSETGRITL 828 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~-~~~l~Glv~~s~ls~--~-~--~~~~-------~~~f~~Gq~V~v~Vl~vd~e~~ri~L 828 (1152)
|..+.|.|..++.+|+||++ ..++.||+|.+.+.+ . + ..+. ...|+.||.|+++|.++|.++++|.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 45899999999999999999 568999999999865 2 2 1111 12599999999999999999988865
Q ss_pred E
Q 001115 829 S 829 (1152)
Q Consensus 829 S 829 (1152)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 184
>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=94.66 E-value=0.071 Score=66.98 Aligned_cols=68 Identities=24% Similarity=0.316 Sum_probs=53.8
Q ss_pred CceEEEEEEEEecCeEEEEEc-CCeEEEEeccccCC--C-C--CCCC-------CCCccCCCEEEEEEEEEecCCCEEEE
Q 001115 586 RLITHGWITKIEKHGCFVRFY-NGVQGFAPRSELGL--D-P--GCEP-------SSMYHVGQVVKCRIMSSIPASRRINL 652 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~~V~~~-~gv~Gflp~sel~~--~-~--~~~~-------~~~f~vGq~v~vrV~~vd~~~~ri~l 652 (1152)
|..+.|.|+.+.++|+||++. +++.||+|.+.+.. + . ..+. ...|++||.|+++|.++|.++++|.+
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 348999999999999999994 57999999999843 1 1 1111 12599999999999999999888865
Q ss_pred E
Q 001115 653 S 653 (1152)
Q Consensus 653 S 653 (1152)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 185
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.61 E-value=0.1 Score=60.99 Aligned_cols=71 Identities=20% Similarity=0.317 Sum_probs=58.0
Q ss_pred CCCEEEEEEEEEecCeEEEEe----CCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEEeCC---CCEEEEccCccccc
Q 001115 232 EGMVLTAYVKSIEDHGYILHF----GLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRT---RKVVYLSSDPDTVS 304 (1152)
Q Consensus 232 ~g~~l~~~V~svedhG~ivd~----Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~---~~~v~ls~~~~~~~ 304 (1152)
.|.+++|.|..++.++++||+ |-.++.|+||+++.-+.. .|++|+.+.|.|..+... +-.+.||.....+.
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 599999999999999999998 433489999999865544 899999999999999654 45688886554443
No 186
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=94.34 E-value=0.11 Score=66.32 Aligned_cols=75 Identities=21% Similarity=0.304 Sum_probs=61.8
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEECCC-eEEEEeccCCCCcccc-----------CccccccCCCEEEEEEEEEeCCC
Q 001115 756 ASHIHPNSVVHGYVCNIIETGCFVRFLGR-LTGFAPRSKAVDGQRA-----------DLSKTYYVGQSVRSNILDVNSET 823 (1152)
Q Consensus 756 ~~~~~~G~~v~G~V~~i~~~GvfV~~~~~-l~Glv~~s~ls~~~~~-----------~~~~~f~~Gq~V~v~Vl~vd~e~ 823 (1152)
|-.-++|..+.|+|..++.+|+||.+.+. ++|++|.+.+.+.+.. .....|..||.|.+++.+++...
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 34456899999999999999999999765 9999999999853211 12336999999999999999998
Q ss_pred CeEEEEe
Q 001115 824 GRITLSL 830 (1152)
Q Consensus 824 ~ri~LSl 830 (1152)
+++.+++
T Consensus 697 ~~i~~~~ 703 (706)
T COG0557 697 RKIDFEL 703 (706)
T ss_pred cceEEEe
Confidence 8888775
No 187
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=93.90 E-value=0.027 Score=60.16 Aligned_cols=73 Identities=21% Similarity=0.205 Sum_probs=67.0
Q ss_pred CCceEEEEEEEEecCeEEEEE--cCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeC
Q 001115 585 DRLITHGWITKIEKHGCFVRF--YNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMK 657 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~--~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~ 657 (1152)
+++++.+-|..|.+-|+||.+ ||++.|++-.||||.+++...+...++|..=-|.|+.+|.+++-|.||.+.-
T Consensus 16 v~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV 90 (304)
T KOG2916|consen 16 VEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV 90 (304)
T ss_pred cccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence 599999999999999999998 5899999999999988777777889999999999999999999999998753
No 188
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=93.69 E-value=0.18 Score=64.39 Aligned_cols=71 Identities=24% Similarity=0.334 Sum_probs=59.6
Q ss_pred cCCceEEEEEEEEecCeEEEEEcCC-eEEEEeccccCCCC-----------CCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 584 TDRLITHGWITKIEKHGCFVRFYNG-VQGFAPRSELGLDP-----------GCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~~G~~V~~~~g-v~Gflp~sel~~~~-----------~~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
+.|+...|+|+++..+|+||.+.+. +.|++|.+.+...+ .......|++|+.|+++++++|...+++.
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~ 700 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKID 700 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceE
Confidence 5799999999999999999999764 89999999996321 12223469999999999999999999888
Q ss_pred EEE
Q 001115 652 LSF 654 (1152)
Q Consensus 652 lS~ 654 (1152)
+++
T Consensus 701 ~~~ 703 (706)
T COG0557 701 FEL 703 (706)
T ss_pred EEe
Confidence 876
No 189
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=93.04 E-value=0.34 Score=48.85 Aligned_cols=63 Identities=22% Similarity=0.378 Sum_probs=49.7
Q ss_pred cCCcEEEEEEEEEeCCeEEEEe--------CCCeeEEEEeeeccCCccccccccccCCCCCCEEEEEEEeee
Q 001115 1062 DVGSLVQAEITEIKPLELRLKF--------GIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKS 1125 (1152)
Q Consensus 1062 ~~G~~v~~~V~~i~~~~l~V~L--------~~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~ 1125 (1152)
.+|++|.|||..+...+..+.+ .+...|.++.-|+.... .+...+.+.|++||+|.|+|++..
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tE-kdrv~v~ksFrPgDiVlAkVis~~ 137 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATE-KDRVKVYKSFRPGDIVLAKVISLG 137 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccc-cchhhhhhccCCCcEEEEEEeecC
Confidence 4699999999999988865553 45568999998887542 223567789999999999999954
No 190
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=91.90 E-value=0.65 Score=43.05 Aligned_cols=61 Identities=23% Similarity=0.455 Sum_probs=49.6
Q ss_pred cccccccccCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE
Q 001115 488 GLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 488 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1152)
++++.+.+ ..|.+|.|+|..+.++-+++++++.+.++|+.... + .++|..|.+|..|+...
T Consensus 14 S~fi~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~------~-~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 14 SPFIQLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAV------N-GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred ChhhhcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecccc------c-ccccccCCEEEEEECCH
Confidence 34555555 58999999999999999999999999999986432 2 25799999999998654
No 191
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=91.60 E-value=0.67 Score=45.30 Aligned_cols=59 Identities=24% Similarity=0.242 Sum_probs=43.5
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCcccccc------------c-cCCCCccccCCEEEEEEEEE
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFE------------I-VKPGKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~------------~-~~~~~~~kvG~~V~~rVl~v 556 (1152)
+|+++.|+|.+.+..|+.|.++-.-+-+||...|.+.. . ..-+--|..|+.|++||..+
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 69999999999999999999986667999998887421 1 12223347999999999887
No 192
>PRK10811 rne ribonuclease E; Reviewed
Probab=89.69 E-value=0.78 Score=58.31 Aligned_cols=71 Identities=24% Similarity=0.265 Sum_probs=52.5
Q ss_pred cCCceEEEEEEEEec--CeEEEEEcCCeEEEEeccccCCCCC---------CCCCCCccCCCEEEEEEEEEecCCCEEEE
Q 001115 584 TDRLITHGWITKIEK--HGCFVRFYNGVQGFAPRSELGLDPG---------CEPSSMYHVGQVVKCRIMSSIPASRRINL 652 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~--~G~~V~~~~gv~Gflp~sel~~~~~---------~~~~~~f~vGq~v~vrV~~vd~~~~ri~l 652 (1152)
.+|.++.|+|.+|.+ .++||+++.+-.||||.+++..... ......++.||.|-|.|..-.-..+--.|
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 479999999999997 5899999999999999998842211 12234688999999999875433333333
Q ss_pred EE
Q 001115 653 SF 654 (1152)
Q Consensus 653 S~ 654 (1152)
|.
T Consensus 117 Tt 118 (1068)
T PRK10811 117 TT 118 (1068)
T ss_pred ee
Confidence 33
No 193
>PRK10811 rne ribonuclease E; Reviewed
Probab=89.36 E-value=0.89 Score=57.79 Aligned_cols=61 Identities=18% Similarity=0.252 Sum_probs=48.9
Q ss_pred CCCCEEEEEEEEEec--ceEEEEECCCeEEEEeccCCCCcccc---------CccccccCCCEEEEEEEEEe
Q 001115 760 HPNSVVHGYVCNIIE--TGCFVRFLGRLTGFAPRSKAVDGQRA---------DLSKTYYVGQSVRSNILDVN 820 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~--~GvfV~~~~~l~Glv~~s~ls~~~~~---------~~~~~f~~Gq~V~v~Vl~vd 820 (1152)
.+|.+|.|.|.+|.+ .++||+++.+..||+|.+++...+.. +....+++||.|.|.|..-.
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 479999999999976 58999999999999999888543221 12446889999999998733
No 194
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=89.34 E-value=1.1 Score=45.30 Aligned_cols=68 Identities=21% Similarity=0.242 Sum_probs=51.5
Q ss_pred CCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEeCCcccccc--ccCCCCccccCCEEEEEEEEE-eCCeEEEee
Q 001115 498 PGMVVKGKVIAVDSFGAIVQF--------PGGVKALCPLPHMSEFE--IVKPGKKFKVGAELVFRVLGV-KSKRITVTH 565 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i--------~~~v~g~vp~~hls~~~--~~~~~~~~kvG~~V~~rVl~v-~~~~i~LS~ 565 (1152)
.|+||.++|..++..-+.|+| ...+.|+|+..++.... ..++-+.|++||-|.++|++. .....+||.
T Consensus 68 ~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTt 146 (193)
T KOG3409|consen 68 VGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTT 146 (193)
T ss_pred cCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEE
Confidence 588888888888777666665 35788999998776542 345667899999999999997 555666665
No 195
>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=87.91 E-value=0.72 Score=38.72 Aligned_cols=59 Identities=29% Similarity=0.300 Sum_probs=47.5
Q ss_pred CCEEEEEEEEEecceEEEEEC--CCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeC
Q 001115 762 NSVVHGYVCNIIETGCFVRFL--GRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNS 821 (1152)
Q Consensus 762 G~~v~G~V~~i~~~GvfV~~~--~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~ 821 (1152)
|+.+++.|..+.+.-+.|++. +.+..+--.|.+++.+..+ ++.|++||.+.+.+...+.
T Consensus 1 ~S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~-seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFD-SEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred CCccchhhhhhhhceEEEEeeccccEEEEEchhhcccccccc-ceeeeccceEEEEEecCcc
Confidence 345678889998888899984 6788888889999887766 5689999999998876554
No 196
>PRK11712 ribonuclease G; Provisional
Probab=86.88 E-value=1.1 Score=54.20 Aligned_cols=59 Identities=15% Similarity=0.178 Sum_probs=45.0
Q ss_pred cCCceEEEEEEEEec--CeEEEEEcCCeEEEEeccccCCCC------------CCCCCCCccCCCEEEEEEEE
Q 001115 584 TDRLITHGWITKIEK--HGCFVRFYNGVQGFAPRSELGLDP------------GCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 584 ~~G~~~~G~V~~i~~--~G~~V~~~~gv~Gflp~sel~~~~------------~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.+|.++.|.|.++.+ .++||+++.+-.||+|.+++.... .....+.++.||.+-|.|+.
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 589999999999999999873100 01123347788888888875
No 197
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=85.93 E-value=4.6 Score=40.70 Aligned_cols=64 Identities=25% Similarity=0.396 Sum_probs=44.6
Q ss_pred CCceEEEEEEEEecCeEEEEEcCCeEEEEeccccC----CCCCCC-C------CCCccCCCEEEEEEEEEecCCCE
Q 001115 585 DRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELG----LDPGCE-P------SSMYHVGQVVKCRIMSSIPASRR 649 (1152)
Q Consensus 585 ~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~----~~~~~~-~------~~~f~vGq~v~vrV~~vd~~~~r 649 (1152)
.|++++|+|+++.+.|+|++. |.++-|+..-.+. ..+.++ | .....+|..|+++|+..-.+...
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 6788776543331 112222 1 12477888888888876554433
No 198
>PRK11712 ribonuclease G; Provisional
Probab=84.82 E-value=2.2 Score=51.78 Aligned_cols=61 Identities=18% Similarity=0.191 Sum_probs=47.9
Q ss_pred CCCCCEEEEEEEEEec--ceEEEEECCCeEEEEeccCCCCcc------------ccCccccccCCCEEEEEEEEE
Q 001115 759 IHPNSVVHGYVCNIIE--TGCFVRFLGRLTGFAPRSKAVDGQ------------RADLSKTYYVGQSVRSNILDV 819 (1152)
Q Consensus 759 ~~~G~~v~G~V~~i~~--~GvfV~~~~~l~Glv~~s~ls~~~------------~~~~~~~f~~Gq~V~v~Vl~v 819 (1152)
..+|.++.|.|.+|.+ .++||+++.+-.||+|.+++.... ..+..+.+++||.|.|.|..=
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 3479999999999977 489999999999999999873210 111234589999999999973
No 199
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=84.42 E-value=5.1 Score=40.43 Aligned_cols=58 Identities=19% Similarity=0.290 Sum_probs=40.9
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCC----ccccccccC-C------CCccccCCEEEEEEEEE
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLP----HMSEFEIVK-P------GKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~----hls~~~~~~-~------~~~~kvG~~V~~rVl~v 556 (1152)
-|++|.|+|+++...|+|++++ -++-++-.. |+-..+..+ | +.+.++|..|++.|+.+
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~G-Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigt 149 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSG-PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGT 149 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEecc-ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEE
Confidence 5999999999999999999998 455554321 111112222 1 23578899999999988
No 200
>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=82.10 E-value=5.5 Score=37.14 Aligned_cols=54 Identities=19% Similarity=0.422 Sum_probs=45.7
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEe
Q 001115 760 HPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVN 820 (1152)
Q Consensus 760 ~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd 820 (1152)
..|..+.|.|.++.+.-+|++|.+.+.++++..... .+.|..|..|.+++.+..
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~-------~~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN-------GEKYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc-------ccccccCCEEEEEECCHh
Confidence 369999999999999999999999999999977653 246888999999887543
No 201
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=76.56 E-value=12 Score=36.64 Aligned_cols=60 Identities=15% Similarity=0.083 Sum_probs=42.0
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCc-------------cccCccccccCCCEEEEEEEEEe
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG-------------QRADLSKTYYVGQSVRSNILDVN 820 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~-------------~~~~~~~~f~~Gq~V~v~Vl~vd 820 (1152)
+|+++.|+|.+-+..|+.|++.===+-++|.+.|.+. +..+-...|..|+.|+.||.++.
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 5999999999999999999973223468998888742 11222345678999999999865
No 202
>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=64.10 E-value=32 Score=28.85 Aligned_cols=62 Identities=24% Similarity=0.277 Sum_probs=41.9
Q ss_pred CcEEEEEEEEEeCCeEEEEeCCceEE---EEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEec
Q 001115 322 GMMVSTRVQSILENGVMLSFLTYFTG---TVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTL 391 (1152)
Q Consensus 322 G~~V~g~V~~v~~~Gl~v~~~~~~~G---~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl 391 (1152)
|+.+.-.|..++++|-..=..+.+.| .....|+.. ....+||+++|.|+-+|--+-.+.+||
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 56677778888887755444444444 344555543 245689999999999997766776664
No 203
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=62.77 E-value=78 Score=35.47 Aligned_cols=114 Identities=13% Similarity=0.164 Sum_probs=67.5
Q ss_pred EEEEEEEEEecc----eEEEEcCCC---cEEEEeccccCChhhcccccccccCCCCCccCCCCEEEEEEEEEecCCcccc
Q 001115 136 KLWGVVAEVNEK----DLVICLPGG---LRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIG 208 (1152)
Q Consensus 136 ~vlG~V~~i~~~----~l~vslp~~---l~G~v~~~~is~~~~~~~~~~~~~~~l~~~f~vGq~v~~~V~~~~~~~~~~~ 208 (1152)
.+-|+|.+|... .+.|.|..+ +...|.-..+.+ | -+.+|+.|++.|.+.
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 578999999754 233555432 334443333221 1 256999999998753
Q ss_pred eeEEEEecchHHHhcCCCccccCCCCEEEEEEEEEecCeEEE----EeC-CCceeeeecCCCCCCCCCCcCCCCcEEEEE
Q 001115 209 KRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYIL----HFG-LPSFTGFLPRNNLAENSGIDVKPGLLLQGV 283 (1152)
Q Consensus 209 ~~~i~LS~~p~~vn~~l~~~~l~~g~~l~~~V~svedhG~iv----d~G-i~~~~gFl~~~~~~~~~~~~l~~G~~~~~~ 283 (1152)
.|.|+..+. .....-..+.|+|.+++.+|..+ +++ -..+.+-++...+ ....+.+|+.+.+.
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 466654321 11233457999999999876544 441 1124444554332 23378999999998
Q ss_pred EEE
Q 001115 284 VRS 286 (1152)
Q Consensus 284 V~~ 286 (1152)
+..
T Consensus 252 iKa 254 (263)
T PRK10676 252 FNA 254 (263)
T ss_pred EEc
Confidence 875
No 204
>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=59.79 E-value=41 Score=29.34 Aligned_cols=59 Identities=22% Similarity=0.184 Sum_probs=44.2
Q ss_pred eEEEEEEEEecCeEE-EEEcCCeEEEEeccc-cCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEE
Q 001115 588 ITHGWITKIEKHGCF-VRFYNGVQGFAPRSE-LGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRIN 651 (1152)
Q Consensus 588 ~~~G~V~~i~~~G~~-V~~~~gv~Gflp~se-l~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~ 651 (1152)
.+.|.|+...+++.| |++.+|..-++|++- |... .-...+|+.|.+-+-.+|..+++|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~-----rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMH-----YIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhc-----cEEECCCCEEEEEECcccCCcEeEE
Confidence 358999999988875 588888886666542 1111 1246799999999999999888875
No 205
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=57.50 E-value=53 Score=29.99 Aligned_cols=66 Identities=17% Similarity=0.161 Sum_probs=50.0
Q ss_pred EEEEEEEEEecceEEE-EECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115 764 VVHGYVCNIIETGCFV-RFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS 833 (1152)
Q Consensus 764 ~v~G~V~~i~~~GvfV-~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~ 833 (1152)
.+.|.|..+.+.+.|- ++.+|..-+++++-=- ..-.-..-+|+.|.+-+...|.+++||.--.+..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKm----R~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~~ 74 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRM----RKHRIRILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccce----eeeeEEecCCCEEEEEECcccCCceeEEEEecCC
Confidence 4889999998887764 8888888887765321 1111246689999999999999999999887743
No 206
>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=56.77 E-value=17 Score=30.80 Aligned_cols=49 Identities=24% Similarity=0.342 Sum_probs=34.1
Q ss_pred CEEEEEEEEEecCe----EEEEeCCCc-eeeeecCCCCCCCCCCcCCCCcEEEEEEE
Q 001115 234 MVLTAYVKSIEDHG----YILHFGLPS-FTGFLPRNNLAENSGIDVKPGLLLQGVVR 285 (1152)
Q Consensus 234 ~~l~~~V~svedhG----~ivd~Gi~~-~~gFl~~~~~~~~~~~~l~~G~~~~~~V~ 285 (1152)
..+.|.|..+|+.| +.+++|-.. +.+.++...+. ...|++|+.+.+.+.
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 666776444 67777765432 236899999999875
No 207
>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=56.72 E-value=51 Score=28.76 Aligned_cols=60 Identities=20% Similarity=0.200 Sum_probs=44.9
Q ss_pred EEEEEEEEEecceEE-EEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEE
Q 001115 764 VVHGYVCNIIETGCF-VRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRIT 827 (1152)
Q Consensus 764 ~v~G~V~~i~~~Gvf-V~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~ 827 (1152)
.+.|.|....+.+.| |++.+|..-+++++-=- ..-.-...+|+.|.+.+-..|.+++||.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKm----r~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKI----RMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcc----hhccEEECCCCEEEEEECcccCCcEeEE
Confidence 478999999888866 48888888888765321 1112246789999999999998888875
No 208
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=55.44 E-value=56 Score=29.86 Aligned_cols=64 Identities=20% Similarity=0.131 Sum_probs=48.7
Q ss_pred eEEEEEEEEecCeEE-EEEcCCeEEEEeccc-cCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEee
Q 001115 588 ITHGWITKIEKHGCF-VRFYNGVQGFAPRSE-LGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMM 656 (1152)
Q Consensus 588 ~~~G~V~~i~~~G~~-V~~~~gv~Gflp~se-l~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~ 656 (1152)
.+.|+|+...+++.| |++.||..=+.|+|- |...+ -...+||.|.+-+-.||..+++|+--.+.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r-----IrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR-----IRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee-----EEecCCCEEEEEECcccCCceeEEEEecC
Confidence 358999999988876 588888776666552 11111 13579999999999999999999988874
No 209
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=51.16 E-value=21 Score=43.60 Aligned_cols=64 Identities=16% Similarity=0.154 Sum_probs=51.9
Q ss_pred ccCCCCCEEEEEEEEEecc--eEEEEECCCeEEEEeccCCCCccccCc-----cccccCCCEEEEEEEEEeC
Q 001115 757 SHIHPNSVVHGYVCNIIET--GCFVRFLGRLTGFAPRSKAVDGQRADL-----SKTYYVGQSVRSNILDVNS 821 (1152)
Q Consensus 757 ~~~~~G~~v~G~V~~i~~~--GvfV~~~~~l~Glv~~s~ls~~~~~~~-----~~~f~~Gq~V~v~Vl~vd~ 821 (1152)
....+|.++.|.|.+|.+. .+||+++.+=.||+|.+++.+ +...+ +..++.||.+-+.|..-..
T Consensus 33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~ 103 (487)
T COG1530 33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR 103 (487)
T ss_pred cEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence 3455799999999999774 799999999999999999988 33322 3578999999999887543
No 210
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=48.84 E-value=22 Score=43.46 Aligned_cols=60 Identities=17% Similarity=0.152 Sum_probs=45.2
Q ss_pred ccCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEeCCccccccccCCC-----CccccCCEEEEEEEE
Q 001115 495 DVKPGMVVKGKVIAVDSF--GAIVQFPGGVKALCPLPHMSEFEIVKPG-----KKFKVGAELVFRVLG 555 (1152)
Q Consensus 495 ~l~~G~iv~g~V~~v~~~--G~~V~i~~~v~g~vp~~hls~~~~~~~~-----~~~kvG~~V~~rVl~ 555 (1152)
...+|.++.|+|++|.+. .+||+++..-.||+|..|+.+ ....+. ..++.|+.+-+-|+.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~k 100 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVK 100 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEe
Confidence 456899999999999986 799999999999999999887 322222 244566666555544
No 211
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=48.01 E-value=12 Score=40.48 Aligned_cols=68 Identities=19% Similarity=0.228 Sum_probs=52.9
Q ss_pred CCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChhhcccc----cccccCCCCCccCCCCEEEEEEEEEecC
Q 001115 133 AGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEI----EANEDNLLPTIFHVGQLVSCIVLQLDDD 203 (1152)
Q Consensus 133 ~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~~~~~----~~~~~~~l~~~f~vGq~v~~~V~~~~~~ 203 (1152)
.|.+|.|.|.+|...---+++..++.+++.+..+.-+ ... .++++..+.+.|+.|++|.|-|.++..+
T Consensus 85 vGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLP---Gg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~d 156 (301)
T KOG3013|consen 85 VGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLP---GGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHD 156 (301)
T ss_pred cCCEEEEEeeeeecceeEEecccccceEEEeecccCC---chhhhccchhhHHHHHHHhhccCeehHHHHHhccC
Confidence 4999999999999999999999999999999988633 111 1111234567899999999988876544
No 212
>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=47.89 E-value=1.1e+02 Score=25.78 Aligned_cols=56 Identities=18% Similarity=0.125 Sum_probs=35.1
Q ss_pred CCCCEEEEEEEEEecCCCeEEEEccccccccccccccccCC--CCEEEEEEEEEeCCeEEEEe
Q 001115 458 KEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKP--GMVVKGKVIAVDSFGAIVQF 518 (1152)
Q Consensus 458 ~vG~~v~~rVi~~~~~~~~~~lS~k~~~~~~~~~~~~~l~~--G~iv~g~V~~v~~~G~~V~i 518 (1152)
.+|+++++.|.+.. .++....-.+.- ....+..-.| |+.++.+|++..++-++-++
T Consensus 3 ~~G~~~~VlVe~~~-~~g~~~gr~~~~----~~V~v~~~~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 3 YVGKTLEVLVEELG-DEGQGIGRTDNG----KVVFVPGGLPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -TTEEEEEEEEEE--TTSEEEEEET-T----EEEEETT--T--TEEEEEEEEEE-SSEEEEEE
T ss_pred cCCcEEEEEEEEec-CCCEEEEEeCCC----eEEEECCCCCCCCCEEEEEEEEeeCCcEEEEE
Confidence 58999999999998 556555444321 1122233355 99999999999998776543
No 213
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=46.85 E-value=45 Score=32.75 Aligned_cols=53 Identities=23% Similarity=0.547 Sum_probs=45.2
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccccccCCCCccccCCEEEEEEEEE
Q 001115 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1152)
..|..|.|+|-.+...-+++++++.+...|....+. .+.|..|..|..|++..
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n-------~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN-------GEAYQKGARVRLRLIDL 133 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC-------HHHhhcCceEEEEEcCh
Confidence 359999999999999999999999999999765442 35899999999998765
No 214
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=45.91 E-value=39 Score=34.96 Aligned_cols=59 Identities=29% Similarity=0.283 Sum_probs=42.7
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCcccccc--------------cc-CC-CC-ccccCCEEEEEEEEE
Q 001115 498 PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFE--------------IV-KP-GK-KFKVGAELVFRVLGV 556 (1152)
Q Consensus 498 ~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~~--------------~~-~~-~~-~~kvG~~V~~rVl~v 556 (1152)
.|+++.|+|.+.+..|+.|.++-.=+-+||..-|.+-. .+ -| .+ -|.+|..|++||...
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 69999999999999999999984456788876554421 01 02 22 236899999999775
No 215
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=44.62 E-value=47 Score=32.65 Aligned_cols=61 Identities=23% Similarity=0.404 Sum_probs=48.7
Q ss_pred CCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 001115 761 PNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLS 829 (1152)
Q Consensus 761 ~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LS 829 (1152)
.|..|.|.|-++...-+|++|.+.+...+....++ .+.|..|..|..++++..- ..||+-|
T Consensus 82 ~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n-------~e~Y~~GaRVrlRl~DlEL-s~rFLGs 142 (173)
T KOG4078|consen 82 KGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN-------GEAYQKGARVRLRLIDLEL-SERFLGS 142 (173)
T ss_pred CCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC-------HHHhhcCceEEEEEcChhH-hhhhhcC
Confidence 48999999999999999999999999999887765 3468889999988886542 2344433
No 216
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=41.71 E-value=2.9e+02 Score=29.36 Aligned_cols=121 Identities=21% Similarity=0.159 Sum_probs=65.9
Q ss_pred cEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCCCcccCCCEEEEEE-EEEEC-----CCCEEEEEEcccchhhhhcc
Q 001115 876 SVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAI-LDVAK-----AERLVDLSLKTVFIDRFREA 949 (1152)
Q Consensus 876 ~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~~~~~~G~~v~a~V-l~vd~-----~~~~v~LSlk~s~~~~~~~~ 949 (1152)
+.++|+|.++.+.-++++..... .-+.+..=....+++||.|+|.= +.-++ +..+-..+++|-+-
T Consensus 40 ~tiEGrVvEV~~~~i~iesk~yn---~~v~i~~d~~~nvKVGD~VKaTG~m~rnf~~ym~A~sVEk~~~~~G~h------ 110 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSKQYE---EPVSVYIDSLSNVKVGDEVKATGSMMRNFTEYMVATAVENTTNKLGMH------ 110 (213)
T ss_pred ceeeeEEEEEeCCEEEEEeccCC---CceEEEecCCCCcccCcEEEEchHHHHhhHHhhhhhhheeeccCccee------
Confidence 57899999999988888776431 11322222235679999998751 01010 11111111221111
Q ss_pred cchhhhhhhccccccccccCCCCEEEEEEEEEec---------CEEEEEEcCCCce--EEEEEecccccccCCcCCCCCC
Q 001115 950 NSNRQAQKKKRKREASKDLGVHQTVNAIVEIVKE---------NYLVLSLPEYNHS--IGYASVSDYNTQKFPQKQFLNG 1018 (1152)
Q Consensus 950 ~~~~~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~---------~~l~V~l~~~~~~--~~~~~~s~~~~~~~~~~~f~~G 1018 (1152)
++..-.=+-+.|.|..+.. +|+.|.-|...+- ...+.++ ....|.+|
T Consensus 111 ---------------~~e~g~pdYvIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V~V~LT-------~GQkFnVG 168 (213)
T PRK06763 111 ---------------MKEDGSPDYVIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLIIDVFLT-------KGQVFHVG 168 (213)
T ss_pred ---------------ecccCCcceEEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEEEEEec-------cCCEEecC
Confidence 1111122457788887733 5788888643332 3334433 23569999
Q ss_pred CEEEEEEEe
Q 001115 1019 QSVIATVMA 1027 (1152)
Q Consensus 1019 q~v~~~V~~ 1027 (1152)
+.|++.-..
T Consensus 169 DkVKV~~~~ 177 (213)
T PRK06763 169 DKVKVDMKY 177 (213)
T ss_pred CEEEEEeee
Confidence 999987544
No 217
>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=41.68 E-value=1.4e+02 Score=25.32 Aligned_cols=47 Identities=21% Similarity=0.385 Sum_probs=33.7
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeEEEEeCCccccccccCCCCccccCCEEEEEEEEE
Q 001115 501 VVKGKVIAVDSFGAIVQFPG-GVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 501 iv~g~V~~v~~~G~~V~i~~-~v~g~vp~~hls~~~~~~~~~~~kvG~~V~~rVl~v 556 (1152)
-++|+|..+.+..+.++.++ |.+-++|...+. .+..+++++..+--+
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 47899999999999999997 788888876543 234555666655444
No 218
>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=40.71 E-value=2.3e+02 Score=24.10 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=35.1
Q ss_pred EEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.|+|+...+ ||.+..-.++-.-|+|.+++.... -..+..|+.|.+.+..
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 689988874 566655544558999999996442 1357899999999987
No 219
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=39.46 E-value=1.7e+02 Score=32.76 Aligned_cols=115 Identities=10% Similarity=0.039 Sum_probs=65.8
Q ss_pred EEEEEEEEEecc--eEEEE--ECCC---eEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccC
Q 001115 764 VVHGYVCNIIET--GCFVR--FLGR---LTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCS 836 (1152)
Q Consensus 764 ~v~G~V~~i~~~--GvfV~--~~~~---l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~ 836 (1152)
.+.|+|..|... ...|+ +..+ +.+.+.. ....+ -.+.+|+.|.+.|..-+ +.+.....
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~-----~s~~~--L~l~~G~~v~~~Ika~~-----V~l~~~~~--- 193 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITA-----QSAER--LGLDEGKEVLVLIKAPW-----VGITQDPA--- 193 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCH-----HHHhh--cCCCCCCeEEEEEECCE-----EEEEcCCC---
Confidence 588999999755 45554 4332 4444432 22222 25779999998877533 44432110
Q ss_pred CCchhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEEEEEEEecceEE--EEec--CCCCeEEEEEeEeeCCC
Q 001115 837 STDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVV--VSFE--EHSDVYGFITHHQLAGA 912 (1152)
Q Consensus 837 ~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~~g~~--v~l~--~~~~v~G~i~~s~l~~~ 912 (1152)
...+.-..+.|+|.++...|.. |.+. ++..+...|+...+.+-
T Consensus 194 ---------------------------------~~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~~L 240 (263)
T PRK10676 194 ---------------------------------VAQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAARL 240 (263)
T ss_pred ---------------------------------CCCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHHhc
Confidence 0122346789999999866543 3333 21124444444333334
Q ss_pred cccCCCEEEEEEEE
Q 001115 913 TVESGSVIQAAILD 926 (1152)
Q Consensus 913 ~~~~G~~v~a~Vl~ 926 (1152)
.+++|+.|.+.+-.
T Consensus 241 ~L~~G~~V~a~iKa 254 (263)
T PRK10676 241 SLQQGDAVTAYFNA 254 (263)
T ss_pred CCCCCCEEEEEEEc
Confidence 68899999888754
No 220
>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=38.40 E-value=1.3e+02 Score=25.66 Aligned_cols=49 Identities=24% Similarity=0.289 Sum_probs=34.7
Q ss_pred EEEEEEEEEeCCCCEEEEccCccccccccccccccccccccCCCcEEEEEEEEEe
Q 001115 279 LLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSIL 333 (1152)
Q Consensus 279 ~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~pG~~V~g~V~~v~ 333 (1152)
.+...|.++++...+++|+-... -+-.+..+++.|.||+.|...-..+.
T Consensus 4 ~veG~I~~id~~~~titLdDGks------y~lp~ef~~~~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKS------YKLPEEFDFDGLKPGMKVVVFYDEVD 52 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCE------EECCCcccccccCCCCEEEEEEEccC
Confidence 35678999999999998874211 11224677999999999876655544
No 221
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=38.14 E-value=1.4e+02 Score=31.80 Aligned_cols=61 Identities=13% Similarity=0.067 Sum_probs=43.7
Q ss_pred cCCCCEEEEEEEEEecCEEEEEEcCCCceEEEEEecccc-cccCCcCCCCCCCEEEEEEEeecC
Q 001115 968 LGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYN-TQKFPQKQFLNGQSVIATVMALPS 1030 (1152)
Q Consensus 968 l~~G~~v~g~V~~i~~~~l~V~l~~~~~~~~~~~~s~~~-~~~~~~~~f~~Gq~v~~~V~~~d~ 1030 (1152)
..+||.|.|.|.....+.-||.|- +.-.+.++...+. ..+.---.+++|+.|+|+|..-++
T Consensus 63 P~~~D~VIGiV~~~~gd~ykVDig--g~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKSGDIYKVDIG--GSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCCEEEEEEEeccCceEEEecC--CCCeeeeeeccccCccccCCCccccccEEEEEEEecCC
Confidence 457999999999999999999992 2224555544442 122222359999999999998775
No 222
>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=37.99 E-value=2e+02 Score=25.18 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=31.4
Q ss_pred EEEEEEecCCCEEEEEEeeCCC-C------------ccccccccCCCEEEEEEEEEeCC
Q 001115 638 CRIMSSIPASRRINLSFMMKPT-R------------VSEDDLVKLGSLVSGVVDVVTPN 683 (1152)
Q Consensus 638 vrV~~vd~~~~ri~lS~k~~~~-~------------~~~~~~l~vG~iv~g~V~~v~~~ 683 (1152)
.+|.++|++.+.+.++..+-.. . ......+++|+.|...+....+.
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~~ 59 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDDG 59 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETTC
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCCC
Confidence 3688999999999999987543 1 22345789999999988775444
No 223
>PLN02741 riboflavin synthase
Probab=36.09 E-value=5.6e+02 Score=27.31 Aligned_cols=135 Identities=20% Similarity=0.203 Sum_probs=0.0
Q ss_pred EEEEEEEec-CeEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEE-----EEEEEeCCCCEEEEccCccccccccccc
Q 001115 237 TAYVKSIED-HGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQG-----VVRSIDRTRKVVYLSSDPDTVSKCVTKD 310 (1152)
Q Consensus 237 ~~~V~sved-hG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~-----~V~~~~~~~~~v~ls~~~~~~~~~~~~~ 310 (1152)
.|.|.+++. ++--..+.+. ...++. .+.+|.-+-+ +|.+++ +..+.+.+-|..+.
T Consensus 9 ~G~I~~i~~~~~~~~~l~i~-~~~~~~----------~l~~G~SIAvnGvCLTV~~~~--~~~f~vdvipETl~------ 69 (194)
T PLN02741 9 MGEVKSLGVTDDGGFDLKIE-ASTVLD----------GVKLGDSIAVNGTCLTVTEFD--GDEFTVGLAPETLR------ 69 (194)
T ss_pred EEEEEEEEecCCCcEEEEEE-cchhhc----------ccccCCEEEECcEEEEEEEEC--CCEEEEEEEHHHhh------
Q ss_pred cccccccccCCCcEEE-----------------------EEEEEEeCCe----EEEEeCCce------EEEEeccccccC
Q 001115 311 LKGISIDLLVPGMMVS-----------------------TRVQSILENG----VMLSFLTYF------TGTVDIFHLQNT 357 (1152)
Q Consensus 311 ~~~~~~~~l~pG~~V~-----------------------g~V~~v~~~G----l~v~~~~~~------~G~v~~~~l~~~ 357 (1152)
..++..+.+|+.|+ |+|.++.+.| +.++++..+ .|.|-+.=+|
T Consensus 70 --~T~L~~l~~G~~VNLEral~~g~rlgGH~V~GHVd~~~~i~~~~~~~~~~~~~i~~p~~~~~yi~~KGsIavdGvS-- 145 (194)
T PLN02741 70 --KTSLGELKTGSLVNLERALRPGSRMGGHFVQGHVDGTGTIVEQEPEGDSLWVKVKADPELLKYIVPKGFIAVDGTS-- 145 (194)
T ss_pred --hCccccCCCCCEEeeccCCcCCCccCCeeEeEECcEEEEEEEEEECCCcEEEEEEECHHHHcccccCcEEEEeeEE--
Q ss_pred CCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhhcCCCCCCCCCCCCeEE
Q 001115 358 FPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYD 412 (1152)
Q Consensus 358 ~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~~~~~~~~~~~~G~iv~ 412 (1152)
-.|..++.....+.+++-||... ......+++|+.+.
T Consensus 146 -----------------LTV~~v~~~~~~f~v~lIP~T~~-~T~l~~~k~Gd~VN 182 (194)
T PLN02741 146 -----------------LTVVDVDDEEGCFNFMLVPYTQQ-KVVIPLKKVGDKVN 182 (194)
T ss_pred -----------------EEEEEeecCCCEEEEEEcHHHHh-hcccccCCCCCEEE
No 224
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=34.70 E-value=62 Score=27.30 Aligned_cols=49 Identities=18% Similarity=0.298 Sum_probs=30.6
Q ss_pred cEEEEEEEEEecce----EEEEecCCCCeEEEEEeEeeCCCcccCCCEEEEEE
Q 001115 876 SVIEGKVHESNDFG----VVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAI 924 (1152)
Q Consensus 876 ~~v~g~V~~i~~~g----~~v~l~~~~~v~G~i~~s~l~~~~~~~G~~v~a~V 924 (1152)
....|+|..+...| +.+.+.+...+..++.......-.+++|+.|.+.+
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 45789999999988 44444543125666655444333578899887765
No 225
>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=33.12 E-value=3e+02 Score=23.31 Aligned_cols=50 Identities=16% Similarity=0.057 Sum_probs=35.4
Q ss_pred EEEEEEEEec---ceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEE
Q 001115 765 VHGYVCNIIE---TGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILD 818 (1152)
Q Consensus 765 v~G~V~~i~~---~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~ 818 (1152)
.+|+|+...+ ||....-.++-+-|+|.+++.... -..+..|+.|...+..
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 4788988864 555554445568999999987543 2468899999998877
No 226
>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=32.14 E-value=2.1e+02 Score=27.06 Aligned_cols=68 Identities=15% Similarity=0.280 Sum_probs=39.7
Q ss_pred EEEEEEEEEecce--EEEEECC---CeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEee
Q 001115 764 VVHGYVCNIIETG--CFVRFLG---RLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLK 831 (1152)
Q Consensus 764 ~v~G~V~~i~~~G--vfV~~~~---~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk 831 (1152)
.+.|+|.++...| +|+.+-. .+..++............+...+..|+.|.+.=.=...+.+.+.+...
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~ 75 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVK 75 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeC
Confidence 4789999998765 8888843 355556544432222223333488999988853222233455555443
No 227
>PRK15463 cold shock-like protein CspF; Provisional
Probab=31.96 E-value=1.9e+02 Score=25.32 Aligned_cols=51 Identities=16% Similarity=0.088 Sum_probs=36.4
Q ss_pred EEEEEEEEec-C--eEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEE
Q 001115 236 LTAYVKSIED-H--GYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSI 287 (1152)
Q Consensus 236 l~~~V~sved-h--G~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~ 287 (1152)
+.|.|+.-.+ . |+|-.-+ .+-.-|++.+.+.......+.+|+.|.+.+..-
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~-g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSD-GRKDVQVHISALNLRDAEELTTGLRVEFCRING 58 (70)
T ss_pred ceEEEEEEeCCCceEEEecCC-CCccEEEEehhhhhcCCCCCCCCCEEEEEEEEC
Confidence 4799999887 3 5554432 245679999888643234899999999988763
No 228
>PRK06386 replication factor A; Reviewed
Probab=31.46 E-value=9.2e+02 Score=28.36 Aligned_cols=189 Identities=12% Similarity=0.121 Sum_probs=96.3
Q ss_pred EEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccC--CCchhhhhhhhhHHHHHH
Q 001115 777 CFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCS--STDASFMQEHFLLEEKIA 854 (1152)
Q Consensus 777 vfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~--~~~~~~~~~~~~~~e~~~ 854 (1152)
++.-+.++=+|.++... |.. ...++.|++|...=..++.=++++.|.+-..... ..+. .++
T Consensus 38 ~~~gllgDeTG~I~fT~--W~~----~~~l~~Gd~v~i~na~v~~~~G~~~Lnv~~~t~v~~~~d~-----------~ie 100 (358)
T PRK06386 38 YYYGIIGDETGTVPFTA--WEF----PDAVKSGDVIEIKYCYSKEYNGKIRIYFDSRSEVMLKPDE-----------NIE 100 (358)
T ss_pred EEEEEEECCcceEEEEe--cCC----cccCCCCCEEEEEeEEEeeECCEEEEEEcCceEEEecCcc-----------ccc
Confidence 44444556688887765 432 2468899999887666666577888777422110 0000 000
Q ss_pred HhhcCcCCCcccccccCccccc---EEEEEEEEEecc--------eEEEEecCCCCeEEEEEeEeeCCCcccCCCEEEEE
Q 001115 855 MLQSSKHNGSELKWVEGFIIGS---VIEGKVHESNDF--------GVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAA 923 (1152)
Q Consensus 855 ~~~~~~~~~~~~~~~~~~~vG~---~v~g~V~~i~~~--------g~~v~l~~~~~v~G~i~~s~l~~~~~~~G~~v~a~ 923 (1152)
. .+. .....+.++.+|. .|.|+|.++.+. |.+-++-. .+-+|.|+.+... ..++.|+.+...
T Consensus 101 -v---~~~-~~~~KI~DL~~g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~l-gDeTGrIr~TlW~-~~l~eGd~v~i~ 173 (358)
T PRK06386 101 -V---KRT-YKLVKIRDLSLVTPYVSVIGKITGITKKEYDSDGTSKIVYQGYI-EDDTARVRISSFG-KPLEDNRFVRIE 173 (358)
T ss_pred -c---ccc-cCccEeEeccCCCCceEEEEEEEEccCceEecCCCccEEEEEEE-EcCCCeEEEEEcc-ccccCCCEEEEe
Confidence 0 000 0011256777773 478999877542 11111111 0224566665553 368899999877
Q ss_pred EEEEECCCCEEEEEEcccc-hhhhhcccchhhhhhhccccccccccCCC---CEEEEEEEEEecC-EEEEEEcCCCc
Q 001115 924 ILDVAKAERLVDLSLKTVF-IDRFREANSNRQAQKKKRKREASKDLGVH---QTVNAIVEIVKEN-YLVLSLPEYNH 995 (1152)
Q Consensus 924 Vl~vd~~~~~v~LSlk~s~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~G---~~v~g~V~~i~~~-~l~V~l~~~~~ 995 (1152)
=..++.-++.++|++-..- +....... +. +.....+.++..+ .++.|.|..+.+. +++=.-|.+++
T Consensus 174 na~v~e~~G~~el~v~~~t~I~~~~~~i-----ev-~~~~~~I~di~~~~g~v~i~G~iv~i~~gsgli~rCP~C~R 244 (358)
T PRK06386 174 NARVSQYNGYIEISVGNKSVIKEVESDI-----NL-ESRNIFIFEIKSPVGGITIMGFIVSVGQGSRIFTKCSVCNK 244 (358)
T ss_pred eeEEEccCCeEEEEeCCeEEEEECCCCc-----cc-CccccchhhhhccCCeEEEEEEEEEEcCCcEeEecCcCCCe
Confidence 5556666778888764321 11100000 00 0112233444443 4788888887654 33323344444
No 229
>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=31.40 E-value=66 Score=26.42 Aligned_cols=19 Identities=11% Similarity=0.059 Sum_probs=16.8
Q ss_pred EEEEEEEecceEEEEcCCC
Q 001115 138 WGVVAEVNEKDLVICLPGG 156 (1152)
Q Consensus 138 lG~V~~i~~~~l~vslp~~ 156 (1152)
+|+|.+....-+.|++++.
T Consensus 17 ~GqVqS~i~~rvTVnF~~a 35 (52)
T PF12073_consen 17 IGQVQSNIGGRVTVNFEHA 35 (52)
T ss_pred ceEEEEecCCeEEEeeccC
Confidence 6999999999999999753
No 230
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=31.35 E-value=5.3e+02 Score=29.29 Aligned_cols=117 Identities=17% Similarity=0.102 Sum_probs=71.3
Q ss_pred CCCCEEEEEEEEEecCEEEEEEcCCCceEEEEEecccccccCCcCCCCCCCEEEEEEEeecCCCCccEEEEEeccccccc
Q 001115 969 GVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISETE 1048 (1152)
Q Consensus 969 ~~G~~v~g~V~~i~~~~l~V~l~~~~~~~~~~~~s~~~~~~~~~~~f~~Gq~v~~~V~~~d~~~~~~~l~l~~~~~~~~~ 1048 (1152)
..|..+.|.|....+.|-...+.-. ...+.. +....++|+.+..+|.+-|. .+.|.-
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~---~~~l~v--------~~~~a~~g~~~R~~I~a~DV-----slal~~------- 286 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALG---DQHLWV--------PKLDAPVGARLRIRIQARDV-----SLALQK------- 286 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecC---ceEEEe--------eccCCCCCCcEEEEEEccce-----EEEecC-------
Confidence 5688899999888766555444211 122222 22346789999999988773 222211
Q ss_pred ccccccccccCCCcCCcEEEEEEEEEeCCe--EEEEeCCCe-eEEEEeeeccCCccccccccccCCCCCCEEEEEEEeee
Q 001115 1049 TSSSKRAKKKSSYDVGSLVQAEITEIKPLE--LRLKFGIGF-HGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKS 1125 (1152)
Q Consensus 1049 ~~~~~~~~~~~~~~~G~~v~~~V~~i~~~~--l~V~L~~~~-~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~ 1125 (1152)
.+..+.=-+++|+|+.|.+.. +.|+|.-+- .=...+|+.+- +.| .+++||.|-|.|-++.
T Consensus 287 ---------P~~~SirNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~sr-------d~L-~l~~G~~v~AqIKsVs 349 (352)
T COG4148 287 ---------PEQTSIRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWAR-------DEL-ALKPGQWVYAQIKSVS 349 (352)
T ss_pred ---------ccccchhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhhH-------Hhh-cCCCCCeEEEEEEEEE
Confidence 233445567888998888643 666665431 11233443322 345 7899999999998775
No 231
>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=30.87 E-value=2.7e+02 Score=23.29 Aligned_cols=56 Identities=16% Similarity=0.145 Sum_probs=34.0
Q ss_pred CCCcEEEEEEEEEeCCCCEEEEccCccccccccccccccccccccCC--CcEEEEEEEEEeCCeEEEEe
Q 001115 275 KPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVP--GMMVSTRVQSILENGVMLSF 341 (1152)
Q Consensus 275 ~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~p--G~~V~g~V~~v~~~Gl~v~~ 341 (1152)
.+|+.+.+.|.+....+..+-=+.+ .....+..-.| |+.+.++|++..++-+...+
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 5799999999998744333221110 11223444477 99999999999998887553
No 232
>PRK07211 replication factor A; Reviewed
Probab=30.76 E-value=1.1e+03 Score=28.98 Aligned_cols=258 Identities=15% Similarity=0.151 Sum_probs=0.0
Q ss_pred cccccCCCCCCCE---EEEEEEEEec-------------ceEEEEcCCCcEEEEeccccCChhhcccccccccCCCCCcc
Q 001115 124 NKITLKNISAGMK---LWGVVAEVNE-------------KDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIF 187 (1152)
Q Consensus 124 e~l~~k~l~~G~~---vlG~V~~i~~-------------~~l~vslp~~l~G~v~~~~is~~~~~~~~~~~~~~~l~~~f 187 (1152)
+....+.|.|||- +.|.|.++.+ .-..+.|.+ -+|-|++|-..+. .... .+.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D-eTG~Ir~TlW~d~-ad~~---------~~~L 120 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD-ETGSVRVAFWDEQ-AVAA---------EEEL 120 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc-CCCeEEEEEechH-hHhh---------hccc
Q ss_pred CCCCEEEEEEEEEecCCcccceeEEEEecc----------hHHHhcCCCccccCCC---CEEEEEEEEEec---------
Q 001115 188 HVGQLVSCIVLQLDDDKKEIGKRKIWLSLR----------LSLLYKGLSLETVQEG---MVLTAYVKSIED--------- 245 (1152)
Q Consensus 188 ~vGq~v~~~V~~~~~~~~~~~~~~i~LS~~----------p~~vn~~l~~~~l~~g---~~l~~~V~sved--------- 245 (1152)
++|+.++ |.......-.+ ++|++. |-.+.......+|.+| -.|.|.|.++.+
T Consensus 121 e~GdV~~--I~~~~~~~ys~----~El~i~~ve~~~d~~i~~~~~~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dG 194 (485)
T PRK07211 121 EVGQVLR--IKGRPKDGYNG----LEVSVDKVEPDPDAEIDVQIGDTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDG 194 (485)
T ss_pred CCCCEEE--EeceEeccccc----eEEEEeeEEEcccccccccccCCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCC
Q ss_pred -CeEEEEeCCCceeeeecCCCCCCCCCC--cCCCCcEEEEEEEEEeCCCCEEEEccCcccccccccccccc----ccccc
Q 001115 246 -HGYILHFGLPSFTGFLPRNNLAENSGI--DVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKG----ISIDL 318 (1152)
Q Consensus 246 -hG~ivd~Gi~~~~gFl~~~~~~~~~~~--~l~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~----~~~~~ 318 (1152)
-|.+.++=+.+-+|.+...-|...... .+.+|+++...=-.+......+.|++.....-.....+.+. ..+..
T Consensus 195 seGkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~~vp~~~~I~d 274 (485)
T PRK07211 195 SEGRVSNLTVGDETGRVRVTLWDDRADLAEELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVEYVPDTTPIES 274 (485)
T ss_pred CeeEEEEEEEEcCCCeEEEEEechhhhhhccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcccccccccccHhh
Q ss_pred cCCCcEEEEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeCCCCEEEEecchhhhcC
Q 001115 319 LVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHN 398 (1152)
Q Consensus 319 l~pG~~V~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~~~k~v~LSl~p~~~~~ 398 (1152)
+.+|+.|+ +.|.|....-....... -|+..+.|=+.+...+.+|.++| |
T Consensus 275 l~~g~~vd------------------V~GvV~~v~~~rtf~r~-------dG~~~~vr~l~l~D~TG~IrvTL------W 323 (485)
T PRK07211 275 LEIDETVD------------------IAGVVRSADPKRTFDRD-------DGSEGQVRNVRIQDDTGDIRVAL------W 323 (485)
T ss_pred cCCCCcee------------------EEEEEEEccCcEEEEcC-------CCCEeEEEEEEEEcCCCcEEEEE------e
Q ss_pred CCCCC-CCCCCCeEEceEEEEEeCCc--eEEEEeC
Q 001115 399 RAPPS-HVKVGDIYDQSKVVRVDRGL--GLLLDIP 430 (1152)
Q Consensus 399 ~~~~~-~~~~G~iv~~~~V~~v~~~~--G~~v~l~ 430 (1152)
..... .+.+|++|. .+=.++..+| |+-|.++
T Consensus 324 g~~A~~~i~~GdvV~-Ikg~~V~dg~~ggleLS~g 357 (485)
T PRK07211 324 GEKADLDIGPGDEVV-AADVEIQDGWQDDLEASAG 357 (485)
T ss_pred CccccCCCCCCCEEE-EEccEEEecCCCCEEEEec
No 233
>PF11580 DUF3239: Protein of unknown function (DUF3239); InterPro: IPR021632 This entry contains possible membrane proteins, however this cannot be confirmed. Currently they have no known function. ; PDB: 3C8I_B.
Probab=30.20 E-value=1.4e+02 Score=29.51 Aligned_cols=81 Identities=19% Similarity=0.181 Sum_probs=35.2
Q ss_pred CCcCCcEEEEEEEEEeCCeEE-EEeC---CCeeEEEEeeeccCCccccccccccCCCCCCEEEEEEEeeecCCCCCCCce
Q 001115 1060 SYDVGSLVQAEITEIKPLELR-LKFG---IGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFL 1135 (1152)
Q Consensus 1060 ~~~~G~~v~~~V~~i~~~~l~-V~L~---~~~~G~v~~te~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~~~~~~~k~~~ 1135 (1152)
-|.-|+.++|.|.++.+..+. +-|- -.-.+.-...=+.-.. ...|.-.+++|+.|.|.=+..+.+........
T Consensus 10 ~Y~~~~LvPavV~ev~pr~v~llalvd~~~d~~~~p~~Al~~r~v---~~ipg~~~~vG~rVP~vAv~~~~~~~~~~~~W 86 (128)
T PF11580_consen 10 LYDNGPLVPAVVAEVNPRDVVLLALVDTAVDPAAPPRWALATRTV---TAIPGHRRKVGERVPSVAVYTGRRSRDDSGRW 86 (128)
T ss_dssp ------EEEEEEEEE-SS-EEEEEEEE-BSSTTS---EEEEEEEE---S--TT-S-STT-EEEEEEEE-EEEECSSSCEE
T ss_pred hhhcCCCCcEEEEEecCcceehhhhhhhcCCCCCCceEEEEEEEe---ecCCCcccccCCEeeeEEEeccccCCCccccc
Confidence 467799999999999998732 2221 1111111111111111 14666679999999998887442223333456
Q ss_pred EEEEeecC
Q 001115 1136 WELSIKPS 1143 (1152)
Q Consensus 1136 ~~LSlr~s 1143 (1152)
.++|-.|=
T Consensus 87 ~~~sPmPI 94 (128)
T PF11580_consen 87 QEFSPMPI 94 (128)
T ss_dssp CEEEEEEG
T ss_pred eeccceee
Confidence 67776553
No 234
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=29.87 E-value=1.8e+02 Score=31.09 Aligned_cols=58 Identities=19% Similarity=0.137 Sum_probs=46.5
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeCCccccc-cccCCCCccccCCEEEEEEEEE
Q 001115 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEF-EIVKPGKKFKVGAELVFRVLGV 556 (1152)
Q Consensus 497 ~~G~iv~g~V~~v~~~G~~V~i~~~v~g~vp~~hls~~-~~~~~~~~~kvG~~V~~rVl~v 556 (1152)
.+|+.|-|.|+.-...+..|+|++.-.|.+|..-+... +..+| .+++|+-|-|+|...
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a 122 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDA 122 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--ccccccEEEEEEEec
Confidence 47999999999999999999999767788887655432 33444 689999999999764
No 235
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=29.83 E-value=2.4e+02 Score=25.25 Aligned_cols=57 Identities=19% Similarity=0.238 Sum_probs=40.4
Q ss_pred cEEEEEEEEEecceEE-EEecCCCCeEEEEEeEeeCCC------cccCCCEEEEEEEEEECCCCEEEEE
Q 001115 876 SVIEGKVHESNDFGVV-VSFEEHSDVYGFITHHQLAGA------TVESGSVIQAAILDVAKAERLVDLS 937 (1152)
Q Consensus 876 ~~v~g~V~~i~~~g~~-v~l~~~~~v~G~i~~s~l~~~------~~~~G~~v~a~Vl~vd~~~~~v~LS 937 (1152)
-.+.|+|.+.-..+.| |.+++ |..-..|+++. ...+||.|.+..-..+..+..+..-
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~ed-----g~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~R 70 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELEN-----GHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYR 70 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecC-----CcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEE
Confidence 3568999999988876 66665 33334455532 4678999999999888777766543
No 236
>PRK10943 cold shock-like protein CspC; Provisional
Probab=29.45 E-value=2.1e+02 Score=24.95 Aligned_cols=51 Identities=16% Similarity=0.092 Sum_probs=35.9
Q ss_pred eEEEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 588 ITHGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 588 ~~~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
...|+|+...+ ||++-.-.++-.-|+|+|.+.... -..+..||.|.+.+..
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 45799988874 455544445678999999985321 1246899999998765
No 237
>PRK15464 cold shock-like protein CspH; Provisional
Probab=28.72 E-value=2.4e+02 Score=24.77 Aligned_cols=51 Identities=16% Similarity=0.106 Sum_probs=35.8
Q ss_pred EEEEEEEEec-CeE--EEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEE
Q 001115 236 LTAYVKSIED-HGY--ILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSI 287 (1152)
Q Consensus 236 l~~~V~sved-hG~--ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~ 287 (1152)
++|+|+.-.+ .|| |..-+ .+-.-|++.+.+....-..+.+|+.|.+.+..-
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~-g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSD-GRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNG 58 (70)
T ss_pred ceEEEEEEECCCCeEEEccCC-CCccEEEEehhehhcCCCCCCCCCEEEEEEEEC
Confidence 4799999887 454 43332 234679999887533223799999999999873
No 238
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=28.47 E-value=2.4e+02 Score=24.64 Aligned_cols=51 Identities=16% Similarity=0.103 Sum_probs=35.4
Q ss_pred eEEEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 588 ITHGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 588 ~~~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.+.|+|+...+ ||++-.-.++-+-|+|+|.+.... -..+.+||.|.+.+..
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 45799988873 555444445578999999985321 1246899999998765
No 239
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=28.00 E-value=2.5e+02 Score=25.13 Aligned_cols=66 Identities=18% Similarity=0.118 Sum_probs=47.0
Q ss_pred CceEEEEEEEEecCeE-EEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEe
Q 001115 586 RLITHGWITKIEKHGC-FVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM 655 (1152)
Q Consensus 586 G~~~~G~V~~i~~~G~-~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k 655 (1152)
...+.|+|....+++- .|++.+|..=+.|++-=--. -.-.+.+|+.|.+....+|..+++|.--.+
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 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 3456799999988775 58888888877776532111 012367999999999999988888775543
No 240
>PRK09289 riboflavin synthase subunit alpha; Provisional
Probab=27.98 E-value=7.6e+02 Score=26.30 Aligned_cols=48 Identities=19% Similarity=0.155 Sum_probs=28.6
Q ss_pred EEEEEEecCCCEEEEEEeeCCCCccccccccCCCEEE-----EEEEEEeCCcEEEEE
Q 001115 638 CRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVS-----GVVDVVTPNAVVVYV 689 (1152)
Q Consensus 638 vrV~~vd~~~~ri~lS~k~~~~~~~~~~~l~vG~iv~-----g~V~~v~~~g~~V~l 689 (1152)
++|.++.+..+...+.++.+. ...++.+|+-+. -+|.++.++.+.+.+
T Consensus 10 g~V~~i~~~~~~~~~~i~~~~----~~~~l~~g~SIAvnGvcLTV~~~~~~~f~~~l 62 (194)
T PRK09289 10 GTVESIEPKGDGLRLTIEAGK----LLSDLKLGDSIAVNGVCLTVTEIDGDSFTVDV 62 (194)
T ss_pred EEEEEEEEcCCcEEEEEEcCc----cccccccCCEEEEccEEEEEEEEcCCEEEEEE
Confidence 566777776666666665421 123477886643 267777666666555
No 241
>PRK15464 cold shock-like protein CspH; Provisional
Probab=27.67 E-value=2e+02 Score=25.22 Aligned_cols=50 Identities=12% Similarity=0.081 Sum_probs=35.1
Q ss_pred EEEEEEEEec-CeE-EEEE-cCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 589 THGWITKIEK-HGC-FVRF-YNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 589 ~~G~V~~i~~-~G~-~V~~-~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
..|+|+...+ .|+ |+.- .++-.-|+|++.+.... ...+..||.|.+.|..
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 3699998874 444 5544 34568999999985321 1247899999998875
No 242
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=27.57 E-value=6.7e+02 Score=32.96 Aligned_cols=56 Identities=16% Similarity=0.176 Sum_probs=34.2
Q ss_pred cCCCCEEEEEEEEEeC-CeEEEEeCCCeEEEEeCCcccc----ccccCCCCccccCCEEEE
Q 001115 496 VKPGMVVKGKVIAVDS-FGAIVQFPGGVKALCPLPHMSE----FEIVKPGKKFKVGAELVF 551 (1152)
Q Consensus 496 l~~G~iv~g~V~~v~~-~G~~V~i~~~v~g~vp~~hls~----~~~~~~~~~~kvG~~V~~ 551 (1152)
+.||+.|...+-.... .|++..+.+.+--++|..+.-. ++.....+.|++|+.|++
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKV 468 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKV 468 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEE
Confidence 7889988765555433 4666666655555555422222 223345578899999876
No 243
>PRK10943 cold shock-like protein CspC; Provisional
Probab=25.93 E-value=3e+02 Score=23.99 Aligned_cols=53 Identities=15% Similarity=0.102 Sum_probs=37.7
Q ss_pred CEEEEEEEEEec---CeEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEE
Q 001115 234 MVLTAYVKSIED---HGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSI 287 (1152)
Q Consensus 234 ~~l~~~V~sved---hG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~ 287 (1152)
|.++|.|+.-.+ +|+|-.-+ .+-.-|++.+.+....-..+.+|+.|.+.+..-
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPAD-GSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDG 57 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCC-CCeeEEEEhhHccccCCCCCCCCCEEEEEEEEC
Confidence 467899998877 46665543 235679998887533113799999999988763
No 244
>PRK15463 cold shock-like protein CspF; Provisional
Probab=25.34 E-value=2.4e+02 Score=24.75 Aligned_cols=49 Identities=14% Similarity=0.098 Sum_probs=34.5
Q ss_pred EEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.|+|+.... ||++-.-.++-+-|+|++.+...- ...+..||.|.+.+..
T Consensus 6 ~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g----~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD----AEELTTGLRVEFCRIN 57 (70)
T ss_pred eEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC----CCCCCCCCEEEEEEEE
Confidence 699998874 454444445678999999985321 1246899999998764
No 245
>PRK13020 riboflavin synthase subunit alpha; Provisional
Probab=24.48 E-value=9.1e+02 Score=26.01 Aligned_cols=50 Identities=12% Similarity=0.086 Sum_probs=30.5
Q ss_pred EEEEEEEecCCCEEEEEEeeCCCCccccccccCCCEEE-----EEEEEEeCCcEEEEE
Q 001115 637 KCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVS-----GVVDVVTPNAVVVYV 689 (1152)
Q Consensus 637 ~vrV~~vd~~~~ri~lS~k~~~~~~~~~~~l~vG~iv~-----g~V~~v~~~g~~V~l 689 (1152)
.++|.++.+..+...+.++.+ ......+.+|+-|. -+|.++.++.+.+.+
T Consensus 9 vg~I~~i~~~~~~~~l~i~~~---~~~~~~l~~g~SIavnGVcLTV~~v~~~~f~~~l 63 (206)
T PRK13020 9 TAEVVAIHKKDGLNTLEIAFP---PELLEGLEIGASVAVNGVCLTVTKIEGDRVFFDV 63 (206)
T ss_pred EEEEEEEEECCCcEEEEEEeC---hhHhccCCCCCEEEECCEEEEEEEECCCEEEEEE
Confidence 356777777666666666532 12234667776543 367777776666655
No 246
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=24.33 E-value=7.8e+02 Score=26.28 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=30.2
Q ss_pred cEEEEEEEEEec---------ceEEEEecCCCCeEEEEEeEeeCCCcccCCCEEEEEEEE
Q 001115 876 SVIEGKVHESND---------FGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILD 926 (1152)
Q Consensus 876 ~~v~g~V~~i~~---------~g~~v~l~~~~~v~G~i~~s~l~~~~~~~G~~v~a~Vl~ 926 (1152)
+-+-|+|.++-. ..+.|+-+...+-...|++.--...+|++||+|++--..
T Consensus 118 dYvIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V~V~LT~GQkFnVGDkVKV~~~~ 177 (213)
T PRK06763 118 DYVIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLIIDVFLTKGQVFHVGDKVKVDMKY 177 (213)
T ss_pred ceEEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEEEEEeccCCEEecCCEEEEEeee
Confidence 345667777643 134455554334344454443345789999999887544
No 247
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.31 E-value=92 Score=32.96 Aligned_cols=80 Identities=14% Similarity=0.147 Sum_probs=54.9
Q ss_pred cccccCCCccccCCCCCEEEEEEEEEec--ceEEEEEC----CCeEEEEeccCCCCccccCc------cccccCCCEEEE
Q 001115 747 NSAQQLPSDASHIHPNSVVHGYVCNIIE--TGCFVRFL----GRLTGFAPRSKAVDGQRADL------SKTYYVGQSVRS 814 (1152)
Q Consensus 747 ~~~~~~~~~~~~~~~G~~v~G~V~~i~~--~GvfV~~~----~~l~Glv~~s~ls~~~~~~~------~~~f~~Gq~V~v 814 (1152)
+.+..++ ++.++..|+++-|+.....+ ||++|.+. .-.++|+|.-++...+-..| ...|-..-.|.+
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 77889999999999999965 56777652 23678888777665544344 334556778888
Q ss_pred EEEEEeCCCCeEE
Q 001115 815 NILDVNSETGRIT 827 (1152)
Q Consensus 815 ~Vl~vd~e~~ri~ 827 (1152)
.|.++|...+-|.
T Consensus 141 ~V~evnk~~~EIe 153 (247)
T COG4044 141 EVNEVNKLAQEIE 153 (247)
T ss_pred EEEeccchhhhhh
Confidence 8998886555443
No 248
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=23.51 E-value=2.9e+02 Score=24.52 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=34.7
Q ss_pred EEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 590 HGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 590 ~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
.|+|+-... ||++..-.++-.-|+|+|.+...- -..+..||.|.+.+..
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 488888763 455545455688999999985321 1246899999999875
No 249
>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=22.70 E-value=1.9e+02 Score=24.53 Aligned_cols=50 Identities=22% Similarity=0.236 Sum_probs=30.8
Q ss_pred cEEEEEEEEEecceEEEEec--CCC--CeEEEEEeEeeCCCcccCCCEEEEEEE
Q 001115 876 SVIEGKVHESNDFGVVVSFE--EHS--DVYGFITHHQLAGATVESGSVIQAAIL 925 (1152)
Q Consensus 876 ~~v~g~V~~i~~~g~~v~l~--~~~--~v~G~i~~s~l~~~~~~~G~~v~a~Vl 925 (1152)
..+.|+|.++...|..+.+. ..+ -+...++...+.+-.+++|+.|.+.+-
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 56789999998877554333 211 233444443333446889998887763
No 250
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=22.16 E-value=58 Score=34.39 Aligned_cols=19 Identities=37% Similarity=0.805 Sum_probs=16.5
Q ss_pred cceEEEEECCCeEEEEecc
Q 001115 774 ETGCFVRFLGRLTGFAPRS 792 (1152)
Q Consensus 774 ~~GvfV~~~~~l~Glv~~s 792 (1152)
+.||||-|.||+.||+-+.
T Consensus 49 DiGCFvlFDGGFsGLVviN 67 (229)
T PF11813_consen 49 DIGCFVLFDGGFSGLVVIN 67 (229)
T ss_pred CcceEEEecCCcceEEEEe
Confidence 4699999999999998753
No 251
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=21.87 E-value=4e+02 Score=25.90 Aligned_cols=54 Identities=11% Similarity=-0.023 Sum_probs=38.4
Q ss_pred EEEEEEEEecCCCEEEEEEeeCCCC-c------------cccccccCCCEEEEEEEEEeCCcEEEEE
Q 001115 636 VKCRIMSSIPASRRINLSFMMKPTR-V------------SEDDLVKLGSLVSGVVDVVTPNAVVVYV 689 (1152)
Q Consensus 636 v~vrV~~vd~~~~ri~lS~k~~~~~-~------------~~~~~l~vG~iv~g~V~~v~~~g~~V~l 689 (1152)
.+.+|.++|++.+++.++..+-+.. | .....+++|+.|.-.+..-.+..++..|
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~~~~~~~~i~~i 111 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQGNLSLLQDI 111 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEEEEEcCCcEEEEEE
Confidence 4788999999999999999765431 1 2235789999999887754444444444
No 252
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=21.74 E-value=1.2e+03 Score=26.54 Aligned_cols=114 Identities=24% Similarity=0.278 Sum_probs=69.9
Q ss_pred CCCCEEEEEEEEE-ecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCC
Q 001115 760 HPNSVVHGYVCNI-IETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSST 838 (1152)
Q Consensus 760 ~~G~~v~G~V~~i-~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~ 838 (1152)
+.|.++.|.|..- ..||+-+--.+...-++|.- ...+|+.++.+|-.-| +.++++...
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 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKL------------DAPVGARLRIRIQARD-----VSLALQKPE---- 288 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecCceEEEeecc------------CCCCCCcEEEEEEccc-----eEEEecCcc----
Confidence 5699999999887 45666554344444444432 3558999999887644 455555432
Q ss_pred chhhhhhhhhHHHHHHHhhcCcCCCcccccccCcccccEEEEEEEEEecce--EEEEecCCCC-eEEEEEeEeeC--CCc
Q 001115 839 DASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFG--VVVSFEEHSD-VYGFITHHQLA--GAT 913 (1152)
Q Consensus 839 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~~g--~~v~l~~~~~-v~G~i~~s~l~--~~~ 913 (1152)
..++=.+..|+|+.+.+.+ +-|.++.+++ +.++| +..+ +-.
T Consensus 289 --------------------------------~~SirNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Ari--t~~srd~L~ 334 (352)
T COG4148 289 --------------------------------QTSIRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARI--TPWARDELA 334 (352)
T ss_pred --------------------------------ccchhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEc--cHhhHHhhc
Confidence 1234456677888877654 4445544322 23333 3332 236
Q ss_pred ccCCCEEEEEEEEEE
Q 001115 914 VESGSVIQAAILDVA 928 (1152)
Q Consensus 914 ~~~G~~v~a~Vl~vd 928 (1152)
+++|+.|-|.|-.+.
T Consensus 335 l~~G~~v~AqIKsVs 349 (352)
T COG4148 335 LKPGQWVYAQIKSVS 349 (352)
T ss_pred CCCCCeEEEEEEEEE
Confidence 899999999998765
No 253
>PRK09890 cold shock protein CspG; Provisional
Probab=21.62 E-value=4e+02 Score=23.30 Aligned_cols=50 Identities=12% Similarity=0.053 Sum_probs=34.4
Q ss_pred EEEEEEEEec---CeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEE
Q 001115 589 THGWITKIEK---HGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMS 642 (1152)
Q Consensus 589 ~~G~V~~i~~---~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~ 642 (1152)
..|+|....+ ||++-.-.++-.-|+|++.+..... ..+.+||.|.+.+..
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 3799988763 4554443345789999999853311 246899999997754
Done!