Query gi|254780456|ref|YP_003064869.1| 30S ribosomal protein S1 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 576
No_of_seqs 221 out of 2846
Neff 7.8
Searched_HMMs 39220
Date Sun May 29 19:09:21 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780456.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06299 rpsA 30S ribosomal pr 100.0 0 0 986.1 53.2 554 7-564 1-556 (556)
2 PRK12269 bifunctional cytidyla 100.0 0 0 951.8 47.7 544 6-560 297-860 (863)
3 TIGR00717 rpsA ribosomal prote 100.0 0 0 936.2 44.2 518 9-530 1-534 (534)
4 COG0539 RpsA Ribosomal protein 100.0 0 0 852.3 47.6 537 8-558 2-539 (541)
5 PRK13806 rpsA 30S ribosomal pr 100.0 0 0 765.9 38.6 444 4-451 10-462 (489)
6 PRK07899 rpsA 30S ribosomal pr 100.0 0 0 627.6 32.4 351 5-359 16-369 (484)
7 PRK00087 4-hydroxy-3-methylbut 100.0 0 0 621.5 33.3 354 6-362 283-644 (670)
8 PRK06299 rpsA 30S ribosomal pr 100.0 0 0 582.5 38.1 418 24-447 102-527 (556)
9 TIGR00717 rpsA ribosomal prote 100.0 0 0 578.0 36.2 422 9-440 94-534 (534)
10 PRK06676 rpsA 30S ribosomal pr 100.0 0 0 577.7 34.0 355 7-365 1-359 (390)
11 PRK13806 rpsA 30S ribosomal pr 100.0 0 0 576.4 33.5 442 108-564 31-488 (489)
12 PRK12269 bifunctional cytidyla 100.0 0 0 547.0 35.9 416 24-444 396-829 (863)
13 COG0539 RpsA Ribosomal protein 100.0 0 0 525.2 31.2 428 105-545 16-448 (541)
14 PRK06676 rpsA 30S ribosomal pr 100.0 0 0 518.3 30.5 365 191-565 11-389 (390)
15 PRK00087 4-hydroxy-3-methylbut 100.0 0 0 471.7 28.9 365 189-563 296-670 (670)
16 PRK07400 30S ribosomal protein 100.0 0 0 463.0 19.3 298 6-315 13-313 (314)
17 PRK07899 rpsA 30S ribosomal pr 100.0 0 0 455.4 25.4 333 105-446 30-369 (484)
18 PRK07400 30S ribosomal protein 100.0 0 0 380.8 13.5 288 191-494 25-314 (314)
19 KOG1070 consensus 100.0 0 0 331.4 27.7 525 14-541 497-1334(1710)
20 KOG1070 consensus 100.0 0 0 297.4 29.5 467 68-539 468-1241(1710)
21 PRK08059 general stress protei 99.9 3.1E-24 7.9E-29 164.2 5.0 115 192-314 1-116 (119)
22 PRK08059 general stress protei 99.9 3.1E-21 7.8E-26 146.0 10.3 108 454-563 2-114 (119)
23 PRK07252 hypothetical protein; 99.8 9.2E-20 2.3E-24 137.1 9.5 109 456-566 1-113 (120)
24 PRK08582 hypothetical protein; 99.8 5E-20 1.3E-24 138.7 6.7 82 194-276 2-84 (139)
25 PRK07252 hypothetical protein; 99.8 5.5E-20 1.4E-24 138.4 6.6 76 195-270 1-77 (120)
26 PRK05807 hypothetical protein; 99.8 2.9E-19 7.3E-24 134.1 6.6 108 456-567 3-115 (136)
27 PRK05807 hypothetical protein; 99.8 1E-18 2.6E-23 130.7 8.5 78 194-272 2-79 (136)
28 PRK08582 hypothetical protein; 99.8 1.4E-18 3.6E-23 129.9 9.1 80 280-361 3-82 (139)
29 cd05689 S1_RPS1_repeat_ec4 S1_ 99.8 1.7E-18 4.3E-23 129.4 7.6 72 280-351 1-72 (72)
30 cd05708 S1_Rrp5_repeat_sc12 S1 99.7 3.3E-18 8.5E-23 127.6 7.3 73 458-531 2-74 (77)
31 cd04452 S1_IF2_alpha S1_IF2_al 99.7 1.1E-17 2.9E-22 124.3 10.0 75 457-531 2-76 (76)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 99.7 1.2E-17 3.1E-22 124.2 10.0 77 451-529 7-83 (83)
33 cd05708 S1_Rrp5_repeat_sc12 S1 99.7 1.9E-17 4.7E-22 123.1 10.1 72 196-267 1-74 (77)
34 cd04461 S1_Rrp5_repeat_hs8_sc7 99.7 4.6E-18 1.2E-22 126.8 6.9 77 189-265 6-83 (83)
35 cd05691 S1_RPS1_repeat_ec6 S1_ 99.7 2.1E-17 5.3E-22 122.8 9.6 73 459-533 1-73 (73)
36 PRK03987 translation initiatio 99.7 3E-17 7.6E-22 121.8 10.2 76 282-358 8-85 (262)
37 cd04452 S1_IF2_alpha S1_IF2_al 99.7 8.5E-18 2.2E-22 125.1 6.9 72 196-267 2-76 (76)
38 cd05698 S1_Rrp5_repeat_hs6_sc5 99.7 3.5E-17 8.8E-22 121.4 9.7 70 459-530 1-70 (70)
39 cd05691 S1_RPS1_repeat_ec6 S1_ 99.7 1.4E-17 3.6E-22 123.8 7.3 71 198-268 1-72 (73)
40 cd05690 S1_RPS1_repeat_ec5 S1_ 99.7 2.1E-17 5.4E-22 122.7 7.3 68 283-350 1-68 (69)
41 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.7 6.5E-17 1.7E-21 119.8 9.7 69 459-529 1-69 (69)
42 cd05698 S1_Rrp5_repeat_hs6_sc5 99.7 3.6E-17 9.1E-22 121.3 6.9 69 198-266 1-70 (70)
43 cd05684 S1_DHX8_helicase S1_DH 99.7 5.5E-17 1.4E-21 120.2 7.7 74 283-358 1-77 (79)
44 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.7 4.9E-17 1.3E-21 120.5 6.6 69 283-352 1-69 (69)
45 COG1098 VacB Predicted RNA bin 99.7 1.1E-16 2.8E-21 118.4 8.1 83 455-540 2-84 (129)
46 cd05706 S1_Rrp5_repeat_sc10 S1 99.7 2.8E-16 7.2E-21 115.9 10.0 73 456-530 1-73 (73)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 99.7 2.9E-16 7.4E-21 115.8 9.1 69 459-530 1-69 (69)
48 cd05684 S1_DHX8_helicase S1_DH 99.7 1.3E-16 3.2E-21 118.0 7.2 73 198-272 1-78 (79)
49 cd05692 S1_RPS1_repeat_hs4 S1_ 99.7 9.1E-17 2.3E-21 118.9 6.4 68 198-266 1-69 (69)
50 COG1098 VacB Predicted RNA bin 99.7 5.1E-17 1.3E-21 120.4 4.6 78 194-272 2-80 (129)
51 cd05706 S1_Rrp5_repeat_sc10 S1 99.7 1.5E-16 3.8E-21 117.6 6.9 72 195-266 1-73 (73)
52 cd05688 S1_RPS1_repeat_ec3 S1_ 99.7 1.4E-16 3.5E-21 117.8 6.4 67 197-263 1-67 (68)
53 cd05685 S1_Tex S1_Tex: The C-t 99.7 1.7E-16 4.2E-21 117.3 6.5 68 459-528 1-68 (68)
54 cd05707 S1_Rrp5_repeat_sc11 S1 99.7 5.3E-16 1.4E-20 114.2 8.8 68 459-528 1-68 (68)
55 cd05685 S1_Tex S1_Tex: The C-t 99.7 5.7E-16 1.5E-20 114.1 8.6 67 198-264 1-68 (68)
56 cd05689 S1_RPS1_repeat_ec4 S1_ 99.6 2.8E-16 7E-21 116.0 6.6 68 196-263 2-71 (72)
57 cd05707 S1_Rrp5_repeat_sc11 S1 99.6 2.5E-16 6.3E-21 116.3 5.7 67 198-264 1-68 (68)
58 COG2996 Predicted RNA-bindinin 99.6 2.7E-13 6.9E-18 97.8 20.7 213 280-534 3-220 (287)
59 pfam00575 S1 S1 RNA binding do 99.6 2.9E-15 7.5E-20 109.7 10.1 73 456-530 2-74 (74)
60 cd04472 S1_PNPase S1_PNPase: P 99.6 1.4E-15 3.6E-20 111.7 8.3 68 459-529 1-68 (68)
61 PRK03987 translation initiatio 99.6 5.6E-16 1.4E-20 114.1 6.0 77 195-271 6-85 (262)
62 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 1.1E-15 2.7E-20 112.4 7.3 69 196-265 2-72 (73)
63 cd05690 S1_RPS1_repeat_ec5 S1_ 99.6 8.8E-16 2.3E-20 112.9 6.6 66 198-263 1-68 (69)
64 cd04472 S1_PNPase S1_PNPase: P 99.6 6.6E-16 1.7E-20 113.7 5.5 66 198-264 1-67 (68)
65 pfam00575 S1 S1 RNA binding do 99.6 2.2E-15 5.6E-20 110.5 7.7 71 196-266 3-74 (74)
66 COG1093 SUI2 Translation initi 99.6 1.1E-14 2.7E-19 106.3 10.2 76 282-358 11-88 (269)
67 cd05688 S1_RPS1_repeat_ec3 S1_ 99.6 7.6E-15 1.9E-19 107.2 8.8 66 459-527 2-67 (68)
68 PRK11824 polynucleotide phosph 99.6 9.4E-15 2.4E-19 106.7 9.1 79 452-533 615-693 (694)
69 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 8.4E-15 2.1E-19 107.0 8.2 71 457-529 2-72 (73)
70 PRK11824 polynucleotide phosph 99.6 3.8E-15 9.7E-20 109.1 6.2 79 363-443 615-693 (694)
71 COG2996 Predicted RNA-bindinin 99.6 9.5E-13 2.4E-17 94.5 17.6 208 109-355 4-218 (287)
72 cd04465 S1_RPS1_repeat_ec2_hs2 99.6 3.8E-15 9.8E-20 109.0 4.9 67 111-177 1-67 (67)
73 COG2183 Tex Transcriptional ac 99.5 1.1E-13 2.8E-18 100.2 7.6 86 450-537 650-735 (780)
74 COG2183 Tex Transcriptional ac 99.5 6.5E-14 1.6E-18 101.6 6.1 77 365-442 654-730 (780)
75 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 1.2E-12 3E-17 94.0 9.5 66 27-92 1-69 (70)
76 TIGR03591 polynuc_phos polyrib 99.4 2.4E-13 6.2E-18 98.1 5.8 72 453-527 613-684 (684)
77 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 4.3E-13 1.1E-17 96.6 6.8 70 459-530 1-70 (70)
78 TIGR03591 polynuc_phos polyrib 99.4 1.5E-12 3.7E-17 93.4 7.4 73 363-437 612-684 (684)
79 cd04460 S1_RpoE S1_RpoE: RpoE, 99.4 1.9E-12 4.8E-17 92.7 7.8 78 199-276 1-94 (99)
80 COG1093 SUI2 Translation initi 99.4 6.4E-13 1.6E-17 95.6 4.6 77 195-271 9-88 (269)
81 cd04473 S1_RecJ_like S1_RecJ_l 99.4 2.3E-12 6E-17 92.2 7.4 69 272-351 7-75 (77)
82 smart00316 S1 Ribosomal protei 99.3 1.1E-11 2.7E-16 88.2 9.9 72 457-530 1-72 (72)
83 cd05705 S1_Rrp5_repeat_hs14 S1 99.3 1E-11 2.6E-16 88.3 8.6 71 456-528 1-74 (74)
84 PTZ00248 eukaryotic translatio 99.3 1.4E-11 3.5E-16 87.5 9.3 76 196-271 16-94 (324)
85 cd04465 S1_RPS1_repeat_ec2_hs2 99.3 2.1E-11 5.2E-16 86.5 9.6 67 459-530 1-67 (67)
86 cd00164 S1_like S1_like: Ribos 99.3 5.7E-12 1.5E-16 89.8 6.5 63 463-527 2-64 (65)
87 cd05705 S1_Rrp5_repeat_hs14 S1 99.3 1.1E-11 2.8E-16 88.1 7.5 70 195-264 1-74 (74)
88 cd00164 S1_like S1_like: Ribos 99.3 1.7E-11 4.4E-16 86.9 8.1 63 202-264 2-65 (65)
89 smart00316 S1 Ribosomal protei 99.3 1.8E-11 4.7E-16 86.7 8.1 71 282-353 2-72 (72)
90 TIGR02063 RNase_R ribonuclease 99.3 2.2E-11 5.6E-16 86.3 7.9 73 456-529 670-753 (755)
91 cd04473 S1_RecJ_like S1_RecJ_l 99.2 4.2E-11 1.1E-15 84.6 8.6 65 453-528 11-75 (77)
92 cd04460 S1_RpoE S1_RpoE: RpoE, 99.2 3.6E-11 9.2E-16 85.0 8.1 68 461-531 2-85 (99)
93 cd05702 S1_Rrp5_repeat_hs11_sc 99.2 2.1E-11 5.4E-16 86.3 6.7 62 283-345 1-64 (70)
94 COG1185 Pnp Polyribonucleotide 99.2 3.7E-11 9.5E-16 84.9 7.2 103 427-533 586-691 (692)
95 TIGR02063 RNase_R ribonuclease 99.2 5.8E-11 1.5E-15 83.7 7.8 72 368-439 671-753 (755)
96 COG1185 Pnp Polyribonucleotide 99.2 2.8E-11 7.2E-16 85.6 5.7 100 340-442 586-690 (692)
97 cd05704 S1_Rrp5_repeat_hs13 S1 99.2 1.5E-10 3.7E-15 81.3 8.0 70 195-266 1-72 (72)
98 cd04471 S1_RNase_R S1_RNase_R: 99.1 3.2E-10 8.2E-15 79.2 8.7 33 283-315 2-35 (83)
99 cd05703 S1_Rrp5_repeat_hs12_sc 99.1 2.7E-10 7E-15 79.6 7.6 70 459-530 1-72 (73)
100 cd04471 S1_RNase_R S1_RNase_R: 99.1 5.5E-10 1.4E-14 77.8 9.1 70 459-529 2-82 (83)
101 cd05702 S1_Rrp5_repeat_hs11_sc 99.1 1.6E-10 4.1E-15 81.0 5.9 58 459-518 1-60 (70)
102 cd05703 S1_Rrp5_repeat_hs12_sc 99.1 8.6E-10 2.2E-14 76.6 9.5 71 283-353 1-72 (73)
103 PTZ00248 eukaryotic translatio 99.1 5.9E-11 1.5E-15 83.7 2.5 81 278-359 12-95 (324)
104 cd05704 S1_Rrp5_repeat_hs13 S1 99.1 7.6E-10 1.9E-14 77.0 8.1 71 456-530 1-72 (72)
105 cd05693 S1_Rrp5_repeat_hs1_sc1 99.0 3.3E-09 8.4E-14 73.1 9.2 73 458-532 3-97 (100)
106 cd05693 S1_Rrp5_repeat_hs1_sc1 99.0 9.3E-10 2.4E-14 76.4 5.6 37 196-232 2-39 (100)
107 PRK11642 exoribonuclease R; Pr 98.9 5E-09 1.3E-13 72.0 7.7 74 455-529 640-724 (813)
108 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 5.3E-09 1.3E-13 71.9 7.5 69 459-529 1-71 (71)
109 PRK11642 exoribonuclease R; Pr 98.9 7.1E-09 1.8E-13 71.1 8.1 73 368-440 642-725 (813)
110 KOG1067 consensus 98.9 2E-09 5E-14 74.5 5.0 78 453-532 663-740 (760)
111 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 9E-09 2.3E-13 70.4 7.1 64 288-352 7-71 (71)
112 KOG1067 consensus 98.8 1.1E-08 2.7E-13 70.0 5.5 80 366-447 665-744 (760)
113 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.7 8.7E-08 2.2E-12 64.5 6.9 66 459-528 1-66 (66)
114 cd05694 S1_Rrp5_repeat_hs2_sc2 98.7 2.6E-07 6.6E-12 61.6 9.3 68 24-94 2-70 (74)
115 COG1095 RPB7 DNA-directed RNA 98.6 1.1E-07 2.7E-12 64.0 7.1 72 196-267 80-167 (183)
116 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.6 2.8E-07 7.3E-12 61.3 8.9 65 198-264 1-66 (66)
117 COG1095 RPB7 DNA-directed RNA 98.6 1.7E-07 4.4E-12 62.7 7.5 34 370-404 82-115 (183)
118 PRK04163 exosome complex RNA-b 98.6 1.1E-05 2.9E-10 51.6 15.5 199 326-569 26-230 (232)
119 TIGR00448 rpoE DNA-directed RN 98.6 3.2E-07 8.1E-12 61.1 7.5 73 195-267 79-172 (184)
120 cd05694 S1_Rrp5_repeat_hs2_sc2 98.5 4.2E-07 1.1E-11 60.4 7.8 68 280-354 2-70 (74)
121 PRK05054 exoribonuclease II; P 98.5 5.5E-07 1.4E-11 59.6 7.5 72 456-528 557-642 (644)
122 PRK05054 exoribonuclease II; P 98.5 7.8E-07 2E-11 58.7 7.9 70 368-437 558-641 (644)
123 PRK08563 DNA-directed RNA poly 98.5 7.4E-07 1.9E-11 58.8 7.4 32 198-229 82-113 (182)
124 cd04455 S1_NusA S1_NusA: N-uti 98.4 1.7E-06 4.4E-11 56.6 9.0 63 25-91 2-66 (67)
125 PRK08563 DNA-directed RNA poly 98.4 1.7E-06 4.4E-11 56.6 8.7 71 370-441 82-167 (182)
126 PTZ00162 RNA polymerase II sub 98.4 3E-06 7.6E-11 55.2 9.6 34 197-230 81-114 (170)
127 KOG2916 consensus 98.4 8.6E-07 2.2E-11 58.5 6.5 74 196-269 15-91 (304)
128 COG1107 Archaea-specific RecJ- 98.4 7.6E-06 1.9E-10 52.7 11.2 207 118-349 55-279 (715)
129 PRK09202 nusA transcription el 98.3 1.7E-05 4.4E-10 50.5 11.7 32 110-141 135-166 (428)
130 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.3 6.1E-06 1.6E-10 53.3 9.4 71 457-530 5-79 (86)
131 PTZ00162 RNA polymerase II sub 98.3 2E-06 5.2E-11 56.2 6.8 32 370-402 82-113 (170)
132 TIGR00448 rpoE DNA-directed RN 98.3 1.4E-06 3.6E-11 57.1 5.8 71 370-441 82-172 (184)
133 PRK12328 nusA transcription el 98.3 1.9E-05 4.9E-10 50.3 11.4 64 281-352 137-204 (375)
134 PRK12327 nusA transcription el 98.3 1.7E-05 4.3E-10 50.6 10.9 57 282-346 134-190 (353)
135 cd04455 S1_NusA S1_NusA: N-uti 98.2 1.1E-05 2.8E-10 51.7 9.1 56 458-522 3-58 (67)
136 KOG1856 consensus 98.2 2.5E-06 6.5E-11 55.6 5.7 82 454-535 981-1063(1299)
137 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.2 4.9E-06 1.2E-10 53.9 6.9 34 197-230 6-40 (86)
138 TIGR01953 NusA transcription t 98.2 2.3E-06 5.9E-11 55.8 4.9 107 233-351 92-217 (366)
139 TIGR01953 NusA transcription t 98.2 2.1E-05 5.4E-10 50.0 9.5 111 148-265 94-218 (366)
140 PRK12328 nusA transcription el 98.2 2.2E-06 5.6E-11 56.0 4.5 109 149-265 88-204 (375)
141 PRK04163 exosome complex RNA-b 98.2 4.5E-05 1.1E-09 48.0 11.1 105 240-354 27-136 (232)
142 KOG1856 consensus 98.2 2.3E-06 5.8E-11 55.9 4.2 77 278-355 981-1060(1299)
143 PRK12327 nusA transcription el 98.1 1.2E-06 3E-11 57.6 2.4 64 196-265 133-198 (353)
144 PRK09202 nusA transcription el 98.0 2E-06 5.2E-11 56.2 2.2 64 196-265 134-199 (428)
145 cd04453 S1_RNase_E S1_RNase_E: 98.0 1.9E-05 4.8E-10 50.3 7.0 72 280-351 5-80 (88)
146 PRK12329 nusA transcription el 98.0 8.5E-05 2.2E-09 46.4 10.2 64 281-351 152-223 (457)
147 COG1107 Archaea-specific RecJ- 98.0 1.6E-05 4E-10 50.8 5.9 70 18-90 114-183 (715)
148 PRK09521 exosome complex RNA-b 97.9 9.3E-05 2.4E-09 46.1 8.4 60 195-254 62-133 (187)
149 PRK09521 exosome complex RNA-b 97.9 0.00027 6.9E-09 43.3 10.6 70 280-353 62-142 (187)
150 COG0557 VacB Exoribonuclease R 97.9 6.9E-05 1.8E-09 46.9 7.5 74 455-529 619-703 (706)
151 COG0557 VacB Exoribonuclease R 97.9 0.00012 3E-09 45.5 8.7 72 368-439 621-703 (706)
152 PRK12329 nusA transcription el 97.8 0.00022 5.7E-09 43.8 9.7 64 196-265 152-224 (457)
153 COG1097 RRP4 RNA-binding prote 97.8 0.002 5.1E-08 38.0 14.3 162 368-565 63-228 (239)
154 KOG2916 consensus 97.8 1.5E-05 3.7E-10 51.0 2.5 81 278-359 11-94 (304)
155 COG1096 Predicted RNA-binding 97.8 0.00015 3.9E-09 44.8 7.7 72 192-266 59-141 (188)
156 cd04454 S1_Rrp4_like S1_Rrp4_l 97.8 0.00027 6.9E-09 43.3 8.8 60 458-519 6-65 (82)
157 TIGR02696 pppGpp_PNP guanosine 97.7 1.1E-05 2.7E-10 51.8 1.5 73 453-528 648-724 (725)
158 COG1097 RRP4 RNA-binding prote 97.7 0.0011 2.9E-08 39.5 11.7 105 241-354 30-138 (239)
159 cd04453 S1_RNase_E S1_RNase_E: 97.7 0.00018 4.5E-09 44.4 7.4 16 42-57 25-40 (88)
160 cd04454 S1_Rrp4_like S1_Rrp4_l 97.7 0.00016 4E-09 44.7 7.1 21 27-47 7-27 (82)
161 PRK11712 ribonuclease G; Provi 97.7 0.00045 1.2E-08 41.9 8.8 38 23-60 35-74 (489)
162 COG1096 Predicted RNA-binding 97.6 0.00026 6.6E-09 43.4 7.4 96 241-342 27-133 (188)
163 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.6 0.0005 1.3E-08 41.7 7.8 70 281-351 5-83 (92)
164 TIGR02696 pppGpp_PNP guanosine 97.5 6.3E-05 1.6E-09 47.1 2.5 69 368-437 652-723 (725)
165 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.0004 1E-08 42.3 5.3 69 459-529 1-71 (72)
166 PRK10811 rne ribonuclease E; R 97.4 0.0018 4.7E-08 38.3 8.7 61 23-83 35-109 (1063)
167 PRK10811 rne ribonuclease E; R 97.3 0.00068 1.7E-08 40.9 6.0 35 109-143 37-74 (1063)
168 PRK11712 ribonuclease G; Provi 97.3 0.0017 4.2E-08 38.5 7.5 66 194-259 35-115 (489)
169 pfam10246 MRP-S35 Mitochondria 97.3 0.0016 4E-08 38.7 7.4 73 6-82 2-75 (105)
170 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.2 0.00045 1.1E-08 42.0 4.2 69 370-439 1-71 (72)
171 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.1 0.0023 5.9E-08 37.7 7.0 32 198-229 2-33 (88)
172 pfam10447 EXOSC1 Exosome compo 97.0 0.0021 5.3E-08 38.0 6.2 13 283-295 5-17 (72)
173 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.6 0.016 4E-07 32.6 7.7 29 370-399 2-30 (88)
174 TIGR00757 RNaseEG ribonuclease 96.5 0.0011 2.9E-08 39.5 1.8 99 22-122 23-137 (464)
175 COG1530 CafA Ribonucleases G a 96.5 0.025 6.5E-07 31.4 8.3 60 23-82 34-102 (487)
176 KOG3409 consensus 96.5 0.018 4.5E-07 32.3 7.5 14 414-427 122-135 (193)
177 KOG3409 consensus 95.9 0.038 9.8E-07 30.3 6.8 59 282-340 68-135 (193)
178 TIGR00757 RNaseEG ribonuclease 95.8 0.0051 1.3E-07 35.6 2.1 39 194-232 24-65 (464)
179 KOG4078 consensus 95.6 0.032 8.2E-07 30.7 5.4 51 370-428 83-133 (173)
180 COG1530 CafA Ribonucleases G a 95.5 0.035 8.9E-07 30.5 5.4 73 192-265 32-112 (487)
181 KOG3298 consensus 94.9 0.14 3.6E-06 26.8 7.0 25 198-222 82-106 (170)
182 KOG3298 consensus 94.7 0.17 4.4E-06 26.3 7.0 27 370-397 82-108 (170)
183 CHL00010 infA translation init 94.5 0.23 5.7E-06 25.6 7.2 65 286-355 9-74 (78)
184 PRK12442 translation initiatio 94.3 0.24 6.2E-06 25.4 7.1 65 286-355 9-74 (87)
185 TIGR00358 3_prime_RNase VacB a 94.2 0.029 7.4E-07 31.0 2.2 74 455-529 595-683 (684)
186 PRK00276 infA translation init 93.4 0.4 1E-05 24.1 6.8 60 286-350 9-69 (72)
187 TIGR00358 3_prime_RNase VacB a 93.3 0.071 1.8E-06 28.7 2.8 53 25-83 14-68 (684)
188 cd04451 S1_IF1 S1_IF1: Transla 92.5 0.5 1.3E-05 23.5 6.2 58 286-348 3-61 (64)
189 cd05790 S1_Rrp40 S1_Rrp40: Rrp 91.5 0.75 1.9E-05 22.4 8.4 67 282-352 6-73 (86)
190 TIGR00008 infA translation ini 90.7 0.78 2E-05 22.3 5.6 59 286-349 7-66 (69)
191 TIGR02062 RNase_B exoribonucle 89.6 0.38 9.6E-06 24.3 3.2 71 455-526 579-661 (664)
192 cd05700 S1_Rrp5_repeat_hs9 S1_ 88.7 1.3 3.3E-05 21.0 6.9 64 283-351 1-64 (65)
193 KOG1004 consensus 84.8 2.1 5.4E-05 19.7 7.1 61 369-431 65-125 (230)
194 KOG1999 consensus 83.7 2.4 6.1E-05 19.4 10.8 32 274-305 454-486 (1024)
195 PRK12366 replication factor A; 82.2 2.7 7E-05 19.0 26.8 74 410-483 455-540 (649)
196 cd05701 S1_Rrp5_repeat_hs10 S1 81.3 2.8 7E-05 19.0 4.3 12 504-515 45-56 (69)
197 TIGR02142 modC_ABC molybdate A 79.3 2.9 7.5E-05 18.8 3.9 56 271-342 226-283 (361)
198 KOG4134 consensus 76.9 1.6 4.2E-05 20.4 2.0 55 196-255 106-161 (253)
199 COG4776 Rnb Exoribonuclease II 75.2 0.68 1.7E-05 22.7 -0.3 68 458-526 561-640 (645)
200 PRK10409 hydrogenase isoenzyme 74.5 4.7 0.00012 17.6 5.2 48 29-78 4-52 (90)
201 KOG3013 consensus 72.1 5.3 0.00013 17.3 3.6 32 196-227 84-116 (301)
202 COG0361 InfA Translation initi 70.2 5.9 0.00015 17.0 7.0 65 283-352 6-71 (75)
203 smart00357 CSP Cold shock prot 66.9 6.9 0.00018 16.6 6.8 10 507-516 39-48 (64)
204 PRK08559 nusG transcription an 65.1 7.5 0.00019 16.4 3.9 16 337-352 114-129 (153)
205 KOG3754 consensus 56.9 5 0.00013 17.5 1.1 32 63-94 40-71 (640)
206 TIGR00074 hypC_hupF hydrogenas 55.4 11 0.00028 15.4 4.4 76 30-111 5-84 (88)
207 COG0298 HypC Hydrogenase matur 49.8 14 0.00035 14.8 5.2 68 29-108 4-75 (82)
208 TIGR01067 rplN_bact ribosomal 49.7 14 0.00035 14.8 4.9 14 280-293 58-71 (128)
209 pfam09883 DUF2110 Uncharacteri 46.9 15 0.00039 14.5 9.1 31 283-314 76-106 (226)
210 KOG0125 consensus 44.2 17 0.00043 14.3 3.6 70 221-295 96-170 (376)
211 PRK12336 translation initiatio 41.7 18 0.00047 14.0 6.2 47 456-518 145-191 (201)
212 TIGR00705 SppA_67K signal pept 40.9 19 0.00048 14.0 3.9 97 25-128 41-149 (614)
213 TIGR01843 type_I_hlyD type I s 39.3 20 0.00051 13.8 9.2 98 194-291 278-382 (434)
214 PRK00116 ruvA Holliday junctio 39.1 20 0.00051 13.8 8.6 19 285-303 4-22 (198)
215 COG0195 NusA Transcription elo 37.2 21 0.00055 13.6 5.5 39 306-351 2-41 (190)
216 pfam04270 Strep_his_triad Stre 35.5 11 0.00028 15.3 0.1 27 118-144 14-40 (53)
217 PRK13901 ruvA Holliday junctio 35.4 23 0.00058 13.4 8.0 19 285-303 4-22 (196)
218 TIGR01363 strep_his_triad stre 35.0 9.9 0.00025 15.6 -0.2 35 459-496 336-371 (376)
219 KOG3297 consensus 34.9 23 0.0006 13.4 5.8 23 243-265 81-103 (202)
220 pfam11813 DUF3334 Protein of u 33.1 25 0.00064 13.2 2.4 18 209-226 48-66 (227)
221 pfam06108 DUF952 Protein of un 32.5 20 0.00052 13.8 1.1 34 394-431 25-58 (92)
222 TIGR02860 spore_IV_B stage IV 30.8 27 0.0007 13.0 11.4 212 132-395 86-310 (423)
223 COG1862 YajC Preprotein transl 30.4 28 0.00071 12.9 6.2 13 188-200 37-49 (97)
224 pfam01938 TRAM TRAM domain. Th 30.1 28 0.00072 12.9 4.6 16 458-473 4-19 (59)
225 pfam00358 PTS_EIIA_1 phosphoen 29.6 29 0.00073 12.9 4.4 26 288-313 49-76 (133)
226 PRK10949 protease 4; Provision 28.3 30 0.00077 12.7 5.0 57 68-129 107-163 (618)
227 cd00210 PTS_IIA_glc PTS_IIA, P 27.3 31 0.0008 12.6 4.3 26 288-313 44-71 (124)
228 cd04322 LysRS_N LysRS_N: N-ter 26.2 33 0.00084 12.5 8.3 18 286-303 4-23 (108)
229 pfam07703 A2M_N_2 Alpha-2-macr 25.9 33 0.00085 12.5 9.5 15 240-254 9-23 (136)
230 TIGR02037 degP_htrA_DO proteas 25.4 34 0.00087 12.4 4.3 23 243-265 123-145 (484)
231 COG2106 Uncharacterized conser 25.4 34 0.00087 12.4 5.5 23 196-218 104-126 (272)
232 TIGR02222 chap_CsaA export-rel 25.0 35 0.00089 12.4 4.9 21 70-90 72-93 (107)
233 COG0179 MhpD 2-keto-4-pentenoa 23.7 37 0.00094 12.2 2.3 29 434-466 207-236 (266)
234 TIGR01648 hnRNP-R-Q hnRNP-R, Q 23.3 37 0.00095 12.2 2.8 32 183-217 250-281 (611)
235 pfam01330 RuvA_N RuvA N termin 23.1 38 0.00097 12.1 7.1 30 30-59 5-35 (61)
236 PRK05585 yajC preprotein trans 22.7 38 0.00098 12.1 6.5 13 188-200 47-59 (107)
237 PRK03598 hypothetical protein; 21.6 41 0.001 11.9 8.7 40 27-74 32-71 (331)
238 smart00815 AMA-1 Apical membra 21.2 39 0.00099 12.0 0.8 13 292-304 13-25 (240)
239 TIGR00739 yajC preprotein tran 21.0 42 0.0011 11.9 6.3 31 188-218 31-69 (86)
240 pfam07405 DUF1506 Protein of u 20.9 42 0.0011 11.9 3.2 27 240-266 101-127 (133)
241 pfam01176 eIF-1a Translation i 20.7 42 0.0011 11.8 6.3 57 286-348 5-62 (65)
242 COG5009 MrcA Membrane carboxyp 20.3 43 0.0011 11.8 6.0 54 197-250 345-404 (797)
243 PRK13289 nitric oxide dioxygen 20.3 43 0.0011 11.8 2.7 13 240-252 184-196 (399)
No 1
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=986.06 Aligned_cols=554 Identities=55% Similarity=0.924 Sum_probs=538.4
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCC
Q ss_conf 06889999885402146389877999999981998999947960367899750566435563789879999999747998
Q gi|254780456|r 7 SREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFG 86 (576)
Q Consensus 7 ~~~~f~~ll~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g 86 (576)
+.++|++||++++...++++|++|+|+|+++++++++||+|+|++|+||++||.+......+++||+|+|+|++.+++.|
T Consensus 1 ~~e~F~~Lle~s~~~~~~~~G~iV~G~Vv~i~~~~v~VdiG~K~eG~I~~~E~~~~~~~~~~~vGd~i~v~v~~~~d~~G 80 (556)
T PRK06299 1 MTESFAALLEESLKEEELREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNDQGELEVKVGDEVEVYLERIEDGFG 80 (556)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCC
T ss_conf 96479999974234457889998999999997999999968883578799993477677467999999999999878897
Q ss_pred EEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCC
Q ss_conf 59996878755575899999852897699999999679559997440200000112345433345555530231113354
Q gi|254780456|r 87 EAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMD 166 (576)
Q Consensus 87 ~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d 166 (576)
+++||++++.....|+.+.+||++|++|+|+|++.+||||+|+++|++||||+||++.++++|++.++|++++|+|+++|
T Consensus 81 ~i~LS~~ka~~~~~w~~l~~a~e~~~~v~g~i~~~vKGG~~V~i~gv~aFlP~Sq~d~~~v~d~~~~vG~~l~~kIi~~d 160 (556)
T PRK06299 81 ETVLSREKAKRLEAWDKLEEAYENGEIVEGVINGKVKGGFTVDLNGVRAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLD 160 (556)
T ss_pred EEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEEE
T ss_conf 49998799775788999999975898799999999778099998898999785882575556617657966999999975
Q ss_pred CCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCE
Q ss_conf 32331122121112222212111000112223302467887531471777448315788642024444433113326972
Q gi|254780456|r 167 KRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQ 246 (576)
Q Consensus 167 ~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~ 246 (576)
++++++++|||+++++....++.++++.+++|++++|+|+++++||+||++||++||+|++++||+|+.||++.|++||+
T Consensus 161 ~~~~~iVvSrr~~lee~~~~~~~~~~~~l~~G~vv~G~V~~i~~~GaFVdlggvdGllhiseiSw~rv~~p~~~~~~G~~ 240 (556)
T PRK06299 161 KKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNVGDE 240 (556)
T ss_pred CCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCE
T ss_conf 23580897328988888888899999852479727899999705758999589589998567155666998992668988
Q ss_pred EEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf 58999987476527998521555432100000004896658999981596699985142000000111101113557421
Q gi|254780456|r 247 VKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSK 326 (576)
Q Consensus 247 v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~ 326 (576)
++++|+++|++++||+||+|++.+|||..+.++|++|++++|+|+++++||+||+|.+|++||+|+|||||++++.+|.+
T Consensus 241 v~vkVl~id~e~~risLslK~l~~dPw~~~~~~~~~G~~v~g~V~~i~~fGafVel~~gveGlvhiSelsw~~~~~~p~~ 320 (556)
T PRK06299 241 VKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSK 320 (556)
T ss_pred EEEEEEEECCCCCEEEEEEECCCCCHHHHHHHHCCCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHCCCCCCCCCHHH
T ss_conf 99999988265638999970356785576786478999899999998276079995499589988787167544479789
Q ss_pred EECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCC
Q ss_conf 00378457999998621550478752034543210000012222213699999850169997068841354005530012
Q gi|254780456|r 327 ILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNR 406 (576)
Q Consensus 327 ~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~ 406 (576)
.|++||.|+|+|+++|+++++|+||+|++++|||+.+.++||+|++++|+|++++++|+||+++++++|++|.+|+||+.
T Consensus 321 ~~~~G~~V~~kIl~id~~~~risLS~K~~~~nPw~~~~~~~~vG~~v~g~V~~i~~fG~fv~l~~gv~GlvH~sdlSW~~ 400 (556)
T PRK06299 321 VVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKIKNITDFGAFVGLEGGIDGLVHLSDISWDK 400 (556)
T ss_pred HCCCCCEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHCCCCC
T ss_conf 54479779999999724436888863236679789998635556479999999664369998527732377853545555
Q ss_pred CCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEE
Q ss_conf 20012342111234226885215654553201132210111000011004789879999999708908999617798499
Q gi|254780456|r 407 PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINS 486 (576)
Q Consensus 407 ~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G 486 (576)
...++.+.|++||.++|+|+++|++++|++||+||+.++||+.+. +.|++|++++|+|.++.++|+||.+. +|+.|
T Consensus 401 ~~~~~~~~~k~Gd~v~vkVL~iD~e~~rIsLgiKql~~dPw~~~~--~~~k~G~iv~g~V~~i~~~G~fV~l~--~gieg 476 (556)
T PRK06299 401 KGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFA--KKHKKGSIVTGTVTEVKDKGAFVELA--DGVEG 476 (556)
T ss_pred CCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEHHCCCCCHHHHH--HHCCCCCEEEEEEEEEECCCEEEEEC--CCEEE
T ss_conf 641056642689669999999816676798870431278168787--63899899999999997895699938--99099
Q ss_pred EEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCCCC--CCCHHHHHHHHHHHH
Q ss_conf 999747182121042011068987999999970576869987036557777999998403445--777999999999874
Q gi|254780456|r 487 FIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDS--GASLGDILGMALKNR 564 (576)
Q Consensus 487 ~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~~~~~--~~tlg~~~~~~lk~~ 564 (576)
|||.|+++..+...+.+.|++||.++|+|+++|++++||+||+|+++++++++++++|+++.+ ++||||+|+++|+++
T Consensus 477 lI~~sels~~~~~~~~~~~~~Gd~v~~~Ii~id~e~rkI~LSiK~le~~~eke~~~~y~~~~~~~~~tLgdiLk~~l~~k 556 (556)
T PRK06299 477 FIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEYGNSDSDATTTLGDLLKAALKGK 556 (556)
T ss_pred EEEHHHCCCHHHHCCCCCCCCCCEEEEEEEEECCCCCEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCC
T ss_conf 99979968002336211168999899999998277799998715955556799999855667777778899998987479
No 2
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=0 Score=951.80 Aligned_cols=544 Identities=35% Similarity=0.597 Sum_probs=515.9
Q ss_pred CHHHHHHHH----HHHHHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEE
Q ss_conf 106889999----8854021463898779999999819989999479603678997505664355637898799999997
Q gi|254780456|r 6 PSREDFATL----LEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERT 81 (576)
Q Consensus 6 ~~~~~f~~l----l~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~ 81 (576)
..++.|..| |.+.+..+.+++|++++|+|++|++++++||+|+|+||+||+.||. .+.++||.|+|++.++
T Consensus 297 ~~~~~~~~~~~~~l~~~~~~~~~~~G~vi~g~Vv~i~~d~V~vdvG~KsEg~ip~~eF~-----~~~~vGD~v~V~ie~~ 371 (863)
T PRK12269 297 NQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFE-----APPKAGDGVRVYVERV 371 (863)
T ss_pred HHHCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCEEEEECCCCCCCCCCHHHCC-----CCCCCCCEEEEEEEEE
T ss_conf 43124135568876665300379986258999999958979996477445532699927-----7889999999999997
Q ss_pred ECCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEE--EEECCCEEEEEC-CCHHHHHCCCCCCCCCCCCCCCCCCEE
Q ss_conf 47998599968787555758999998528976999999--996795599974-402000001123454333455555302
Q gi|254780456|r 82 ENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIF--NQVKGGMTVDLN-GEVAFLPRSQIDIRPVRDVTPLMHEPQ 158 (576)
Q Consensus 82 ~~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~--~~~k~G~~V~i~-gi~~FlP~s~~~~~~~~d~~~~vG~~i 158 (576)
++..++ ||+.||.+...|..++++++.|++|+|+|. ..+||||.|+++ |++||||+||+|.+|++|+.+++|+++
T Consensus 372 e~~~~~--LSr~kA~r~~~w~~le~a~~~~~~v~G~i~~~~~vkgG~~Vdl~~gv~AFLPgSqvd~rpv~d~~~~~g~~~ 449 (863)
T PRK12269 372 TPYGPE--LSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTS 449 (863)
T ss_pred CCCCCE--ECHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEECCCCCEEECCHHHCCCEECCCCHHHCCCCC
T ss_conf 088975--618999878999999999756990799997446104537998588967867665647113688632158874
Q ss_pred EECCCCCCCC-----CCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCC
Q ss_conf 3111335432-----33112212111222221211100011222330246788753147177744831578864202444
Q gi|254780456|r 159 LFEILKMDKR-----RGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHR 233 (576)
Q Consensus 159 ~~~Ii~~d~~-----~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~ 233 (576)
+|+|+++|.. +++|++|||+++++...+++.++++++++|++++|+|+++++||+||++||++||+|++||||+|
T Consensus 450 ~f~iik~~~~~~~r~~~NiVvSRravlEe~~~~~r~~~l~~l~eG~vv~G~VKnitdyGaFvDLGGvDGLLHitDiSW~R 529 (863)
T PRK12269 450 KFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGH 529 (863)
T ss_pred CEEEEEEEHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCEEEEECCCCCEEEEEECCCCCC
T ss_conf 15999953133126778889976798888889999999864436877889998315640589617710146621113578
Q ss_pred CCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECC
Q ss_conf 44331133269725899998747652799852155543210000000489665899998159669998514200000011
Q gi|254780456|r 234 ILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHIS 313 (576)
Q Consensus 234 ~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~s 313 (576)
+.||++++++||+++++||.+|++++||+|++|||.+|||..+.++|++|+++.|+|++++|||+||+|++|++||+|+|
T Consensus 530 v~hPse~~~vG~~i~vkVlk~D~e~~riSLglKQl~~dPW~~i~~ky~vg~~v~gkVtnitdyGaFVEle~GiEGLvHvS 609 (863)
T PRK12269 530 VARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHIS 609 (863)
T ss_pred CCCHHHHHCCCCEEEEEEEEECCCCCEEEECCCCCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCCEEEEEEH
T ss_conf 89989971279779999985256545143113217789767888638899989999999744656999638925788702
Q ss_pred CCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCC
Q ss_conf 11011135574210037845799999862155047875203454321000001222221369999985016999706884
Q gi|254780456|r 314 QISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHL 393 (576)
Q Consensus 314 els~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i 393 (576)
||||++++.+|.+++++||.|+|+|+++|+++|+|+||+||+++|||+.+.++||+|++++|+|+++++||+||.+.+++
T Consensus 610 EmsWtkk~~~P~k~v~~GdeVev~VLeID~ekrRISLg~Kq~~~NPW~~~~~ky~vG~~v~g~I~nitdFGiFv~le~gI 689 (863)
T PRK12269 610 EFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGI 689 (863)
T ss_pred HHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECEEEEEECCCCC
T ss_conf 50202367997980768977999999880322678544101668849999976899898999999853308999747993
Q ss_pred EEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCE
Q ss_conf 13540055300122001234211123422688521565455320113221011100001100478987999999970890
Q gi|254780456|r 394 DGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGG 473 (576)
Q Consensus 394 ~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G 473 (576)
+|++|.+|+||+...+++.+.|+.||+++++||++|.+++||+|++|||..+||+.+. +.+++|++|+|+|.++.++|
T Consensus 690 DGlvH~sDlSW~~~~~~~~~~~kkGd~ve~kVL~Id~ekeRIsLGiKQL~~DP~~~f~--~~~~~G~iVtg~V~~v~d~G 767 (863)
T PRK12269 690 DGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFA--NAYGVGSTVEGEVSSVTDFG 767 (863)
T ss_pred EEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCCCCCHHHHH--HHCCCCCEEEEEEEEEECCC
T ss_conf 6789821067678772656625789879999999747657777401006578789998--63899898999999995694
Q ss_pred EEEEECCCCCEEEEEEHHHCCHHHHCCCHH---HCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCCC--
Q ss_conf 899961779849999974718212104201---106898799999997057686998703655777799999840344--
Q gi|254780456|r 474 IEVSLIDHKGINSFIRRSDLSRDRVDQDPG---RFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSD-- 548 (576)
Q Consensus 474 ~~V~l~~~~gv~G~i~~s~is~~~~~~~~~---~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~~~~-- 548 (576)
+||.+. .|+.||+|.|+++.++.+++++ .|++|++|+|+|+++|.++++|.||+|+++..++++++++|.+..
T Consensus 768 ~~V~l~--~gieg~I~~s~ls~~r~e~~~~~~~rFavGd~vdA~I~~iD~k~RkI~LSIK~le~~~ekEa~~kY~s~~sg 845 (863)
T PRK12269 768 IFVRVP--GGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQRDELSRYMSAPRG 845 (863)
T ss_pred EEEEEC--CCEEEEEEHHHHHHHHHHCHHHHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 799908--991699898981120331846664235899879999998846667799877897767789999986076666
Q ss_pred ---CCCCHHHHHHHH
Q ss_conf ---577799999999
Q gi|254780456|r 549 ---SGASLGDILGMA 560 (576)
Q Consensus 549 ---~~~tlg~~~~~~ 560 (576)
..+||||+||+.
T Consensus 846 ~~~~t~~LG~llke~ 860 (863)
T PRK12269 846 EDEGSFTLGDLMRQT 860 (863)
T ss_pred CCCCCCCHHHHHHHH
T ss_conf 676777589998876
No 3
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of 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 , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=100.00 E-value=0 Score=936.18 Aligned_cols=518 Identities=50% Similarity=0.864 Sum_probs=507.5
Q ss_pred HHHHHHHHHHHCCCCCCC-CCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCC
Q ss_conf 889999885402146389-8779999999819--9899994796036789975056643556378987999999974799
Q gi|254780456|r 9 EDFATLLEESFTKKDLAE-NCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSF 85 (576)
Q Consensus 9 ~~f~~ll~~~~~~~~~~~-G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~ 85 (576)
++|++||++++...+..+ |+++.|.|++|.. ++++||+|+|+||+||.+||.+...+..+++||.|+|++....+..
T Consensus 1 ~~f~~ll~E~~~~~e~~~~G~i~~G~VV~i~~ndd~v~VDvG~KsEg~ip~~Ef~~~~G~l~~~~Gd~v~V~l~~~~~~~ 80 (534)
T TIGR00717 1 EEFAKLLEESLKTEETRPKGSIVKGTVVKINKNDDTVFVDVGLKSEGRIPVEEFLDAQGELEIQVGDEVEVYLDRVEDRI 80 (534)
T ss_pred CCHHHHHHHHCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCHHHCCCCCCCCEEECCCEEEEEEEEECCCC
T ss_conf 97177554100211335688555327899816888999983156312341768268888400005887999998442899
Q ss_pred CEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE--CCCEEEEEC-CCHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 8599968787555758999998528976999999996--795599974-4020000011234543334555553023111
Q gi|254780456|r 86 GEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQV--KGGMTVDLN-GEVAFLPRSQIDIRPVRDVTPLMHEPQLFEI 162 (576)
Q Consensus 86 g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~--k~G~~V~i~-gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~I 162 (576)
|...||+.++++...|..++.++..+++|.|+|..++ ||||+|++. |+.||||.||+|.++++++.+++|.+++|+|
T Consensus 81 g~~~LS~~ka~r~~~~~~l~~~~~~~~~V~G~I~~kvekKGGf~Vdl~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i 160 (534)
T TIGR00717 81 GETVLSREKAQRKEAWIKLEKAYEEGSIVEGKIVGKVEKKGGFIVDLEAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKI 160 (534)
T ss_pred CCCEEECCHHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEE
T ss_conf 97023045257888999999986169845679877660565779992368178616460466266640303430778999
Q ss_pred CCCCCCC-----CCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCC--CEEEECCCEEEEEEEECCCCCCC
Q ss_conf 3354323-----3112212111222221211100011222330246788753147--17774483157886420244444
Q gi|254780456|r 163 LKMDKRR-----GNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYG--VFVDLSGVDGLLHVTDIAWHRIL 235 (576)
Q Consensus 163 i~~d~~~-----~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g--~~V~~~g~~g~i~~~~ls~~~~~ 235 (576)
+.+|+++ ++|++|||++|++....++.+++++|++|+.+.|+|+++++|| +||++||++||||++||||+|+.
T Consensus 161 ~k~d~~rqhrGn~nivvSRr~~lE~~~~~~r~e~le~l~~g~~v~GvVk~iT~fGGv~Fvdlgg~dGLLH~~d~sWkr~~ 240 (534)
T TIGR00717 161 IKLDKKRQHRGNNNIVVSRRAYLEEERSQAREELLEKLKEGEVVKGVVKNITDFGGVAFVDLGGVDGLLHITDMSWKRVK 240 (534)
T ss_pred EEECCHHCCCCCCCEEEEEEEEECHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECCCEEECCCHHHCCCCCCC
T ss_conf 98631001257997699410010425688898887615558576108888889874999981643320350121478878
Q ss_pred CCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCC
Q ss_conf 33113326972589999874765279985215554321000000048966589999815966999851420000001111
Q gi|254780456|r 236 HPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI 315 (576)
Q Consensus 236 ~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sel 315 (576)
||+++++.||+|.++|+.+|.+++||+||||++..|||..+.++||+|+.++|+|++++|||+||+|.+|++||+|.|||
T Consensus 241 ~P~e~~~~G~~~~Vkv~~~D~~~~Ri~LsLK~~~~dPW~~i~~~~~~G~~~~G~Vt~~~dyGvFvEi~eGiEGlvH~SE~ 320 (534)
T TIGR00717 241 HPSEYVKVGQEVKVKVIKFDKEKKRISLSLKQLKEDPWEEIEKKFPVGDKIKGRVTNLTDYGVFVEIEEGIEGLVHVSEI 320 (534)
T ss_pred CCHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHCCCCCEEEEEEEEECCCEEEEEECCCCEEEECCEEE
T ss_conf 83464007988999999652657607787120588830899983889978899999883770799923894234231444
Q ss_pred CCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEE
Q ss_conf 01113557421003784579999986215504787520345432100000122222136999998501699970688413
Q gi|254780456|r 316 SWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDG 395 (576)
Q Consensus 316 s~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g 395 (576)
||.+++.+|++.+++||.|+|.||+||+++|||+|||||++.|||+.|.++||+|++++|+|.++|++|+||.|++|++|
T Consensus 321 sW~kk~~~P~~~v~~Gd~Ve~~vl~iD~~~rR~sLsLKQ~~~nPw~~f~~~hpvG~~v~gki~~iTd~GaFv~Le~GidG 400 (534)
T TIGR00717 321 SWVKKNSHPSKVVKIGDEVEVMVLDIDPERRRISLSLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEDGIDG 400 (534)
T ss_pred ECCCCCCCHHHCEECCCEEEEEEEEEECCCCEEEEEEECCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEECCCCCCE
T ss_conf 05788558158054387999999855456784989751067781589998489885898888888256899973899223
Q ss_pred EEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEE
Q ss_conf 54005530012200123421112342268852156545532011322101110000110047898799999997089089
Q gi|254780456|r 396 MIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIE 475 (576)
Q Consensus 396 ~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~ 475 (576)
|||.+|+||......+...|+.|++|+|+||.+|.+.++|+|++|||.+|||+.+. +.|++|++|.|.|++++++|+|
T Consensus 401 liH~~D~SW~~~~~~~~~~~~~Gd~ie~~vl~~d~~~k~i~LG~KQL~~nP~~~~~--~~yk~g~~v~g~V~~i~dfG~f 478 (534)
T TIGR00717 401 LIHLSDLSWEKKKREADHLYKKGDEIEAKVLAVDKEKKRISLGVKQLTENPWEEFA--EKYKVGSVVKGKVTEIKDFGAF 478 (534)
T ss_pred EEECCCCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHH--HHCCCCCEEEEEEEEECCCEEE
T ss_conf 89564015311785224410278799999999768566688766426988279999--8658996788888898057069
Q ss_pred EEECCCCCEEEEEEHHHCCHHHH---CCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 99617798499999747182121---04201106898799999997057686998703
Q gi|254780456|r 476 VSLIDHKGINSFIRRSDLSRDRV---DQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 476 V~l~~~~gv~G~i~~s~is~~~~---~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|.+ ++||+||||.+++++++. ......|++||.|+|+|+.+|++++++.||+|
T Consensus 479 v~~--~~GveGli~~~el~~~~~GdP~~~~~~~~vGd~v~ak~v~i~~~~~kV~lSv~ 534 (534)
T TIGR00717 479 VEL--PGGVEGLIRKSELSEERDGDPEEKKDEIKVGDEVEAKVVDIDKKNRKVSLSVK 534 (534)
T ss_pred EEC--CCCEEEEEECCCCCCCCCCCHHHHHHHEECCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 980--79737886230177888888112033410686899999997078985888559
No 4
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=852.32 Aligned_cols=537 Identities=54% Similarity=0.882 Sum_probs=516.5
Q ss_pred HHHHHHHHHHH-HCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCC
Q ss_conf 68899998854-02146389877999999981998999947960367899750566435563789879999999747998
Q gi|254780456|r 8 REDFATLLEES-FTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFG 86 (576)
Q Consensus 8 ~~~f~~ll~~~-~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g 86 (576)
.++|..+|+++ .....+.+|++++|+|+++++++++||+|+|++|+||++||......+.+++||.++++|+...+..|
T Consensus 2 ~~~f~~~~~~~~~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~~~~~gd~v~v~v~~~e~~~g 81 (541)
T COG0539 2 EEEFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVEDVVQVGDEVEVLVLRVEDGEG 81 (541)
T ss_pred CHHHHHHHHHHHCCHHCCCCCCEEEEEEEEEECCEEEEEECCCCCCEEEHHHCCCCCCCCEECCCCEEEEEEEEEECCCC
T ss_conf 31579999865321311688878999999993884999836761557688980566655131589889999999836886
Q ss_pred EEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCC
Q ss_conf 59996878755575899999852897699999999679559997440200000112345433345555530231113354
Q gi|254780456|r 87 EAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMD 166 (576)
Q Consensus 87 ~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d 166 (576)
+++||++++....+|+.++.++++|++|.|.|+..+|||++|+++|++||+|+||++.++++|..+++|++++|+|+++|
T Consensus 82 ~~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d 161 (541)
T COG0539 82 ELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELD 161 (541)
T ss_pred EEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEECCHHHHCCCCCCCCCCCCCCEEEEEEEEEC
T ss_conf 08861778887777899998874598389999988448489998787886557871545234652347865899999985
Q ss_pred CCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCE
Q ss_conf 32331122121112222212111000112223302467887531471777448315788642024444433113326972
Q gi|254780456|r 167 KRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQ 246 (576)
Q Consensus 167 ~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~ 246 (576)
++++++++|||+++++...+++.++++++++|++++|+|+++++||+||++||++||+|+++|||.|+.+|++.|++||+
T Consensus 162 ~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~ 241 (541)
T COG0539 162 KKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDE 241 (541)
T ss_pred CCCCCEEEEHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCE
T ss_conf 33484787717776677888799997247887669999998615747999257166886476065555898995356988
Q ss_pred EEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf 58999987476527998521555432100000004896658999981596699985142000000111101113557421
Q gi|254780456|r 247 VKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSK 326 (576)
Q Consensus 247 v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~ 326 (576)
|+|+|+++|++++||+||+|++.+|||..+.++|++|+++.|+|+++++||+||++.+|++||+|+|||||.+... |.+
T Consensus 242 VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~-P~e 320 (541)
T COG0539 242 VKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNV-PSE 320 (541)
T ss_pred EEEEEEEECCCCCEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCCCCEEECHHHCCCCCCC-HHH
T ss_conf 9999999726788699994650469477776414788778899998614747999518843101030413133699-789
Q ss_pred EECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCC
Q ss_conf 00378457999998621550478752034543210000012222213699999850169997068841354005530012
Q gi|254780456|r 327 ILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNR 406 (576)
Q Consensus 327 ~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~ 406 (576)
.+++||.|.|+|+++|+++|||+||||++..|||+.+.+.|++|++++|.|+++|++|+|+.+++|++||+|.+|++|+.
T Consensus 321 vv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~ 400 (541)
T COG0539 321 VVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDR 400 (541)
T ss_pred HCCCCCEEEEEEEEECCCCCEEEEEEHHCCCCHHHHHHHHCCCCCEEEEEEEEECCCCEEECCCCCCCCEEEHHHCCCCC
T ss_conf 53568789999995072016677660000039446534305788767778865525533882588724327877737554
Q ss_pred CCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEE
Q ss_conf 20012342111234226885215654553201132210111000011004789879999999708908999617798499
Q gi|254780456|r 407 PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINS 486 (576)
Q Consensus 407 ~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G 486 (576)
...... .|++|+.++++|+.+|.++++++|++|||.++||..+. ..+++|++++|.|+++.++|+||++. .++.|
T Consensus 401 ~~~~~~-~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~--~~~~~~~~v~~~v~~i~~~G~~v~l~--~~v~G 475 (541)
T COG0539 401 PGEEAE-KYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFS--EKYKKGSVVKGKVKSVKDKGAFVELG--GGVEG 475 (541)
T ss_pred CCCHHH-HHCCCCEEEEEEEEEECCCCEEEEEHHHHCCCCHHHHH--HHCCCCCEEEEEEEEECCCCEEEEEC--CCEEE
T ss_conf 565777-63157679999999703003765222443239256656--54468974899899982670699954--77044
Q ss_pred EEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 999747182121042011068987999999970576869987036557777999998403445777999999
Q gi|254780456|r 487 FIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILG 558 (576)
Q Consensus 487 ~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~~~~~~~tlg~~~~ 558 (576)
|++.++++.. .|++||.++|+|+.+|++++++.||+|+++..++++++..|+ .+...++|++++
T Consensus 476 ~i~~~~~~~~-------~~~~gd~v~a~v~~id~k~~ki~lSik~~~~~eek~~~~~~~-~~~~~s~g~~~~ 539 (541)
T COG0539 476 LIRLSELSRD-------VLKVGDEVEAVVVSIDKKNRKILLSIKALERKEEKEALESYN-KDDDSSLGDILG 539 (541)
T ss_pred EEEHHHHHHH-------HCCCCCEEEEEEEEECCCCCEEEEEECHHHHHHHHHHHHHHC-CCCCCCCCCCCC
T ss_conf 5641053364-------235798899999998177878999733655566788898624-777665552000
No 5
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=0 Score=765.87 Aligned_cols=444 Identities=33% Similarity=0.583 Sum_probs=421.2
Q ss_pred CCCHHHHHHHHHHHHHCC-CCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEE
Q ss_conf 771068899998854021-4638987799999998199899994796036789975056643556378987999999974
Q gi|254780456|r 4 TNPSREDFATLLEESFTK-KDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTE 82 (576)
Q Consensus 4 ~~~~~~~f~~ll~~~~~~-~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~ 82 (576)
.-+..++|++||++++.. .++++|++|+|+|+++++++++||+|+|++|+||++||.+.....++++||+++++|+..+
T Consensus 10 ~~~e~e~F~~LLe~~~~~~~~i~~G~iV~G~Vv~I~~d~v~VDiG~KsEG~Ip~~E~~d~~~~~~~kvGD~Iev~V~~~~ 89 (489)
T PRK13806 10 ELDESASFADLLEAHSGGARNVRVGDRIKAAIVAIGEDSVFVATGSKVDGVIDRRELEDAEGNLPYAVGDRLDLYVVAVN 89 (489)
T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEC
T ss_conf 89956439999961420046777998899999999799899996898289958999257557756589989999999964
Q ss_pred CCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 79985999687875557589999985289769999999967955999744020000011234543334555553023111
Q gi|254780456|r 83 NSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEI 162 (576)
Q Consensus 83 ~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~I 162 (576)
+|++.||+ +......|+.+.++++++++|+|+|++.+||||.|++.|++||||+||++.++.+++..++|++++|+|
T Consensus 90 --dgei~LSr-~~~~~~~~~~l~ea~e~~~~V~g~I~~~vKGG~~V~i~Gv~aFlP~Sqid~r~v~d~~~~vGk~~~~~I 166 (489)
T PRK13806 90 --GGEIRLSK-AMGGQGGAAVLEEARDNGVPVEGKVTGTCKGGFNVEVLRRRAFCPVSQIDLHQVEDPESFVGQTFQFLI 166 (489)
T ss_pred --CCCEEEEH-HHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEE
T ss_conf --98189988-998887899999997589869999999986759999899776423166046666785896796589999
Q ss_pred CCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEE
Q ss_conf 33543233112212111222221211100011222330246788753147177744-83157886420244444331133
Q gi|254780456|r 163 LKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVL 241 (576)
Q Consensus 163 i~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~ 241 (576)
+++|+++++|++|||+++++...+++.++++.+++|++++|+|+++++||+||+++ |++||+|+++|||.|+.||++.|
T Consensus 167 ikid~~~~nIVvSRR~lLe~e~~~~~~~~~~~l~~G~vv~G~V~~i~~~GaFVdl~~GvdGllHiSeiSw~rv~~p~~~~ 246 (489)
T PRK13806 167 TRVEQNGRNIVVSRRALLEREQAESLATFLEGVKEGDVLEGTVTRLAPFGAFVEIAPGVEGMVHISELSWSRVQQADEAV 246 (489)
T ss_pred EEECCCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCEECEEEEEECCCEEEEEECCCCEEEEEHHHCCCCCCCCHHHEE
T ss_conf 99705687078668998888877789999986114880042999975753899937980799983555865668888945
Q ss_pred CCCCEEEEEEEEECCCCC----EEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC
Q ss_conf 269725899998747652----7998521555432100000004896658999981596699985142000000111101
Q gi|254780456|r 242 SIGQQVKVKIIRINQETH----RISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW 317 (576)
Q Consensus 242 ~~G~~v~~~Vl~~d~~~~----~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~ 317 (576)
++||+++++|+++|.+++ ||+||+|++.+|||..+.++|++|+++.|+|+++++||+||+|.+|++||+|+|||||
T Consensus 247 ~vGd~v~vkVl~id~e~~~~~~risLs~Kql~~dPW~~~~~k~~vG~~v~g~V~~i~~fGaFVel~~gieGlvHiSelSw 326 (489)
T PRK13806 247 SVGDRVRVKVLGIGEAPKGKGLRISLSAKQAGGDPWETVGDRLEADQVVEGKVVRLAPFGAFVEVLPGVEGLVHISEMSW 326 (489)
T ss_pred CCCCEEEEEEEEEECCCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEEECCCCCEEEEECCCEEEEEEEHHCCC
T ss_conf 16988999999986445666506986016678895787786367998379999972454069996388079998044255
Q ss_pred CCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEE
Q ss_conf 11355742100378457999998621550478752034543210000012222213699999850169997068841354
Q gi|254780456|r 318 TKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMI 397 (576)
Q Consensus 318 ~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i 397 (576)
+++..+|.+.+++||.|+|+|+++|+++++|+||+|++++|||+.+.+.|++|++++|+|++++++|+||+++++++|||
T Consensus 327 ~~~~~~p~~~~~~Gd~v~vkIl~iD~e~rrisLs~Kq~~~nPw~~~~~~~~~G~~v~g~V~~i~~fG~fV~l~~gi~Gli 406 (489)
T PRK13806 327 TRRVNKPEEVVAPGDTVSVKIKELDPAKRRISLSLRDAEGDPWATAAERFAPGTTVTGTVEKRAQFGLFVNIAPGVTGLL 406 (489)
T ss_pred CCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEHHHCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEECCCCCEEEE
T ss_conf 34578989960668729999999714337899656753469588998763689879999999763489997589908999
Q ss_pred EHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHH---CCCCCCHH
Q ss_conf 0055300122001234211123422688521565455320113221---01110000
Q gi|254780456|r 398 HLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLS---GSAPDVVD 451 (576)
Q Consensus 398 ~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~---~~~~~~~~ 451 (576)
|.+|+||+... ++.+.|+.||.|+|+|+++|++++||+||+|+++ .+||..+.
T Consensus 407 h~sdls~~~~~-~~~~~~k~Gd~V~~~Il~id~~~rrIsLsik~l~~~~~~~w~~~~ 462 (489)
T PRK13806 407 PESIIKSSPQS-KSLAKLNAGDSVTLTVRDINAATRRITLAPADAAGHDDGEWKQFA 462 (489)
T ss_pred EHHHCCCCCCC-CHHHHCCCCCEEEEEEEEECCCCCEEEECHHHHCCCCCCHHHHHC
T ss_conf 98986756442-738628999989999999847778898446663458777366643
No 6
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=627.56 Aligned_cols=351 Identities=38% Similarity=0.678 Sum_probs=339.3
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCC---CCCCCCCCCCEEEEEEEEE
Q ss_conf 7106889999885402146389877999999981998999947960367899750566---4355637898799999997
Q gi|254780456|r 5 NPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGK---GQYTPIKVGDEVEVYVERT 81 (576)
Q Consensus 5 ~~~~~~f~~ll~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~---~~~~~~kvGd~i~v~V~~~ 81 (576)
.+++++|..++++++. ++..|++|+|+|++|++++++||+|+|++|+||.+||+.. ...+.+++||+|+++|++.
T Consensus 16 ~~S~edf~~~le~s~k--~~~eGdIV~GtVv~I~~d~VlVDIG~KsEGiIP~~E~s~~~d~d~~e~vkvGDeIeV~Vi~~ 93 (484)
T PRK07899 16 IGSAEDFLAAIDKTIK--YFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVSVGDEVEALVLTK 93 (484)
T ss_pred CCCHHHHHHHHHHHHH--CCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEE
T ss_conf 9999999998887873--58899889999999978989998268704787999946675778454578999999999987
Q ss_pred ECCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf 47998599968787555758999998528976999999996795599974402000001123454333455555302311
Q gi|254780456|r 82 ENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFE 161 (576)
Q Consensus 82 ~~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~ 161 (576)
+++.|+++||++++.....|+.++++++.+++|+|+|++.+|||++|++ |++||||+||++.++.+|+..++|++++|+
T Consensus 94 ed~eG~vvLSkkkA~~~k~W~~Leea~e~~~vVeGkV~~~vKGGliVdi-GvraFlP~Sqid~r~v~dl~~~vGk~l~~k 172 (484)
T PRK07899 94 EDKEGRLILSKKRAQYERAWGTIEKLKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAK 172 (484)
T ss_pred ECCCCCEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEC-CCEEEEECCCCCCCCCCCHHHHCCCEEEEE
T ss_conf 3788749988899765678999999975798699999999667099982-657998642256510478388779879999
Q ss_pred CCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEE
Q ss_conf 13354323311221211122222121110001122233024678875314717774483157886420244444331133
Q gi|254780456|r 162 ILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVL 241 (576)
Q Consensus 162 Ii~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~ 241 (576)
|+++|+++++|++|||+++++...+++.++++.|++|++++|+|+++++||+||++||++||+|+++|||+|+.||+++|
T Consensus 173 Iieid~~r~nIVlSRRa~LEee~~~~r~e~l~~L~~G~vveG~Vk~It~fGAFVDLGGVDGLvHiSEiSW~Rv~~Psev~ 252 (484)
T PRK07899 173 IIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVV 252 (484)
T ss_pred EEEECCCCCCEEEEHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCEEEEEECCEEEEEEHHHCCCCCCCCHHHHC
T ss_conf 99975766806501999999999889999997477898799999982164689995572378981340356779989957
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCC
Q ss_conf 26972589999874765279985215554321000000048966589999815966999851420000001111011135
Q gi|254780456|r 242 SIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKN 321 (576)
Q Consensus 242 ~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~ 321 (576)
++||+++++|+++|++++||+||+|++.+|||..+.++|++|+++.|+|+++++||+||+|.+|++||||+|||| .++.
T Consensus 253 ~vGd~V~VkVl~iD~Ek~RISLslKql~~dPW~~~~~k~~vG~vv~GkV~~l~~fGAFVel~~GIEGLVHISElS-~~~v 331 (484)
T PRK07899 253 EVGDEVTVEVLDVDLDRERVSLSLKATQEDPWQVFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA-ERHV 331 (484)
T ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCC-CCCC
T ss_conf 799879999987747678898862547788389898648998989999998726605999369967667877645-6444
Q ss_pred CCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCC
Q ss_conf 57421003784579999986215504787520345432
Q gi|254780456|r 322 IHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINP 359 (576)
Q Consensus 322 ~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p 359 (576)
.+|.+.+++||.|+|+|++||++++||+||+||+.++|
T Consensus 332 ~~P~dvv~~GdeV~vkIl~ID~e~rRISLSiKQa~e~~ 369 (484)
T PRK07899 332 EVPEQVVSVGDEVMVKVIDIDLERRRISLSLKQANEDY 369 (484)
T ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEECCEECCCCCC
T ss_conf 79888477998899999987577678542300167898
No 7
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=0 Score=621.54 Aligned_cols=354 Identities=42% Similarity=0.748 Sum_probs=335.0
Q ss_pred CHHHHHHHHHH---HHHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCC---CCCCCCCCEEEEEEE
Q ss_conf 10688999988---540214638987799999998199899994796036789975056643---556378987999999
Q gi|254780456|r 6 PSREDFATLLE---ESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQ---YTPIKVGDEVEVYVE 79 (576)
Q Consensus 6 ~~~~~f~~ll~---~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~---~~~~kvGd~i~v~V~ 79 (576)
.++++|+.+++ ++ ..++++|++|+|+|+++++++++||+|+|++|+||++||..... .+.+++||+++|+|+
T Consensus 283 ~~~~~~~~~~~~~~~s--~k~~~~G~iV~G~Vv~v~~~~v~VDiG~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~ 360 (670)
T PRK00087 283 EVENNFEEQLEYMNEN--EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVL 360 (670)
T ss_pred HHHHHHHHHHHHHHHH--HCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEE
T ss_conf 0245499999987763--34677898799999999389899983678436888999366767773345799998999999
Q ss_pred EEECCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEE
Q ss_conf 97479985999687875557589999985289769999999967955999744020000011234543334555553023
Q gi|254780456|r 80 RTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQL 159 (576)
Q Consensus 80 ~~~~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~ 159 (576)
+++++.|+++||++++.....|+++++||+++++|+|+|++.+||||+|+++|++||||+||++.++.+|++.++|++++
T Consensus 361 k~ed~~G~i~LS~kka~~~~~w~~l~~a~e~~e~V~g~V~~~vKGG~~V~i~gi~~FiP~Sq~~~~~~~d~~~~vG~~~~ 440 (670)
T PRK00087 361 KLENEDGYVVLSKKEADREKAWKELEEAFENGETVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSAYKGQELE 440 (670)
T ss_pred EEECCCCCEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEEECHHHCCCCCCCCHHHHCCCEEE
T ss_conf 98689982998889999888799999998689869999999985859999899899802276156656772787697489
Q ss_pred ECCCCCCCCCC--CEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCC
Q ss_conf 11133543233--1122121112222212111000112223302467887531471777448315788642024444433
Q gi|254780456|r 160 FEILKMDKRRG--NIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHP 237 (576)
Q Consensus 160 ~~Ii~~d~~~~--~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~ 237 (576)
|+|+++|++++ ++++|||+++++....++.++++.+++|++++|+|+++++||+||+|||++||+|++++||+|+.+|
T Consensus 441 ~kIie~d~~k~r~niV~Srr~vlee~~~~~k~~~~~~l~~G~~v~G~V~~i~~~GaFvdlgGvdGLvHiSelSw~rv~~p 520 (670)
T PRK00087 441 VKIIEFDKKRKKTKVVLSRKALLKEEKEKQKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKP 520 (670)
T ss_pred EEEEEECCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCH
T ss_conf 99999844457674897809999988999999999748899889999999973407999779899998434476777898
Q ss_pred CEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC
Q ss_conf 11332697258999987476527998521555432100000004896658999981596699985142000000111101
Q gi|254780456|r 238 SKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW 317 (576)
Q Consensus 238 ~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~ 317 (576)
++.|++||+++++|+++|++++||+||+|++.+|||..+.++|++|+++.|+|+++++||+||+|.+|++||||+|||||
T Consensus 521 ~~~~~~G~~v~vkIl~iD~e~~rIsLs~K~l~~dPw~~~~~~~~~G~~v~g~V~~i~~fGaFVel~~gveGlih~sels~ 600 (670)
T PRK00087 521 SDVLKVGDEIKVYILEIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISEISW 600 (670)
T ss_pred HHHCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCC
T ss_conf 99627897799999998388788987634377894788886489969999999999677079995799789989899484
Q ss_pred CCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCC
Q ss_conf 113557421003784579999986215504787520345432100
Q gi|254780456|r 318 TKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEE 362 (576)
Q Consensus 318 ~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~ 362 (576)
+++.+|.+.|++||.|+|+|+++|+++++|+||+|+++++|+..
T Consensus 601 -~~~~~~~~~~~~Gd~v~~kIl~id~~~krisLSiK~~~~~peke 644 (670)
T PRK00087 601 -KRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPEKE 644 (670)
T ss_pred -CCCCCHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHCCCCCCHH
T ss_conf -32489777489999899999998377788997846531180046
No 8
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=582.54 Aligned_cols=418 Identities=34% Similarity=0.586 Sum_probs=382.2
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCC-CCCCCEEEEEEEEEECCCCEEEEEHHHHHH---HH
Q ss_conf 38987799999998199899994796036789975056643556-378987999999974799859996878755---57
Q gi|254780456|r 24 LAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTP-IKVGDEVEVYVERTENSFGEAVFSRDKALR---EG 99 (576)
Q Consensus 24 ~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~-~kvGd~i~v~V~~~~~~~g~i~lS~~k~~~---~~ 99 (576)
+..|..++|+|.+....|+.|+++ +.+||+|.+++......+. .-+|+.++++|+..+...+.+++|++.... ..
T Consensus 102 ~e~~~~v~g~i~~~vKGG~~V~i~-gv~aFlP~Sq~d~~~v~d~~~~vG~~l~~kIi~~d~~~~~iVvSrr~~lee~~~~ 180 (556)
T PRK06299 102 YENGEIVEGVINGKVKGGFTVDLN-GVRAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAE 180 (556)
T ss_pred HHCCCEEEEEEEEEECCEEEEEEC-CEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEEECCCCEEEEEHHHHHHHHHHH
T ss_conf 758987999999997780999988-9899978588257555661765796699999997523580897328988888888
Q ss_pred HHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCC--CCCEEEECCCCCCCCCCCEEECCC
Q ss_conf 589999985289769999999967955999744020000011234543334555--553023111335432331122121
Q gi|254780456|r 100 VWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPL--MHEPQLFEILKMDKRRGNIVVSRR 177 (576)
Q Consensus 100 ~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~--vG~~i~~~Ii~~d~~~~~ivvS~k 177 (576)
.++++.+.++.|++++|+|.+.++.|.+|+++|+.||+|.|+++..+++++..+ +|+.++++|+.+|+++++|.+|.|
T Consensus 181 ~~~~~~~~l~~G~vv~G~V~~i~~~GaFVdlggvdGllhiseiSw~rv~~p~~~~~~G~~v~vkVl~id~e~~risLslK 260 (556)
T PRK06299 181 EREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 260 (556)
T ss_pred HHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
T ss_conf 89999985247972789999970575899958958999856715566699899266898899999988265638999970
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCC-CCCCCCCEEECCCCEEEEEEEEEC
Q ss_conf 11222221211100011222330246788753147177744-8315788642024-444433113326972589999874
Q gi|254780456|r 178 AVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAW-HRILHPSKVLSIGQQVKVKIIRIN 255 (576)
Q Consensus 178 ~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~-~~~~~~~~~~~~G~~v~~~Vl~~d 255 (576)
++.+ .-+..+.+.+++|++++|+|+++++||+||++. |++||+|+++||| .++.+|++.|++||.|+|+|+++|
T Consensus 261 ~l~~----dPw~~~~~~~~~G~~v~g~V~~i~~fGafVel~~gveGlvhiSelsw~~~~~~p~~~~~~G~~V~~kIl~id 336 (556)
T PRK06299 261 QLGE----DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEID 336 (556)
T ss_pred CCCC----CHHHHHHHHCCCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEC
T ss_conf 3567----855767864789998999999982760799954995899887871675444797895447977999999972
Q ss_pred CCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEE
Q ss_conf 76527998521555432100000004896658999981596699985142000000111101113557421003784579
Q gi|254780456|r 256 QETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVE 335 (576)
Q Consensus 256 ~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~ 335 (576)
++++||+||+|++.+|||+.+.++|++|+++.|+|.++++||+||+|++|++||+|.|++||+++..+|.+.|++||.++
T Consensus 337 ~~~~risLS~K~~~~nPw~~~~~~~~vG~~v~g~V~~i~~fG~fv~l~~gv~GlvH~sdlSW~~~~~~~~~~~k~Gd~v~ 416 (556)
T PRK06299 337 EEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKIKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVE 416 (556)
T ss_pred CCCCEEEEEECCCCCCHHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHCCCCCCCCCHHHHCCCCCEEE
T ss_conf 44368888632366797899986355564799999996643699985277323778535455556410566426896699
Q ss_pred EEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHH
Q ss_conf 99998621550478752034543210000012222213699999850169997068841354005530012200123421
Q gi|254780456|r 336 VVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEY 415 (576)
Q Consensus 336 ~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~ 415 (576)
|+|+++|+++++++||+|++.++||+.+.+.|++|++++|+|+++.++|+||+++++++||||.++++++ ....+.+.|
T Consensus 417 vkVL~iD~e~~rIsLgiKql~~dPw~~~~~~~k~G~iv~g~V~~i~~~G~fV~l~~gieglI~~sels~~-~~~~~~~~~ 495 (556)
T PRK06299 417 AVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELADGVEGFIRASELSRD-RVEDATEVL 495 (556)
T ss_pred EEEEEECCCCCEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCEEEEEEHHHCCCH-HHHCCCCCC
T ss_conf 9999981667679887043127816878763899899999999997895699938990999997996800-233621116
Q ss_pred CCCCCCEEEEEECCCCCCCCCCCHHHHHCCCC
Q ss_conf 11234226885215654553201132210111
Q gi|254780456|r 416 AKGDIVKAVVLDIDVGKERISLGVKQLSGSAP 447 (576)
Q Consensus 416 k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~ 447 (576)
++||.++|+|+++|++++++.||+|+++....
T Consensus 496 ~~Gd~v~~~Ii~id~e~rkI~LSiK~le~~~e 527 (556)
T PRK06299 496 KVGDEVEAKVINIDRKNRRISLSIKALDEAEE 527 (556)
T ss_pred CCCCEEEEEEEEECCCCCEEEEEHHHHHHHHH
T ss_conf 89998999999982777999987159555567
No 9
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of 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 , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=100.00 E-value=0 Score=578.04 Aligned_cols=422 Identities=35% Similarity=0.600 Sum_probs=385.4
Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEEEEE--CCEEEEEECCCEEEEEEHHHHCCCCCCC-CCCCCCEEEEEEEEEECCC
Q ss_conf 889999885402146389877999999981--9989999479603678997505664355-6378987999999974799
Q gi|254780456|r 9 EDFATLLEESFTKKDLAENCVTKGIVVGLE--KDTVVVDVGLKFEGRIPRREFMGKGQYT-PIKVGDEVEVYVERTENSF 85 (576)
Q Consensus 9 ~~f~~ll~~~~~~~~~~~G~iv~G~V~~i~--~~~v~vdig~k~~G~i~~~e~~~~~~~~-~~kvGd~i~v~V~~~~~~~ 85 (576)
+.+.+|+.. ...|+.|.|+|.+.. ..|..||++.+.++|+|.+....-...+ .--+|-.++++|.++|.+.
T Consensus 94 ~~~~~l~~~------~~~~~~V~G~I~~kvekKGGf~Vdl~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i~k~d~~r 167 (534)
T TIGR00717 94 EAWIKLEKA------YEEGSIVEGKIVGKVEKKGGFIVDLEAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKIIKLDKKR 167 (534)
T ss_pred HHHHHHHHH------HHCCCEEEEEEEEEEECCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHH
T ss_conf 899999998------61698456798776605657799923681786164604662666403034307789999863100
Q ss_pred -----CEEEEEHHHH---HHHHHHHHHHHHHHCCCEEEEEEEEEECCC--EEEEECCCHHHHHCCCCCCCCCCCCCCC--
Q ss_conf -----8599968787---555758999998528976999999996795--5999744020000011234543334555--
Q gi|254780456|r 86 -----GEAVFSRDKA---LREGVWEKIEAKFRAGERIEGVIFNQVKGG--MTVDLNGEVAFLPRSQIDIRPVRDVTPL-- 153 (576)
Q Consensus 86 -----g~i~lS~~k~---~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G--~~V~i~gi~~FlP~s~~~~~~~~d~~~~-- 153 (576)
..+++|++.. ...+..+++.+.++.|+.+.|.|.+.++.| .+|+++|++||||.+.|+...++.|+.+
T Consensus 168 qhrGn~nivvSRr~~lE~~~~~~r~e~le~l~~g~~v~GvVk~iT~fGGv~Fvdlgg~dGLLH~~d~sWkr~~~P~e~~~ 247 (534)
T TIGR00717 168 QHRGNNNIVVSRRAYLEEERSQAREELLEKLKEGEVVKGVVKNITDFGGVAFVDLGGVDGLLHITDMSWKRVKHPSEYVK 247 (534)
T ss_pred CCCCCCCEEEEEEEEECHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECCCEEECCCHHHCCCCCCCCCHHHCC
T ss_conf 12579976994100104256888988876155585761088888898749999816433203501214788788346400
Q ss_pred CCCEEEECCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCC-
Q ss_conf 5530231113354323311221211122222121110001122233024678875314717774-48315788642024-
Q gi|254780456|r 154 MHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAW- 231 (576)
Q Consensus 154 vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~- 231 (576)
+|+++.++|+.+|++++||.||.|++- ..-|.++.+.+++|+.++|+|+++++|||||++ .|++||+|.|||||
T Consensus 248 ~G~~~~Vkv~~~D~~~~Ri~LsLK~~~----~dPW~~i~~~~~~G~~~~G~Vt~~~dyGvFvEi~eGiEGlvH~SE~sW~ 323 (534)
T TIGR00717 248 VGQEVKVKVIKFDKEKKRISLSLKQLK----EDPWEEIEKKFPVGDKIKGRVTNLTDYGVFVEIEEGIEGLVHVSEISWV 323 (534)
T ss_pred CCCEEEEEEEEECCCCCEEEEEEECCC----CCCCHHHHHHCCCCCEEEEEEEEECCCEEEEEECCCCEEEECCEEEECC
T ss_conf 798899999965265760778712058----8830899983889978899999883770799923894234231444057
Q ss_pred CCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEE
Q ss_conf 44443311332697258999987476527998521555432100000004896658999981596699985142000000
Q gi|254780456|r 232 HRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAH 311 (576)
Q Consensus 232 ~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~ 311 (576)
....+|++++++||.|+|.||++|++.+||+|||||+.++||..+.++||+|++++|+|.++++||+||+|++|++||||
T Consensus 324 kk~~~P~~~v~~Gd~Ve~~vl~iD~~~rR~sLsLKQ~~~nPw~~f~~~hpvG~~v~gki~~iTd~GaFv~Le~GidGliH 403 (534)
T TIGR00717 324 KKNSHPSKVVKIGDEVEVMVLDIDPERRRISLSLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEDGIDGLIH 403 (534)
T ss_pred CCCCCHHHCEECCCEEEEEEEEEECCCCEEEEEEECCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEECCCCCCEEEE
T ss_conf 88558158054387999999855456784989751067781589998489885898888888256899973899223895
Q ss_pred CCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECC
Q ss_conf 11110111355742100378457999998621550478752034543210000012222213699999850169997068
Q gi|254780456|r 312 ISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDE 391 (576)
Q Consensus 312 ~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~ 391 (576)
.|++||.+....+...|+.|+.|+|.|+.+|.+.++|+|++||+.+|||+.+.+.|+.|++|+|.|++++++|+||++.+
T Consensus 404 ~~D~SW~~~~~~~~~~~~~Gd~ie~~vl~~d~~~k~i~LG~KQL~~nP~~~~~~~yk~g~~v~g~V~~i~dfG~fv~~~~ 483 (534)
T TIGR00717 404 LSDLSWEKKKREADHLYKKGDEIEAKVLAVDKEKKRISLGVKQLTENPWEEFAEKYKVGSVVKGKVTEIKDFGAFVELPG 483 (534)
T ss_pred CCCCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHCCCCCEEEEEEEEECCCEEEEECCC
T ss_conf 64015311785224410278799999999768566688766426988279999865899678888889805706998079
Q ss_pred CCEEEEEHHHHHCCCCC--HHHHHHHCCCCCCEEEEEECCCCCCCCCCCHH
Q ss_conf 84135400553001220--01234211123422688521565455320113
Q gi|254780456|r 392 HLDGMIHLSDLDWNRPG--EKVIAEYAKGDIVKAVVLDIDVGKERISLGVK 440 (576)
Q Consensus 392 ~i~g~i~~~dls~~~~~--~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K 440 (576)
|++||||.+|++.++.+ ......|++||.++|+|+.+|+.++++.||+|
T Consensus 484 GveGli~~~el~~~~~GdP~~~~~~~~vGd~v~ak~v~i~~~~~kV~lSv~ 534 (534)
T TIGR00717 484 GVEGLIRKSELSEERDGDPEEKKDEIKVGDEVEAKVVDIDKKNRKVSLSVK 534 (534)
T ss_pred CEEEEEECCCCCCCCCCCHHHHHHHEECCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 737886230177888888112033410686899999997078985888559
No 10
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=577.69 Aligned_cols=355 Identities=41% Similarity=0.692 Sum_probs=339.6
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCEEEEEE-CCCEEEEEEHHHHCCC---CCCCCCCCCCEEEEEEEEEE
Q ss_conf 0688999988540214638987799999998199899994-7960367899750566---43556378987999999974
Q gi|254780456|r 7 SREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDV-GLKFEGRIPRREFMGK---GQYTPIKVGDEVEVYVERTE 82 (576)
Q Consensus 7 ~~~~f~~ll~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdi-g~k~~G~i~~~e~~~~---~~~~~~kvGd~i~v~V~~~~ 82 (576)
+|++||+.|++ .+++++|++|+|+|++++++++|||+ |++++|+||.+|+++. ++...|++||.|+|+|++++
T Consensus 1 ~~~~fe~~l~~---~~~i~~G~iV~G~V~~I~~~~v~Vdi~G~k~eG~I~~~E~s~~~~~~~~~~~kvGd~V~~~Vl~~~ 77 (390)
T PRK06676 1 MMEEFEESLNS---VKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDTLEVYVLKVE 77 (390)
T ss_pred CHHHHHHHHHH---HHCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEE
T ss_conf 96799998752---006899998999999998998999933863589999999456643584024699899999999998
Q ss_pred CCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 79985999687875557589999985289769999999967955999744020000011234543334555553023111
Q gi|254780456|r 83 NSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEI 162 (576)
Q Consensus 83 ~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~I 162 (576)
++.+++.||++++.....|+.+.+++++|+++.|+|++.+++|++|+++|++||||.||++.++.+++..++|+.+.|+|
T Consensus 78 ~~~~~l~LS~kk~~~~~~w~~~~~~~~~g~~v~g~V~~~~kgG~~V~~~gv~gFlP~S~ls~~~~~~~~~~vGq~v~~kV 157 (390)
T PRK06676 78 DGEGNYLLSKRRLEARKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVGGVRGFIPASLISTRFVEDLSDFKGKTLDVKI 157 (390)
T ss_pred CCCCEEEEEHHHHHHCHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCEEEEEHHHCCCCCCCCCHHHCCEEEEEEE
T ss_conf 89973999967922010088888765379779999999955859999768168775487256445770554371699999
Q ss_pred CCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEEC
Q ss_conf 33543233112212111222221211100011222330246788753147177744831578864202444443311332
Q gi|254780456|r 163 LKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLS 242 (576)
Q Consensus 163 i~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~ 242 (576)
+++|++++++++|||++++......+.++++.+++|++++|+|+++++||+||+++|++||+|++|+||.++.+|.+.|+
T Consensus 158 i~vd~~~~~ivlS~K~~l~~~~~~~~~~~~~~l~~Gdvv~G~V~~i~~~G~FV~lggv~glvh~sels~~~~~~~~~~~k 237 (390)
T PRK06676 158 IELDPEKNRVILSRRAVVEEERAEKKKELLSSLKEGDVVEGKVARLTDFGAFVDIGGVDGLVHISELSHERVNKPSEVVS 237 (390)
T ss_pred EEEECCCCCEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEECCCEEEEEEECCCCHHHHCCHHHHHC
T ss_conf 99853788289703245466676657667763468984789999994563699807767999961057333359888304
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCC
Q ss_conf 69725899998747652799852155543210000000489665899998159669998514200000011110111355
Q gi|254780456|r 243 IGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNI 322 (576)
Q Consensus 243 ~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~ 322 (576)
+||+++|+|+++|+++++|.||+|++.+|||..+.++|++|+++.|+|+++++||+||++.+|++||+|.||+||. +..
T Consensus 238 ~G~~v~~~Vl~id~~~~ri~LslK~l~~dP~~~~~~~~~vG~~v~G~V~~i~~fG~fV~l~~g~~Glih~sels~~-~~~ 316 (390)
T PRK06676 238 VGQEVEVKVLSIDEETERISLSLKDTLPGPWEGVEEKLKEGDVIEGTVKRLTNFGAFVEVLPGVEGLVHISQISHK-HIA 316 (390)
T ss_pred CCCEEEEEEEEEECCCCEEEEEEEECCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCC-CCC
T ss_conf 7975799999994678899999832678956776653369989999999994737999977996899998994753-336
Q ss_pred CCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCC
Q ss_conf 7421003784579999986215504787520345432100000
Q gi|254780456|r 323 HPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSK 365 (576)
Q Consensus 323 ~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~ 365 (576)
+|.+.|++||.|+|+|+++|+++++++||+|+++++||+...+
T Consensus 317 ~p~~~~~~Gd~V~~~Vl~id~e~~ri~LS~K~l~~~p~~e~~~ 359 (390)
T PRK06676 317 KPSEVLEEGQEVKVKVLEVDEEEKRISLSIKALEEAPAEEESR 359 (390)
T ss_pred CHHHCCCCCCEEEEEEEEECCCCCEEEEEEHHCCCCHHHHHHH
T ss_conf 8555278999999999998177898998814134481566666
No 11
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=0 Score=576.41 Aligned_cols=442 Identities=24% Similarity=0.404 Sum_probs=389.9
Q ss_pred HHCCCEEEEEEEEEECCCEEEEECC-CHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEECCCCCCCCCCCC
Q ss_conf 5289769999999967955999744-020000011234543334555553023111335432331122121112222212
Q gi|254780456|r 108 FRAGERIEGVIFNQVKGGMTVDLNG-EVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAE 186 (576)
Q Consensus 108 ~~~g~~v~g~V~~~~k~G~~V~i~g-i~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~~~~ 186 (576)
++.|++|+|+|.+..+.+++|+++. ..|++|..++.... ......+|.++++.|+..+ .+.+.+|++... ..
T Consensus 31 i~~G~iV~G~Vv~I~~d~v~VDiG~KsEG~Ip~~E~~d~~-~~~~~kvGD~Iev~V~~~~--dgei~LSr~~~~----~~ 103 (489)
T PRK13806 31 VRVGDRIKAAIVAIGEDSVFVATGSKVDGVIDRRELEDAE-GNLPYAVGDRLDLYVVAVN--GGEIRLSKAMGG----QG 103 (489)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCC-CCCCCCCCCEEEEEEEEEC--CCCEEEEHHHHH----HH
T ss_conf 7799889999999979989999689828995899925755-7756589989999999964--981899889988----87
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 11100011222330246788753147177744831578864202444443311332697258999987476527998521
Q gi|254780456|r 187 QRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 187 ~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
.+..+.+.++.|.+|+|+|.+...-|+.|+++|++||+|.|+++-.++.++++. +|++++++|+.+|+..++|.+|.|
T Consensus 104 ~~~~l~ea~e~~~~V~g~I~~~vKGG~~V~i~Gv~aFlP~Sqid~r~v~d~~~~--vGk~~~~~Iikid~~~~nIVvSRR 181 (489)
T PRK13806 104 GAAVLEEARDNGVPVEGKVTGTCKGGFNVEVLRRRAFCPVSQIDLHQVEDPESF--VGQTFQFLITRVEQNGRNIVVSRR 181 (489)
T ss_pred HHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHH--CCCEEEEEEEEECCCCCEEEEEHH
T ss_conf 899999997589869999999986759999899776423166046666785896--796589999997056870786689
Q ss_pred CCCCC----CCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEE
Q ss_conf 55543----21000000048966589999815966999851420000001111011135574210037845799999862
Q gi|254780456|r 267 QLEKN----PWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVN 342 (576)
Q Consensus 267 ~l~~d----p~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id 342 (576)
++... ....+.+.+++|+++.|+|.++++||+||+|++|++||+|+||+||.+ ..+|.+.|++||.|+|+|+.+|
T Consensus 182 ~lLe~e~~~~~~~~~~~l~~G~vv~G~V~~i~~~GaFVdl~~GvdGllHiSeiSw~r-v~~p~~~~~vGd~v~vkVl~id 260 (489)
T PRK13806 182 ALLEREQAESLATFLEGVKEGDVLEGTVTRLAPFGAFVEIAPGVEGMVHISELSWSR-VQQADEAVSVGDRVRVKVLGIG 260 (489)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCEECEEEEEECCCEEEEEECCCCEEEEEHHHCCCCC-CCCHHHEECCCCEEEEEEEEEE
T ss_conf 988888777899999861148800429999757538999379807999835558656-6888894516988999999986
Q ss_pred CCCC----EEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCC
Q ss_conf 1550----478752034543210000012222213699999850169997068841354005530012200123421112
Q gi|254780456|r 343 PARK----RISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKG 418 (576)
Q Consensus 343 ~~~~----~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G 418 (576)
.+++ +|+||+|+++++||+.+.+.|++|++++|+|+++++||+||++.+|++|++|.||+||+.+..+|.+.|++|
T Consensus 261 ~e~~~~~~risLs~Kql~~dPW~~~~~k~~vG~~v~g~V~~i~~fGaFVel~~gieGlvHiSelSw~~~~~~p~~~~~~G 340 (489)
T PRK13806 261 EAPKGKGLRISLSAKQAGGDPWETVGDRLEADQVVEGKVVRLAPFGAFVEVLPGVEGLVHISEMSWTRRVNKPEEVVAPG 340 (489)
T ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEEECCCCCEEEEECCCEEEEEEEHHCCCCCCCCCHHHHCCCC
T ss_conf 44566650698601667889578778636799837999997245406999638807999804425534578989960668
Q ss_pred CCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHH
Q ss_conf 34226885215654553201132210111000011004789879999999708908999617798499999747182121
Q gi|254780456|r 419 DIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRV 498 (576)
Q Consensus 419 ~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~ 498 (576)
|.++|+|+++|++++||+||+|++..+||+.+. ++|.+|++|+|+|.+++++|+||.+. +|++||||.|++++.+.
T Consensus 341 d~v~vkIl~iD~e~rrisLs~Kq~~~nPw~~~~--~~~~~G~~v~g~V~~i~~fG~fV~l~--~gi~Glih~sdls~~~~ 416 (489)
T PRK13806 341 DTVSVKIKELDPAKRRISLSLRDAEGDPWATAA--ERFAPGTTVTGTVEKRAQFGLFVNIA--PGVTGLLPESIIKSSPQ 416 (489)
T ss_pred CEEEEEEEEECCCCCEEEEEHHHCCCCCHHHHH--HHCCCCCEEEEEEEEEECCEEEEECC--CCCEEEEEHHHCCCCCC
T ss_conf 729999999714337899656753469588998--76368987999999976348999758--99089999898675644
Q ss_pred CCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCC-C-----CC-CCHHHHHHHHHHHH
Q ss_conf 0420110689879999999705768699870365577779999984034-4-----57-77999999999874
Q gi|254780456|r 499 DQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSS-D-----SG-ASLGDILGMALKNR 564 (576)
Q Consensus 499 ~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~~~-~-----~~-~tlg~~~~~~lk~~ 564 (576)
.++.+.|++||.|+|+|+++|++++||+||+|++..+++. ..++|.+. + +| -+||..|.+++++|
T Consensus 417 ~~~~~~~k~Gd~V~~~Il~id~~~rrIsLsik~l~~~~~~-~w~~~~~~~~~~~~~~g~g~~~~~l~~a~~~k 488 (489)
T PRK13806 417 SKSLAKLNAGDSVTLTVRDINAATRRITLAPADAAGHDDG-EWKQFAPRKEEPRQAGGLGSLGQALQAAMQKR 488 (489)
T ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEECHHHHCCCCCC-HHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCC
T ss_conf 2738628999989999999847778898446663458777-36664310248666787057999999997505
No 12
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=0 Score=546.96 Aligned_cols=416 Identities=27% Similarity=0.523 Sum_probs=290.0
Q ss_pred CCCCCEEEEEEEEEE--CCEEEEEECCCEEEEEEHHHHCCCCCC-CCCCCCCEEEEEEEEEECC-----CCEEEEEHHHH
Q ss_conf 389877999999981--998999947960367899750566435-5637898799999997479-----98599968787
Q gi|254780456|r 24 LAENCVTKGIVVGLE--KDTVVVDVGLKFEGRIPRREFMGKGQY-TPIKVGDEVEVYVERTENS-----FGEAVFSRDKA 95 (576)
Q Consensus 24 ~~~G~iv~G~V~~i~--~~~v~vdig~k~~G~i~~~e~~~~~~~-~~~kvGd~i~v~V~~~~~~-----~g~i~lS~~k~ 95 (576)
+..|..|+|+|.+.. ..|..||+|.+..+|+|-+.+.--... ...-+|...++.|++++.. .+.+++|++-.
T Consensus 396 ~~~~~~v~G~i~~~~~vkgG~~Vdl~~gv~AFLPgSqvd~rpv~d~~~~~g~~~~f~iik~~~~~~~r~~~NiVvSRrav 475 (863)
T PRK12269 396 ERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRRRY 475 (863)
T ss_pred HHCCCEEEEEEEECCCCCCCEEEECCCCCEEECCHHHCCCEECCCCHHHCCCCCCEEEEEEEHHHHCCCCCCEEEECHHH
T ss_conf 75699079999744610453799858896786766564711368863215887415999953133126778889976798
Q ss_pred H---HHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCC--CCCEEEECCCCCCCCCC
Q ss_conf 5---557589999985289769999999967955999744020000011234543334555--55302311133543233
Q gi|254780456|r 96 L---REGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPL--MHEPQLFEILKMDKRRG 170 (576)
Q Consensus 96 ~---~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~--vG~~i~~~Ii~~d~~~~ 170 (576)
. .....+++.+.++.|++++|.|++.++.|.||+++|+.|+++.+.++...++.++.+ +|++++++|+++|++++
T Consensus 476 lEe~~~~~r~~~l~~l~eG~vv~G~VKnitdyGaFvDLGGvDGLLHitDiSW~Rv~hPse~~~vG~~i~vkVlk~D~e~~ 555 (863)
T PRK12269 476 LEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEK 555 (863)
T ss_pred HHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCEEEEECCCCCEEEEEECCCCCCCCCHHHHHCCCCEEEEEEEEECCCCC
T ss_conf 88888999999986443687788999831564058961771014662111357889989971279779999985256545
Q ss_pred CEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCC-CCCCCCCEEECCCCEEE
Q ss_conf 112212111222221211100011222330246788753147177744-8315788642024-44443311332697258
Q gi|254780456|r 171 NIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAW-HRILHPSKVLSIGQQVK 248 (576)
Q Consensus 171 ~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~-~~~~~~~~~~~~G~~v~ 248 (576)
++.+|.|++.+ .-|...-+.+++|+.+.|+|+++++||+||++. |++||+|.|+||| .+..||++.+++||+++
T Consensus 556 riSLglKQl~~----dPW~~i~~ky~vg~~v~gkVtnitdyGaFVEle~GiEGLvHvSEmsWtkk~~~P~k~v~~GdeVe 631 (863)
T PRK12269 556 RINLSLKHFQP----DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVE 631 (863)
T ss_pred EEEECCCCCCC----CCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCCEEEEEEHHHCCCCCCCCHHHCCCCCCEEE
T ss_conf 14311321778----97678886388999899999997446569996389257887025020236799798076897799
Q ss_pred EEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEE
Q ss_conf 99998747652799852155543210000000489665899998159669998514200000011110111355742100
Q gi|254780456|r 249 VKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKIL 328 (576)
Q Consensus 249 ~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~ 328 (576)
|+|+.+|++++||+||+||+.+|||+.+.++|++|+++.|+|.++++||+||.|.++++||+|.|++||+++..+|.+.|
T Consensus 632 v~VLeID~ekrRISLg~Kq~~~NPW~~~~~ky~vG~~v~g~I~nitdFGiFv~le~gIDGlvH~sDlSW~~~~~~~~~~~ 711 (863)
T PRK12269 632 CMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHEL 711 (863)
T ss_pred EEEEEEECCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECEEEEEECCCCCEEEEEHHHCCCCCCCCCHHHHC
T ss_conf 99998803226785441016688499999768998989999998533089997479936789821067678772656625
Q ss_pred CCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCC
Q ss_conf 37845799999862155047875203454321000001222221369999985016999706884135400553001220
Q gi|254780456|r 329 SVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPG 408 (576)
Q Consensus 329 ~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~ 408 (576)
+.||.|+|+|+++|+++++|+|++||+..+||+.+.+.++.|++|+|+|++++++|+||+++.+++||+|.++++-+ ..
T Consensus 712 kkGd~ve~kVL~Id~ekeRIsLGiKQL~~DP~~~f~~~~~~G~iVtg~V~~v~d~G~~V~l~~gieg~I~~s~ls~~-r~ 790 (863)
T PRK12269 712 EVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVEN-RD 790 (863)
T ss_pred CCCCEEEEEEEEECCCCCEEEEECCCCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCEEEEEEHHHHHHH-HH
T ss_conf 78987999999974765777740100657878999863899898999999995694799908991699898981120-33
Q ss_pred HHHH---HHHCCCCCCEEEEEECCCCCCCCCCCHHHHHC
Q ss_conf 0123---42111234226885215654553201132210
Q gi|254780456|r 409 EKVI---AEYAKGDIVKAVVLDIDVGKERISLGVKQLSG 444 (576)
Q Consensus 409 ~~~~---~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~ 444 (576)
+++. +.|.+||.|+|+|+.+|..++++.||+|+++.
T Consensus 791 e~~~~~~~rFavGd~vdA~I~~iD~k~RkI~LSIK~le~ 829 (863)
T PRK12269 791 GDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQR 829 (863)
T ss_pred HCHHHHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHHHH
T ss_conf 184666423589987999999884666779987789776
No 13
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=525.24 Aligned_cols=428 Identities=31% Similarity=0.559 Sum_probs=376.5
Q ss_pred HHHHHCCCEEEEEEEEEECCCEEEEECC-CHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEECCCCCCCCC
Q ss_conf 9985289769999999967955999744-020000011234543334555553023111335432331122121112222
Q gi|254780456|r 105 EAKFRAGERIEGVIFNQVKGGMTVDLNG-EVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEES 183 (576)
Q Consensus 105 ~~a~~~g~~v~g~V~~~~k~G~~V~i~g-i~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~ 183 (576)
...+++|++|.|.|++..+++..|++++ ..|++|.+++...+..+ ...+|+.+++.|.......+.+++|++.+.
T Consensus 16 ~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~-~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~--- 91 (541)
T COG0539 16 DEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVED-VVQVGDEVEVLVLRVEDGEGELVLSRRKAE--- 91 (541)
T ss_pred HHCCCCCCEEEEEEEEEECCEEEEEECCCCCCEEEHHHCCCCCCCC-EECCCCEEEEEEEEEECCCCEEEEEHHHHH---
T ss_conf 3116888789999999938849998367615576889805666551-315898899999998368860886177888---
Q ss_pred CCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEE
Q ss_conf 21211100011222330246788753147177744831578864202444443311332697258999987476527998
Q gi|254780456|r 184 RAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISL 263 (576)
Q Consensus 184 ~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l 263 (576)
....|..+...+..|.+|+|.|.....-|++|+++|+.||+|.|.++..++.++. -.+|.++.++|+.+|+.++++.+
T Consensus 92 ~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~--~~~Gk~~~~kiie~d~~~n~vv~ 169 (541)
T COG0539 92 RERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLD--PLIGKELEFKILELDKKRNNVVL 169 (541)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEECCHHHHCCCCCCCCC--CCCCCEEEEEEEEECCCCCCEEE
T ss_conf 7777899998874598389999988448489998787886557871545234652--34786589999998533484787
Q ss_pred EECCCCCCC----CCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEE
Q ss_conf 521555432----1000000048966589999815966999851420000001111011135574210037845799999
Q gi|254780456|r 264 GMKQLEKNP----WDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVIL 339 (576)
Q Consensus 264 slK~l~~dp----~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl 339 (576)
|.+.....- -..+.+.+++|+++.|+|.++++||+||+|+. ++||+|+|||||. +..+|.+.|++||.|+|+|+
T Consensus 170 SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~-rv~~P~~vvkvGd~VkvkVi 247 (541)
T COG0539 170 SRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWK-RVDHPSEVVKVGDEVKVKVI 247 (541)
T ss_pred EHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCEEEEECC-EEEEEEHHHCCCC-CCCCHHHHCCCCCEEEEEEE
T ss_conf 717776677888799997247887669999998615747999257-1668864760655-55898995356988999999
Q ss_pred EEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCC
Q ss_conf 86215504787520345432100000122222136999998501699970688413540055300122001234211123
Q gi|254780456|r 340 EVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGD 419 (576)
Q Consensus 340 ~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~ 419 (576)
++|+++++++||+|+++++||+.+.+.+++|+.+.|+|++++++|+||++.+|++||+|.||+||..... |.+.+++||
T Consensus 248 ~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~-P~evv~~Gq 326 (541)
T COG0539 248 SLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNV-PSEVVKVGQ 326 (541)
T ss_pred EECCCCCEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCCCCEEECHHHCCCCCCC-HHHHCCCCC
T ss_conf 9726788699994650469477776414788778899998614747999518843101030413133699-789535687
Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHC
Q ss_conf 42268852156545532011322101110000110047898799999997089089996177984999997471821210
Q gi|254780456|r 420 IVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVD 499 (576)
Q Consensus 420 ~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~ 499 (576)
+++|+||.+|++++||+||+||+..+||..+. ..+.+|++++|.|.+++++|+||.+. .|++||+|.+++++....
T Consensus 327 ~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~--~~~~~g~~v~g~v~~~t~~g~fv~le--~gidG~vh~~d~sw~~~~ 402 (541)
T COG0539 327 EVEVKVLDIDPERRRISLGLKQLKENPWEEFA--DKHPVGDVVEGKVKSITDFGAFVELE--GGIDGLVHLSDLSWDRPG 402 (541)
T ss_pred EEEEEEEEECCCCCEEEEEEHHCCCCHHHHHH--HHCCCCCEEEEEEEEECCCCEEECCC--CCCCCEEEHHHCCCCCCC
T ss_conf 89999995072016677660000039446534--30578876777886552553388258--872432787773755456
Q ss_pred CCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHH
Q ss_conf 4201106898799999997057686998703655777799999840
Q gi|254780456|r 500 QDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFG 545 (576)
Q Consensus 500 ~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~ 545 (576)
.+...|+.|+.++|+|+.+|++++|++|++|++....-......+.
T Consensus 403 ~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~ 448 (541)
T COG0539 403 EEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYK 448 (541)
T ss_pred CHHHHHCCCCEEEEEEEEEECCCCEEEEEHHHHCCCCHHHHHHHCC
T ss_conf 5777631576799999997030037652224432392566565446
No 14
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=518.27 Aligned_cols=365 Identities=29% Similarity=0.483 Sum_probs=331.3
Q ss_pred CCCCCCCCCEEEEEEEEEECCCCEEEE-C-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCC
Q ss_conf 001122233024678875314717774-4-83157886420244444331133269725899998747652799852155
Q gi|254780456|r 191 IVQKLEEGQVIEGTVKNITDYGVFVDL-S-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQL 268 (576)
Q Consensus 191 ~~~~l~~G~~v~g~V~~i~~~g~~V~~-~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l 268 (576)
.++.+++|++|+|+|.++.++|+||++ | +++|++|.++++|.+..+|.+.|++||+++|+|++++.+++++.||+|++
T Consensus 11 ~~~~i~~G~iV~G~V~~I~~~~v~Vdi~G~k~eG~I~~~E~s~~~~~~~~~~~kvGd~V~~~Vl~~~~~~~~l~LS~kk~ 90 (390)
T PRK06676 11 SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDTLEVYVLKVEDGEGNYLLSKRRL 90 (390)
T ss_pred HHHCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEHHHH
T ss_conf 20068999989999999989989999338635899999994566435840246998999999999988997399996792
Q ss_pred CC-CCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCE
Q ss_conf 54-32100000004896658999981596699985142000000111101113557421003784579999986215504
Q gi|254780456|r 269 EK-NPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKR 347 (576)
Q Consensus 269 ~~-dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~ 347 (576)
.. .||..+.+.|+.|+++.|+|+++.+.|++|+++ |++||+|.|++|+ ....+|... +|+.++|+|+.+|+++++
T Consensus 91 ~~~~~w~~~~~~~~~g~~v~g~V~~~~kgG~~V~~~-gv~gFlP~S~ls~-~~~~~~~~~--vGq~v~~kVi~vd~~~~~ 166 (390)
T PRK06676 91 EARKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVG-GVRGFIPASLIST-RFVEDLSDF--KGKTLDVKIIELDPEKNR 166 (390)
T ss_pred HHCHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEC-CCEEEEEHHHCCC-CCCCCCHHH--CCEEEEEEEEEEECCCCC
T ss_conf 201008888876537977999999995585999976-8168775487256-445770554--371699999998537882
Q ss_pred EEEEEECCCCC----CCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEE
Q ss_conf 78752034543----21000001222221369999985016999706884135400553001220012342111234226
Q gi|254780456|r 348 ISLGLKQALIN----PWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKA 423 (576)
Q Consensus 348 i~lS~k~~~~~----p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~ 423 (576)
+.||+|++... +|+.+.+.+++|++++|+|++++++|+||+++ +++|++|++|+||.. ..++.+.|++||.++|
T Consensus 167 ivlS~K~~l~~~~~~~~~~~~~~l~~Gdvv~G~V~~i~~~G~FV~lg-gv~glvh~sels~~~-~~~~~~~~k~G~~v~~ 244 (390)
T PRK06676 167 VILSRRAVVEEERAEKKKELLSSLKEGDVVEGKVARLTDFGAFVDIG-GVDGLVHISELSHER-VNKPSEVVSVGQEVEV 244 (390)
T ss_pred EEECCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEECC-CEEEEEEECCCCHHH-HCCHHHHHCCCCEEEE
T ss_conf 89703245466676657667763468984789999994563699807-767999961057333-3598883047975799
Q ss_pred EEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHH
Q ss_conf 88521565455320113221011100001100478987999999970890899961779849999974718212104201
Q gi|254780456|r 424 VVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPG 503 (576)
Q Consensus 424 ~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~ 503 (576)
+|+++|++++++.||+|++..+||..+ .++|++|++++|+|+++++||+||.+. +|+.||||.|++++.++.++.+
T Consensus 245 ~Vl~id~~~~ri~LslK~l~~dP~~~~--~~~~~vG~~v~G~V~~i~~fG~fV~l~--~g~~Glih~sels~~~~~~p~~ 320 (390)
T PRK06676 245 KVLSIDEETERISLSLKDTLPGPWEGV--EEKLKEGDVIEGTVKRLTNFGAFVEVL--PGVEGLVHISQISHKHIAKPSE 320 (390)
T ss_pred EEEEEECCCCEEEEEEEECCCCCHHHH--HHHCCCCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCCCCCCCHHH
T ss_conf 999994678899999832678956776--653369989999999994737999977--9968999989947533368555
Q ss_pred HCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHH-----HHHH--HCCCCCCCHHHHHHHHHHHHH
Q ss_conf 1068987999999970576869987036557777999-----9984--034457779999999998743
Q gi|254780456|r 504 RFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGA-----VAQF--GSSDSGASLGDILGMALKNRG 565 (576)
Q Consensus 504 ~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~-----~~~~--~~~~~~~tlg~~~~~~lk~~~ 565 (576)
.|++||.|+|+|++||++++||+||+|++++...+++ ..++ +.+++++||||+++++||++.
T Consensus 321 ~~~~Gd~V~~~Vl~id~e~~ri~LS~K~l~~~p~~e~~~~~~~~~~~~~~~~~~~~lgd~~~~~~~~~~ 389 (390)
T PRK06676 321 VLEEGQEVKVKVLEVDEEEKRISLSIKALEEAPAEEESRREEYRQYELPEEETGFSLGDLIGDKLKDLK 389 (390)
T ss_pred CCCCCCEEEEEEEEECCCCCEEEEEEHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 278999999999998177898998814134481566666656664146677688538999988875435
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=0 Score=471.67 Aligned_cols=365 Identities=27% Similarity=0.467 Sum_probs=329.2
Q ss_pred CCCCCCCCCCCEEEEEEEEEECCCCEEEECC-CEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECC
Q ss_conf 1000112223302467887531471777448-315788642024444433113326972589999874765279985215
Q gi|254780456|r 189 SEIVQKLEEGQVIEGTVKNITDYGVFVDLSG-VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQ 267 (576)
Q Consensus 189 ~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g-~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~ 267 (576)
.+.+..++.|++|+|+|.++.+.+++|++|. .+|++|++++++....++.+.+++||++++.|++++...+.+.||.+.
T Consensus 296 ~~s~k~~~~G~iV~G~Vv~v~~~~v~VDiG~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G~i~LS~kk 375 (670)
T PRK00087 296 NENEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDGYVVLSKKE 375 (670)
T ss_pred HHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHH
T ss_conf 76334677898799999999389899983678436888999366767773345799998999999986899829988899
Q ss_pred C-CCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCC
Q ss_conf 5-543210000000489665899998159669998514200000011110111355742100378457999998621550
Q gi|254780456|r 268 L-EKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK 346 (576)
Q Consensus 268 l-~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~ 346 (576)
+ ...-|+.+.+.|..|..+.|+|++..+.|+.|+++ |+.||+|.|+++ .+...++.. -+|+.++|+|+.+|++++
T Consensus 376 a~~~~~w~~l~~a~e~~e~V~g~V~~~vKGG~~V~i~-gi~~FiP~Sq~~-~~~~~d~~~--~vG~~~~~kIie~d~~k~ 451 (670)
T PRK00087 376 ADREKAWKELEEAFENGETVKGKVKEVVKGGLLVDYG-GVRAFLPASHVE-LGYVEDLSA--YKGQELEVKIIEFDKKRK 451 (670)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEC-CEEEEECHHHCC-CCCCCCHHH--HCCCEEEEEEEEECCCCC
T ss_conf 9988879999999868986999999998585999989-989980227615-665677278--769748999999844457
Q ss_pred E--EEEEEECCCCC----CCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCC
Q ss_conf 4--78752034543----21000001222221369999985016999706884135400553001220012342111234
Q gi|254780456|r 347 R--ISLGLKQALIN----PWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDI 420 (576)
Q Consensus 347 ~--i~lS~k~~~~~----p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~ 420 (576)
+ +.+|.|+.+.. -.+.+.+.+++|++++|+|+++++||+||+++ |++||+|.||+||.+ ..+|.+.|++||.
T Consensus 452 r~niV~Srr~vlee~~~~~k~~~~~~l~~G~~v~G~V~~i~~~GaFvdlg-GvdGLvHiSelSw~r-v~~p~~~~~~G~~ 529 (670)
T PRK00087 452 KTKVVLSRKALLKEEKEKQKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISWGR-VEKPSDVLKVGDE 529 (670)
T ss_pred CCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEC-CEEEEEEHHHCCCCC-CCCHHHHCCCCCE
T ss_conf 67489780999998899999999974889988999999997340799977-989999843447677-7898996278977
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCC
Q ss_conf 22688521565455320113221011100001100478987999999970890899961779849999974718212104
Q gi|254780456|r 421 VKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQ 500 (576)
Q Consensus 421 i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~ 500 (576)
++++|+++|++++||+||+|++..+||..+. ++|++|++++|+|+++.+||+||.+ .+|++||||.|++|+.+..+
T Consensus 530 v~vkIl~iD~e~~rIsLs~K~l~~dPw~~~~--~~~~~G~~v~g~V~~i~~fGaFVel--~~gveGlih~sels~~~~~~ 605 (670)
T PRK00087 530 IKVYILEIDKENKKLSLSLKKLLPDPWENVE--EKYPVGSIVLGKVVRIAPFGAFVEL--EPGVDGLVHISEISWKRIDK 605 (670)
T ss_pred EEEEEEEECCCCCEEEEEECCCCCCCHHHHH--HHCCCCCEEEEEEEEEECCEEEEEE--CCCCEEEEEHHHCCCCCCCC
T ss_conf 9999999838878898763437789478888--6489969999999999677079995--79978998989948432489
Q ss_pred CHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCC--CCCCCHHHHHHHHHHH
Q ss_conf 20110689879999999705768699870365577779999984034--4577799999999987
Q gi|254780456|r 501 DPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSS--DSGASLGDILGMALKN 563 (576)
Q Consensus 501 ~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~~~~~~~--~~~~tlg~~~~~~lk~ 563 (576)
+.+.|++||.|+++|+++|++++||+||+|+++.+.++++..++.+. +++.||||++++.||.
T Consensus 606 ~~~~~~~Gd~v~~kIl~id~~~krisLSiK~~~~~peke~~~~~~~~~~~~~~tlgdi~~~~~k~ 670 (670)
T PRK00087 606 PEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPEKEGDIEKVKKEKENEVTLGDIEGYLPKS 670 (670)
T ss_pred HHHCCCCCCEEEEEEEEECCCCCEEEEEHHHCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 77748999989999999837778899784653118004689976522665685288975565249
No 16
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=463.05 Aligned_cols=298 Identities=29% Similarity=0.478 Sum_probs=275.1
Q ss_pred CHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCC---CCCCCCCCCCEEEEEEEEEE
Q ss_conf 106889999885402146389877999999981998999947960367899750566---43556378987999999974
Q gi|254780456|r 6 PSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGK---GQYTPIKVGDEVEVYVERTE 82 (576)
Q Consensus 6 ~~~~~f~~ll~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~---~~~~~~kvGd~i~v~V~~~~ 82 (576)
-+|++|+.||+++. .++++|++|+|+|++|+++++|||+|+|++|+||++|+++. ++.+.+++||.++++|+..+
T Consensus 13 ~~~edF~~lLe~~~--~~~k~GdiVeG~V~~I~~~~v~VdiG~k~eG~i~~~E~s~~~~~~~~e~~~vGd~iev~V~~~~ 90 (314)
T PRK07400 13 FTHEDFAALLDKYD--YHFKPGDIVNGTVFSLEPKGALIDIGAKTAAFMPLQEMSINRVEGPSEVLQPGETREFFILSEE 90 (314)
T ss_pred CCHHHHHHHHHHHH--CCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEE
T ss_conf 69999999998752--3699999899999999799899997798079999999366656894301358976999999985
Q ss_pred CCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 79985999687875557589999985289769999999967955999744020000011234543334555553023111
Q gi|254780456|r 83 NSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEI 162 (576)
Q Consensus 83 ~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~I 162 (576)
++.|++.||++++....+|+.+.+++++|++++|+|++.+++|++|++.|++||||.||++.++.++ .++|+.++|+|
T Consensus 91 ~~~g~i~LS~k~~~~~~~w~~l~~~~~~~~~V~gkV~~~~kgG~~V~i~gl~gFiP~Sqls~~~~~~--~~vG~~~~~kI 168 (314)
T PRK07400 91 NEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKE--ELVGEELPLKF 168 (314)
T ss_pred CCCCCEEEEECHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCH--HHCCCEEEEEE
T ss_conf 6889689986043212069999977325987999999996384899976865685524516355632--10697688999
Q ss_pred CCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEEC
Q ss_conf 33543233112212111222221211100011222330246788753147177744831578864202444443311332
Q gi|254780456|r 163 LKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLS 242 (576)
Q Consensus 163 i~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~ 242 (576)
+++|++++++++|+|+++.. ..++.+++|++++|+|++|++||+||+++|++||+|++++||+|+.+|++.|+
T Consensus 169 ieid~~~~rivlS~r~~l~e-------~~~~~l~vG~vv~G~V~~I~~fGaFVdigGvdGLlHiSeiSw~rv~~p~dv~k 241 (314)
T PRK07400 169 LEVDEERNRLVLSHRRALVE-------RKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFN 241 (314)
T ss_pred EEEECCCCCEEEEEEHHHHH-------HHHHCCCCCCEEEEEEEEEECEEEEEEECCCEEEEEHHHCCCCCCCCHHHHCC
T ss_conf 99715668248998333201-------36750889988999999996408899978918999814616544489878267
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCC
Q ss_conf 6972589999874765279985215554321000000048966589999815966999851420000001111
Q gi|254780456|r 243 IGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI 315 (576)
Q Consensus 243 ~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sel 315 (576)
+||+|+|+|+.+|++++||+||+|+|.+|||+.+.++|++|+.+... ..-...++++....+..|++|.|||
T Consensus 242 vGd~V~vkVi~iD~e~~rIsLSiK~l~~dPwd~i~~K~kvgd~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 313 (314)
T PRK07400 242 VNDQMKVMIIDLDAERGRISLSTKQLEPEPGDMLTDPQKVFDKAEEM-AAKYRQMLLEQAEGGEEPIEAAAEL 313 (314)
T ss_pred CCCEEEEEEEEECCCCCEEEEEHHHCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHCC
T ss_conf 99999999999738898899776665558477762577765899999-9999988765231441310012107
No 17
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=455.39 Aligned_cols=333 Identities=28% Similarity=0.525 Sum_probs=187.5
Q ss_pred HHHHHCCCEEEEEEEEEECCCEEEEECC-CHHHHHCCCCCCCCCCCCC--CCCCCEEEECCCCCCCCCCCEEECCCCCCC
Q ss_conf 9985289769999999967955999744-0200000112345433345--555530231113354323311221211122
Q gi|254780456|r 105 EAKFRAGERIEGVIFNQVKGGMTVDLNG-EVAFLPRSQIDIRPVRDVT--PLMHEPQLFEILKMDKRRGNIVVSRRAVLE 181 (576)
Q Consensus 105 ~~a~~~g~~v~g~V~~~~k~G~~V~i~g-i~~FlP~s~~~~~~~~d~~--~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l~ 181 (576)
.+.++.|++|+|+|++..+.+++|+++. ..|++|.++++..+..++. ..+|.++++.|+..+...+++++|++.+.
T Consensus 30 ~k~~~eGdIV~GtVv~I~~d~VlVDIG~KsEGiIP~~E~s~~~d~d~~e~vkvGDeIeV~Vi~~ed~eG~vvLSkkkA~- 108 (484)
T PRK07899 30 IKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVSVGDEVEALVLTKEDKEGRLILSKKRAQ- 108 (484)
T ss_pred HHCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHHHH-
T ss_conf 7358899889999999978989998268704787999946675778454578999999999987378874998889976-
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEE
Q ss_conf 22212111000112223302467887531471777448315788642024444433113326972589999874765279
Q gi|254780456|r 182 ESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRI 261 (576)
Q Consensus 182 ~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i 261 (576)
....+..+-+.++.|.+|+|+|++...-|+.|++ |++||+|.|+++..++.+++.. +|++++++|+.+|+.+++|
T Consensus 109 --~~k~W~~Leea~e~~~vVeGkV~~~vKGGliVdi-GvraFlP~Sqid~r~v~dl~~~--vGk~l~~kIieid~~r~nI 183 (484)
T PRK07899 109 --YERAWGTIEKLKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPY--IGQEIEAKIIELDKNRNNV 183 (484)
T ss_pred --HHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEC-CCEEEEECCCCCCCCCCCHHHH--CCCEEEEEEEEECCCCCCE
T ss_conf --5678999999975798699999999667099982-6579986422565104783887--7987999999975766806
Q ss_pred EEEECCCCCCC----CCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEE
Q ss_conf 98521555432----10000000489665899998159669998514200000011110111355742100378457999
Q gi|254780456|r 262 SLGMKQLEKNP----WDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVV 337 (576)
Q Consensus 262 ~lslK~l~~dp----~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~ 337 (576)
.||.|++.... -..+.+.+++|+++.|+|.++++||+||+|+ |++||+|+||+|| .+..+|.+.|++||.|+|+
T Consensus 184 VlSRRa~LEee~~~~r~e~l~~L~~G~vveG~Vk~It~fGAFVDLG-GVDGLvHiSEiSW-~Rv~~Psev~~vGd~V~Vk 261 (484)
T PRK07899 184 VLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSW-KHIDHPSEVVEVGDEVTVE 261 (484)
T ss_pred EEEHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCEEEEEEC-CEEEEEEHHHCCC-CCCCCHHHHCCCCCEEEEE
T ss_conf 5019999999998899999974778987999999821646899955-7237898134035-6779989957799879999
Q ss_pred EEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCC
Q ss_conf 99862155047875203454321000001222221369999985016999706884135400553001220012342111
Q gi|254780456|r 338 ILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAK 417 (576)
Q Consensus 338 Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~ 417 (576)
|+.+|+++++|+||+|+++++||+.+.++|++|++++|+|+++++||+||++.+|++|+||+|+|| +....+|.+.+++
T Consensus 262 Vl~iD~Ek~RISLslKql~~dPW~~~~~k~~vG~vv~GkV~~l~~fGAFVel~~GIEGLVHISElS-~~~v~~P~dvv~~ 340 (484)
T PRK07899 262 VLDVDLDRERVSLSLKATQEDPWQVFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA-ERHVEVPEQVVSV 340 (484)
T ss_pred EEEECCCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCC-CCCCCCHHHHCCC
T ss_conf 987747678898862547788389898648998989999998726605999369967667877645-6444798884779
Q ss_pred CCCCEEEEEECCCCCCCCCCCHHHHHCCC
Q ss_conf 23422688521565455320113221011
Q gi|254780456|r 418 GDIVKAVVLDIDVGKERISLGVKQLSGSA 446 (576)
Q Consensus 418 G~~i~~~Vl~id~~~~~i~LS~K~l~~~~ 446 (576)
||.|+|+|+.+|++++||+||+||..+++
T Consensus 341 GdeV~vkIl~ID~e~rRISLSiKQa~e~~ 369 (484)
T PRK07899 341 GDEVMVKVIDIDLERRRISLSLKQANEDY 369 (484)
T ss_pred CCEEEEEEEEECCCCCEEECCEECCCCCC
T ss_conf 98899999987577678542300167898
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=0 Score=380.76 Aligned_cols=288 Identities=24% Similarity=0.420 Sum_probs=259.6
Q ss_pred CCCCCCCCCEEEEEEEEEECCCCEEEECC-CEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCC
Q ss_conf 00112223302467887531471777448-31578864202444443311332697258999987476527998521555
Q gi|254780456|r 191 IVQKLEEGQVIEGTVKNITDYGVFVDLSG-VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLE 269 (576)
Q Consensus 191 ~~~~l~~G~~v~g~V~~i~~~g~~V~~~g-~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~ 269 (576)
....+++|++|+|+|.++.++|+||++|+ .+|++|.++++|.+..+|.+.+++|+++++.|++.+.+.+++.||+|++.
T Consensus 25 ~~~~~k~GdiVeG~V~~I~~~~v~VdiG~k~eG~i~~~E~s~~~~~~~~e~~~vGd~iev~V~~~~~~~g~i~LS~k~~~ 104 (314)
T PRK07400 25 YDYHFKPGDIVNGTVFSLEPKGALIDIGAKTAAFMPLQEMSINRVEGPSEVLQPGETREFFILSEENEDGQLTLSIRRIE 104 (314)
T ss_pred HHCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEECHHH
T ss_conf 52369999989999999979989999779807999999936665689430135897699999998568896899860432
Q ss_pred -CCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEE
Q ss_conf -4321000000048966589999815966999851420000001111011135574210037845799999862155047
Q gi|254780456|r 270 -KNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRI 348 (576)
Q Consensus 270 -~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i 348 (576)
.+||+.+.+.+..|.++.|+|+++.++|++|++. |++||||.|++||.. +.+.+ +|+.++|+|+.+|++++++
T Consensus 105 ~~~~w~~l~~~~~~~~~V~gkV~~~~kgG~~V~i~-gl~gFiP~Sqls~~~----~~~~~-vG~~~~~kIieid~~~~ri 178 (314)
T PRK07400 105 YMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRK----PKEEL-VGEELPLKFLEVDEERNRL 178 (314)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEC-CEEEEEEHHHCCCCC----CCHHH-CCCEEEEEEEEEECCCCCE
T ss_conf 12069999977325987999999996384899976-865685524516355----63210-6976889999971566824
Q ss_pred EEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEEC
Q ss_conf 87520345432100000122222136999998501699970688413540055300122001234211123422688521
Q gi|254780456|r 349 SLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDI 428 (576)
Q Consensus 349 ~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~i 428 (576)
.||.|++.. +...+.+++|++++|+|+++++||+||+++ |++||+|+||+||.+ ..+|.+.|++||.++|+|+.+
T Consensus 179 vlS~r~~l~---e~~~~~l~vG~vv~G~V~~I~~fGaFVdig-GvdGLlHiSeiSw~r-v~~p~dv~kvGd~V~vkVi~i 253 (314)
T PRK07400 179 VLSHRRALV---ERKMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEH-IETPHSVFNVNDQMKVMIIDL 253 (314)
T ss_pred EEEEEHHHH---HHHHHCCCCCCEEEEEEEEEECEEEEEEEC-CCEEEEEHHHCCCCC-CCCHHHHCCCCCEEEEEEEEE
T ss_conf 899833320---136750889988999999996408899978-918999814616544-489878267999999999997
Q ss_pred CCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCC
Q ss_conf 565455320113221011100001100478987999999970890899961779849999974718
Q gi|254780456|r 429 DVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLS 494 (576)
Q Consensus 429 d~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is 494 (576)
|++++||+||+|+|.++||+.+. ++|++|+.++ .+..-..+++|+.. .+|..|++|.|+|.
T Consensus 254 D~e~~rIsLSiK~l~~dPwd~i~--~K~kvgd~~~-~~~~~~~~~~~~~~--~~~~~~~~~~~~~~ 314 (314)
T PRK07400 254 DAERGRISLSTKQLEPEPGDMLT--DPQKVFDKAE-EMAAKYRQMLLEQA--EGGEEPIEAAAELE 314 (314)
T ss_pred CCCCCEEEEEHHHCCCCCHHHHH--HHHHHHHHHH-HHHHHHHHHHHHHH--CCCHHHHHHHHCCC
T ss_conf 38898899776665558477762--5777658999-99999998876523--14413100121079
No 19
>KOG1070 consensus
Probab=100.00 E-value=0 Score=331.42 Aligned_cols=525 Identities=20% Similarity=0.266 Sum_probs=382.1
Q ss_pred HHHHHHCCCCCCCCCEEEEEEEEEECCEEEEEEC-CCEEEEEEHHHHCCCCC---CCCCCCCCEEEEEEEEEECCCCEEE
Q ss_conf 9885402146389877999999981998999947-96036789975056643---5563789879999999747998599
Q gi|254780456|r 14 LLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVG-LKFEGRIPRREFMGKGQ---YTPIKVGDEVEVYVERTENSFGEAV 89 (576)
Q Consensus 14 ll~~~~~~~~~~~G~iv~G~V~~i~~~~v~vdig-~k~~G~i~~~e~~~~~~---~~~~kvGd~i~v~V~~~~~~~g~i~ 89 (576)
|.-+++..++++.|++|.|+|.+++++|+.|.+- ....|++|..++.+... +..+++|..++++|+.++...+++.
T Consensus 497 l~lk~~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~ 576 (1710)
T KOG1070 497 LGLKFLRVNDIEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVA 576 (1710)
T ss_pred HCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEECCCEEEECCHHHHHHCCCCCCCCEEEECCCCEEEEEEEECCCCEEE
T ss_conf 41553410353344412238878537847999853854134586764203356633012304662799999973687258
Q ss_pred EEHHHHHHHHHHH---HHHHHHHCCCEEEEEEEEEECCCEEEEE-CCCHHHHHCCCCCCCCCCCCCC--CCCCEEEECCC
Q ss_conf 9687875557589---9999852897699999999679559997-4402000001123454333455--55530231113
Q gi|254780456|r 90 FSRDKALREGVWE---KIEAKFRAGERIEGVIFNQVKGGMTVDL-NGEVAFLPRSQIDIRPVRDVTP--LMHEPQLFEIL 163 (576)
Q Consensus 90 lS~~k~~~~~~~~---~i~~a~~~g~~v~g~V~~~~k~G~~V~i-~gi~~FlP~s~~~~~~~~d~~~--~vG~~i~~~Ii 163 (576)
|+++++....... +... ..+|+...|++++....|++|.+ +|++||+|.|.+++.++.+... .+||++.+.|.
T Consensus 577 l~~K~slv~~~~plp~d~~~-~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~ 655 (1710)
T KOG1070 577 LTLKKSLVNTQLPLPSDFEQ-AIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIV 655 (1710)
T ss_pred EEECHHHHCCCCCCCCCHHH-CCCCCEEEEEEEEECCCCEEEEECCCCCCCCCHHHHHHHHHCCHHHHCCCCCEEEEEEE
T ss_conf 88223343146888642533-58783689877654268728995676565664454310121482663345647999997
Q ss_pred CCCCCCCCEEECCCCCCCCCCCC----------------------C----------------------------------
Q ss_conf 35432331122121112222212----------------------1----------------------------------
Q gi|254780456|r 164 KMDKRRGNIVVSRRAVLEESRAE----------------------Q---------------------------------- 187 (576)
Q Consensus 164 ~~d~~~~~ivvS~k~~l~~~~~~----------------------~---------------------------------- 187 (576)
.+|++++++.+|.|+.-...... .
T Consensus 656 nvd~ek~rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~~~~~~~v~~~~~L~dg~v~~~~~~~~k 735 (1710)
T KOG1070 656 NVDDEKRRMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIVEIVDQGITGVGVFGELVDGSVVVNKVLENK 735 (1710)
T ss_pred ECCCHHCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHCCCCEEEECCCCCEEEEEEEEEECCCCEEECCCHHHH
T ss_conf 42714502302233455587889998877541643321210111462799715851687899999806824772530354
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780456|r 188 -------------------------------------------------------------------------------- 187 (576)
Q Consensus 188 -------------------------------------------------------------------------------- 187 (576)
T Consensus 736 l~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~~~~l~k~~~~~~~v~~is~~~~~~a~~~~~i~~v~~s~~ 815 (1710)
T KOG1070 736 LRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTDLPNNATKLLKGSYALALVRSISKEGKFVAFVSNLIALVKVSHL 815 (1710)
T ss_pred HHHCCHHHEEEECCEEEEEEEEEEHHHHHHHCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHEEHEEECCCCCCEEECCCC
T ss_conf 55145133265145157999972103334100225410013888754751677887454433011220553110102013
Q ss_pred ------------------------------------------------------------CCCCCCCCCCCCEEEEEEEE
Q ss_conf ------------------------------------------------------------11000112223302467887
Q gi|254780456|r 188 ------------------------------------------------------------RSEIVQKLEEGQVIEGTVKN 207 (576)
Q Consensus 188 ------------------------------------------------------------~~~~~~~l~~G~~v~g~V~~ 207 (576)
.....+++.+|.++.|+|++
T Consensus 816 v~s~~~d~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~~~~~~~~~d~~Vd~a~k~~~~~~igsiv~a~v~s 895 (1710)
T KOG1070 816 VDSELDDLTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKFIKVSSNDSDNEVDLAIKSTEDLSIGSIVRAYVKS 895 (1710)
T ss_pred CCCCCCCCCEEEEECCCCEEEEECCHHHHHHHHHHCCHHHCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEEEEE
T ss_conf 34532563202442245269972070277788862360220300478720466777433234542211344678787865
Q ss_pred EECCCCEEEEC-CCEEEEEEEECCC--CCCCCCCEEECCCCEEEEEEEEEC-----CCCCEE------EEEECC--CCCC
Q ss_conf 53147177744-8315788642024--444433113326972589999874-----765279------985215--5543
Q gi|254780456|r 208 ITDYGVFVDLS-GVDGLLHVTDIAW--HRILHPSKVLSIGQQVKVKIIRIN-----QETHRI------SLGMKQ--LEKN 271 (576)
Q Consensus 208 i~~~g~~V~~~-g~~g~i~~~~ls~--~~~~~~~~~~~~G~~v~~~Vl~~d-----~~~~~i------~lslK~--l~~d 271 (576)
+.++++.|.++ ++.|.+|++++-+ .-+.+|...|++||.+.+||++.. |-+..| .||.|. |..+
T Consensus 896 vKp~~L~v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~lpith~i~k~~v~ElSvkps~les~ 975 (1710)
T KOG1070 896 VKPDQLNVLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKDLPITHLISKEQVLELSVKPSELESD 975 (1710)
T ss_pred ECCCCEEEECCCCCCCCEEHHHHHCCCCCCCCHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHCCCHHHHCCC
T ss_conf 55652698501256683006885135432478055225687079999737765557643223465543312586663256
Q ss_pred CCCCCC-CCCC---------------------------------------------------------------------
Q ss_conf 210000-0004---------------------------------------------------------------------
Q gi|254780456|r 272 PWDDVQ-DKYV--------------------------------------------------------------------- 281 (576)
Q Consensus 272 p~~~~~-~~~~--------------------------------------------------------------------- 281 (576)
++...+ ..|+
T Consensus 976 ~~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~~~tv~~ 1055 (1710)
T KOG1070 976 EFNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDKSKTVRA 1055 (1710)
T ss_pred CCCCCCHHHHHCCCEEEEEEECCCCCEEEEECCCCCCCEEEEEECCCHHHHHHCCHHHCCCCCCEEEEEECCCCEEEEEE
T ss_conf 54343355652587699999816501267770555542124200232044442716444445500147862555057883
Q ss_pred -----------CCCEEEEEEEEECCCEEEEEECCCCEEEEECC-CCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEE
Q ss_conf -----------89665899998159669998514200000011-110111355742100378457999998621550478
Q gi|254780456|r 282 -----------EGSKVSGVVTNLTDYGVFVELQSGIEGLAHIS-QISWTKKNIHPSKILSVGQQVEVVILEVNPARKRIS 349 (576)
Q Consensus 282 -----------~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~s-els~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~ 349 (576)
+|+++.|+|.++.+.++.+.+...+.|.++.. +++ +..-.+|.+.|..++.+-|.++.++..++.+.
T Consensus 1056 iG~~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~-d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~le 1134 (1710)
T KOG1070 1056 IGFSKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMS-DSYSMTPVEHFTKIQIVYVCVLSVSALNKGLE 1134 (1710)
T ss_pred CCCCCCCCCCCCCHHHCCEEEEECCCEEEEECCCCCCCCEEEEEEHH-CCCCCCHHHHCCCCCEEEEEEEEEECCCCCCE
T ss_conf 13466778999311212456664256069825873235347743110-15567857734554078888999723555311
Q ss_pred EEEECCCC--------CCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCC
Q ss_conf 75203454--------3210000012222213699999850169997068841354005530012200123421112342
Q gi|254780456|r 350 LGLKQALI--------NPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIV 421 (576)
Q Consensus 350 lS~k~~~~--------~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i 421 (576)
||++.+.. ++.-...++++.|+++.|+|.++.+.|+|+.+++++++|+|++++++. ....+...|++|+.+
T Consensus 1135 Lslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds-~~k~w~k~~~~gklv 1213 (1710)
T KOG1070 1135 LSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDS-FEKEWEKHLPVGKLV 1213 (1710)
T ss_pred EECCCCCCCCCCCCCCCCCCCCHHHCCCCCEEEEEEEEECCCCEEEEECCCEEEEEECCCCCCC-HHHHHHCCCCCCCEE
T ss_conf 2213355667632024875241432255764688999703774899971562899983456640-232221138854443
Q ss_pred EEEEEECCCCCCCCCCCHHHHHC-CCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCC
Q ss_conf 26885215654553201132210-11100001100478987999999970890899961779849999974718212104
Q gi|254780456|r 422 KAVVLDIDVGKERISLGVKQLSG-SAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQ 500 (576)
Q Consensus 422 ~~~Vl~id~~~~~i~LS~K~l~~-~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~ 500 (576)
.++|+.++...+|+.||+|.... ++.........+.+|+...|+|..+.++|+|+++.....+.|++|.+++++.+..+
T Consensus 1214 ~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~ 1293 (1710)
T KOG1070 1214 TGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGEN 1293 (1710)
T ss_pred EEEEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCEEEEECCCCEECCCCCCEEECCHHHHH
T ss_conf 15899852368628999852666884444345566422630043499936875389833750341444310123214442
Q ss_pred CHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHHHH
Q ss_conf 20110689879999999705768699870365577779999
Q gi|254780456|r 501 DPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAV 541 (576)
Q Consensus 501 ~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~~~ 541 (576)
.+..|..|+.++|.+++.|.+.+||.|++|.....++.+..
T Consensus 1294 it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~~~~~dd~~ 1334 (1710)
T KOG1070 1294 ITALYYAGDRVKACVLKEDSEKKRISLGLKSSYLSSEDDAR 1334 (1710)
T ss_pred CCCCEECCCEEEEEEEECCCHHHHHHHHHHHHCCCCHHHHH
T ss_conf 10121124400267631251131210114554268734432
No 20
>KOG1070 consensus
Probab=100.00 E-value=0 Score=297.38 Aligned_cols=467 Identities=19% Similarity=0.295 Sum_probs=327.0
Q ss_pred CCCCCEEEEEEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEE--CCCHHHHHCCCCCCC
Q ss_conf 378987999999974799859996878755575899999852897699999999679559997--440200000112345
Q gi|254780456|r 68 IKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDL--NGEVAFLPRSQIDIR 145 (576)
Q Consensus 68 ~kvGd~i~v~V~~~~~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~i--~gi~~FlP~s~~~~~ 145 (576)
+++|.++.+.+..+-+....+.+|-+++.....+-.+.+ ++.|+.|+|.|.+.++.|+.|.+ +.++||+|..|+++.
T Consensus 468 ~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~ 546 (1710)
T KOG1070 468 YEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDH 546 (1710)
T ss_pred EECCCCCCCCCCEECCCCCEEEEEEEHHHHCCCCCCCCC-CCCCCEEEEEEEEECCCCEEEEEECCCEEEECCHHHHHHC
T ss_conf 114775567601141268579999706754155341035-3344412238878537847999853854134586764203
Q ss_pred CCCCC--CCCCCCEEEECCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEE-CCCEE
Q ss_conf 43334--5555530231113354323311221211122222121110001122233024678875314717774-48315
Q gi|254780456|r 146 PVRDV--TPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDL-SGVDG 222 (576)
Q Consensus 146 ~~~d~--~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~-~g~~g 222 (576)
+..-+ ...+|...+.|++.++..++++.++++..+-.. ......-++.+.+|+++.|++..+.++|+||.| ||++|
T Consensus 547 ~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~-~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsG 625 (1710)
T KOG1070 547 PLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNT-QLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSG 625 (1710)
T ss_pred CCCCCCCEEEECCCCEEEEEEEECCCCEEEEEECHHHHCC-CCCCCCCHHHCCCCCEEEEEEEEECCCCEEEEECCCCCC
T ss_conf 3566330123046627999999736872588822334314-688864253358783689877654268728995676565
Q ss_pred EEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCC---------------------------C-CCC
Q ss_conf 788642024444433113326972589999874765279985215554---------------------------3-210
Q gi|254780456|r 223 LLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEK---------------------------N-PWD 274 (576)
Q Consensus 223 ~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~---------------------------d-p~~ 274 (576)
|+|.+++|++++..+++.|.+||++.++|.++|++++|+.+|+|+... | -|.
T Consensus 626 f~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viV 705 (1710)
T KOG1070 626 FAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIV 705 (1710)
T ss_pred CCCHHHHHHHHHCCHHHHCCCCCEEEEEEEECCCHHCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHCCCCEEE
T ss_conf 66445431012148266334564799999742714502302233455587889998877541643321210111462799
Q ss_pred CCCC----------------------------------------------------------------------------
Q ss_conf 0000----------------------------------------------------------------------------
Q gi|254780456|r 275 DVQD---------------------------------------------------------------------------- 278 (576)
Q Consensus 275 ~~~~---------------------------------------------------------------------------- 278 (576)
.+..
T Consensus 706 ei~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~~~~l~k~~~ 785 (1710)
T KOG1070 706 EIVDQGITGVGVFGELVDGSVVVNKVLENKLRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTDLPNNATKLLKGSY 785 (1710)
T ss_pred ECCCCCEEEEEEEEEECCCCEEECCCHHHHHHHCCHHHEEEECCEEEEEEEEEEHHHHHHHCCCCCCCCCHHHHHHCCCH
T ss_conf 71585168789999980682477253035455145133265145157999972103334100225410013888754751
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780456|r 279 -------------------------------------------------------------------------------- 278 (576)
Q Consensus 279 -------------------------------------------------------------------------------- 278 (576)
T Consensus 786 ~~~~v~~is~~~~~~a~~~~~i~~v~~s~~v~s~~~d~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~~~~~ 865 (1710)
T KOG1070 786 ALALVRSISKEGKFVAFVSNLIALVKVSHLVDSELDDLTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKFIKVS 865 (1710)
T ss_pred HHHHHHHHHHHEEHEEECCCCCCEEECCCCCCCCCCCCCEEEEECCCCEEEEECCHHHHHHHHHHCCHHHCCCEEEEEEC
T ss_conf 67788745443301122055311010201334532563202442245269972070277788862360220300478720
Q ss_pred ----------------CCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC-CCCCCCCCCEECCCCEEEEEEEEE
Q ss_conf ----------------004896658999981596699985142000000111101-113557421003784579999986
Q gi|254780456|r 279 ----------------KYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW-TKKNIHPSKILSVGQQVEVVILEV 341 (576)
Q Consensus 279 ----------------~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~-~~~~~~~~~~~~~G~~v~~~Vl~i 341 (576)
++.+|+++.++|.++.++++.|.+++++.|.||+||.-. .....+|.+.|++|+.|.++|++.
T Consensus 866 ~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~ 945 (1710)
T KOG1070 866 SNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGG 945 (1710)
T ss_pred CCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCEEEECCCCCCCCEEHHHHHCCCCCCCCHHHHCCCCCEEEEEEECC
T ss_conf 46677743323454221134467878786555652698501256683006885135432478055225687079999737
Q ss_pred ECCC-----------CEEEEEEECCCCC--CCCCCC-CCCCC--------------------------------------
Q ss_conf 2155-----------0478752034543--210000-01222--------------------------------------
Q gi|254780456|r 342 NPAR-----------KRISLGLKQALIN--PWEEFS-KSHPP-------------------------------------- 369 (576)
Q Consensus 342 d~~~-----------~~i~lS~k~~~~~--p~~~~~-~~~~~-------------------------------------- 369 (576)
..-+ .-..||.|+++-+ ++..-+ ..++.
T Consensus 946 ~D~k~lpith~i~k~~v~ElSvkps~les~~~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~ 1025 (1710)
T KOG1070 946 HDVKDLPITHLISKEQVLELSVKPSELESDEFNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLH 1025 (1710)
T ss_pred CCCCCCCCCCCCCHHHHHHHCCCHHHHCCCCCCCCCHHHHHCCCEEEEEEECCCCCEEEEECCCCCCCEEEEEECCCHHH
T ss_conf 76555764322346554331258666325654343355652587699999816501267770555542124200232044
Q ss_pred ------------------------------------------CCCEEEEEEEEEEEEEEEEECCCCEEEEEHH-HHHCCC
Q ss_conf ------------------------------------------2213699999850169997068841354005-530012
Q gi|254780456|r 370 ------------------------------------------GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLS-DLDWNR 406 (576)
Q Consensus 370 ------------------------------------------G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~-dls~~~ 406 (576)
|++.-|+|.++++.++.+.++.+..|.++.- +++ +.
T Consensus 1026 ~le~~e~~F~~g~al~~~V~~~~~~~tv~~iG~~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~-d~ 1104 (1710)
T KOG1070 1026 VLELPESLFPLGKALDEYVVRNDKSKTVRAIGFSKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMS-DS 1104 (1710)
T ss_pred HHHCCHHHCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCCCHHHCCEEEEECCCEEEEECCCCCCCCEEEEEEHH-CC
T ss_conf 44271644444550014786255505788313466778999311212456664256069825873235347743110-15
Q ss_pred CCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHC--CC----CCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECC
Q ss_conf 20012342111234226885215654553201132210--11----1000011004789879999999708908999617
Q gi|254780456|r 407 PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSG--SA----PDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLID 480 (576)
Q Consensus 407 ~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~--~~----~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~ 480 (576)
...+|.+.|..++.+.+.++.++..++.+.||++.... .| -..+....+++.|+++.|+|.++.+.|+|+.++
T Consensus 1105 ~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls- 1183 (1710)
T KOG1070 1105 YSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS- 1183 (1710)
T ss_pred CCCCHHHHCCCCCEEEEEEEEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCHHHCCCCCEEEEEEEEECCCCEEEEEC-
T ss_conf 5678577345540788889997235553112213355667632024875241432255764688999703774899971-
Q ss_pred CCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHHHHHH
Q ss_conf 79849999974718212104201106898799999997057686998703655777799
Q gi|254780456|r 481 HKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKG 539 (576)
Q Consensus 481 ~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~~~~~ 539 (576)
.++.+|+|+|++++.+...+..+|.+|+.+.++|+.++...+|+.||+|.........
T Consensus 1184 -~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~ 1241 (1710)
T KOG1070 1184 -RKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVK 1241 (1710)
T ss_pred -CCEEEEEECCCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCCHH
T ss_conf -5628999834566402322211388544431589985236862899985266688444
No 21
>PRK08059 general stress protein 13; Validated
Probab=99.90 E-value=3.1e-24 Score=164.15 Aligned_cols=115 Identities=30% Similarity=0.533 Sum_probs=90.1
Q ss_pred CCCCCCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCC
Q ss_conf 01122233024678875314717774-48315788642024444433113326972589999874765279985215554
Q gi|254780456|r 192 VQKLEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEK 270 (576)
Q Consensus 192 ~~~l~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~ 270 (576)
++++++|++|.|+|++|.+||+||++ +|++||+|++++||.++.+|++.|++||+|+|+|+++|+++++|.||+|++.+
T Consensus 1 i~k~kvGdiv~G~V~~I~~fG~FV~l~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~ri~LSlK~l~~ 80 (119)
T PRK08059 1 MEQYEVGVVVTGKVTGIQDYGAFVALDEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHGKISLSIRATEE 80 (119)
T ss_pred CCCCCCCCEEEEEEEEEECEEEEEEEECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEECCCCCC
T ss_conf 98789999999999999740489999439537888788245666799997058998999999998999999875035764
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCC
Q ss_conf 32100000004896658999981596699985142000000111
Q gi|254780456|r 271 NPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQ 314 (576)
Q Consensus 271 dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~se 314 (576)
|||..... ....+.+..++| |-.|++.+..++|-||
T Consensus 81 ~P~~~~~k-------~~~~~~~~~~~g-~~~l~~~l~~~l~~s~ 116 (119)
T PRK08059 81 APERKRKK-------GKILIPNPSEQG-FNTLRDKLEEWIEQSE 116 (119)
T ss_pred CCCCCCCC-------CCCCCCCCCCCC-CCCHHHHHHHHHHHHH
T ss_conf 83422323-------444567765667-4258998999998755
No 22
>PRK08059 general stress protein 13; Validated
Probab=99.86 E-value=3.1e-21 Score=146.00 Aligned_cols=108 Identities=23% Similarity=0.217 Sum_probs=63.1
Q ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHH
Q ss_conf 00478987999999970890899961779849999974718212104201106898799999997057686998703655
Q gi|254780456|r 454 SSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALE 533 (576)
Q Consensus 454 ~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~ 533 (576)
++|++|++|+|+|+++.+||+||++. +|++||||+|++++.++.++.+.|++||.|+|+|+++|++++||.||+|++.
T Consensus 2 ~k~kvGdiv~G~V~~I~~fG~FV~l~--~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~ri~LSlK~l~ 79 (119)
T PRK08059 2 EQYEVGVVVTGKVTGIQDYGAFVALD--EETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHGKISLSIRATE 79 (119)
T ss_pred CCCCCCCEEEEEEEEEECEEEEEEEE--CCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEECCCCC
T ss_conf 87899999999999997404899994--3953788878824566679999705899899999999899999987503576
Q ss_pred HHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHH
Q ss_conf 77779999984034-----4577799999999987
Q gi|254780456|r 534 IAEEKGAVAQFGSS-----DSGASLGDILGMALKN 563 (576)
Q Consensus 534 ~~~~~~~~~~~~~~-----~~~~tlg~~~~~~lk~ 563 (576)
.+.++...+.+.+. +.-++||+.++..||.
T Consensus 80 ~~P~~~~~k~~~~~~~~~~~g~~~l~~~l~~~l~~ 114 (119)
T PRK08059 80 EAPERKRKKGKILIPNPSEQGFNTLRDKLEEWIEQ 114 (119)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 48342232344456776566742589989999987
No 23
>PRK07252 hypothetical protein; Provisional
Probab=99.81 E-value=9.2e-20 Score=137.05 Aligned_cols=109 Identities=19% Similarity=0.206 Sum_probs=82.3
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHH
Q ss_conf 47898799999997089089996177984999997471821210420110689879999999705768699870365577
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIA 535 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~ 535 (576)
+++|+++.|+|+++.+||+||++. +|++||||+|+|++.++.++.+.|++||.|+|+|+++|++++||+||+|+++++
T Consensus 1 lkvGdiv~G~V~~I~~fGaFV~l~--~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~rIsLSiK~l~e~ 78 (120)
T PRK07252 1 MKIGDKLKGTITGIKPYGAFVALE--NGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTKKASLSMRTLEEE 78 (120)
T ss_pred CCCCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEECCHHHHCCC
T ss_conf 988889999999997545799957--995788886660102004999947899999999999868999886136332245
Q ss_pred HHHHHHHHHHCCC---CC-CCHHHHHHHHHHHHHC
Q ss_conf 7799999840344---57-7799999999987431
Q gi|254780456|r 536 EEKGAVAQFGSSD---SG-ASLGDILGMALKNRGN 566 (576)
Q Consensus 536 ~~~~~~~~~~~~~---~~-~tlg~~~~~~lk~~~~ 566 (576)
+....-..+.++. .+ .++.+-+-..++.+.+
T Consensus 79 ~~~~~~~~~~~~~~~~~gf~~~~~~l~~~~~e~~~ 113 (120)
T PRK07252 79 KQHFPHRHRFSNSRHKIGFRPLEEQLPQWIEEALQ 113 (120)
T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 34576655445555357945899988999999999
No 24
>PRK08582 hypothetical protein; Provisional
Probab=99.81 E-value=5e-20 Score=138.65 Aligned_cols=82 Identities=30% Similarity=0.630 Sum_probs=57.3
Q ss_pred CCCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCC
Q ss_conf 1222330246788753147177744-831578864202444443311332697258999987476527998521555432
Q gi|254780456|r 194 KLEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNP 272 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp 272 (576)
.+++|++++|+|++|++|||||+++ |++||+|++++||.++.++++.|++||+|+|+|+++|. +++|.||+|++.++|
T Consensus 2 sievG~iv~G~V~~I~~fGaFV~l~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~-~gKI~LSiK~~~~~p 80 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVED-DGKIGLSIKKAKDRP 80 (139)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEHHHCCCCC
T ss_conf 7447879999998996417899956996678873662566568999957899999999998889-997051655545487
Q ss_pred CCCC
Q ss_conf 1000
Q gi|254780456|r 273 WDDV 276 (576)
Q Consensus 273 ~~~~ 276 (576)
|..-
T Consensus 81 ~~~~ 84 (139)
T PRK08582 81 RRQH 84 (139)
T ss_pred CCCC
T ss_conf 6554
No 25
>PRK07252 hypothetical protein; Provisional
Probab=99.80 E-value=5.5e-20 Score=138.39 Aligned_cols=76 Identities=36% Similarity=0.654 Sum_probs=40.2
Q ss_pred CCCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCC
Q ss_conf 22233024678875314717774-48315788642024444433113326972589999874765279985215554
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEK 270 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~ 270 (576)
+++|+++.|+|++|.+||+||++ +|++||+|++++||.++.+|.+.|++||.|+|+|+++|+++++|+||+|++.+
T Consensus 1 lkvGdiv~G~V~~I~~fGaFV~l~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~rIsLSiK~l~e 77 (120)
T PRK07252 1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTKKASLSMRTLEE 77 (120)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEECCHHHHCC
T ss_conf 98888999999999754579995799578888666010200499994789999999999986899988613633224
No 26
>PRK05807 hypothetical protein; Provisional
Probab=99.78 E-value=2.9e-19 Score=134.06 Aligned_cols=108 Identities=19% Similarity=0.300 Sum_probs=57.2
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHHH
Q ss_conf 47898799999997089089996177984999997471821210420110689879999999705768699870365577
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIA 535 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~~ 535 (576)
+++|++++|+|++|++||+||+| +|..||||+|++++.++.++.+.|++||.|+|+|+++| +++||.||+|+....
T Consensus 3 levG~iv~G~V~~I~~fGaFV~l---~g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD-~~gkI~LSiK~~~~~ 78 (136)
T PRK05807 3 LEAGSILEGTVVNITNFGAFVEV---EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMPQ 78 (136)
T ss_pred CCCCCEEEEEEEEEECCEEEEEE---CCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCEEEHHHCCCC
T ss_conf 45788999999999724479997---89276898567077643699996789999999999989-999814332223887
Q ss_pred HHHHHHHHH--H---CCCCCCCHHHHHHHHHHHHHCC
Q ss_conf 779999984--0---3445777999999999874311
Q gi|254780456|r 536 EEKGAVAQF--G---SSDSGASLGDILGMALKNRGND 567 (576)
Q Consensus 536 ~~~~~~~~~--~---~~~~~~tlg~~~~~~lk~~~~~ 567 (576)
++...-..+ . ......++.+.|..+||+-...
T Consensus 79 ~~~~~p~~~~~~~~~~~~~~~~Fe~~ls~flKdSeer 115 (136)
T PRK05807 79 KKSVKPAEIDWQKEKKKNNNSNFEDRLSKFLKDSEER 115 (136)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 6667855455333346667789899998772416999
No 27
>PRK05807 hypothetical protein; Provisional
Probab=99.77 E-value=1e-18 Score=130.67 Aligned_cols=78 Identities=38% Similarity=0.640 Sum_probs=68.9
Q ss_pred CCCCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCC
Q ss_conf 1222330246788753147177744831578864202444443311332697258999987476527998521555432
Q gi|254780456|r 194 KLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNP 272 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp 272 (576)
.+++|++++|+|++|++||+||+|+|.+||||++++||.++.++++.|++||+|+|+|+++| ++++|.||+|++.+.|
T Consensus 2 slevG~iv~G~V~~I~~fGaFV~l~g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD-~~gkI~LSiK~~~~~~ 79 (136)
T PRK05807 2 TLEAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMPQK 79 (136)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCEEEHHHCCCCC
T ss_conf 74578899999999972447999789276898567077643699996789999999999989-9998143322238876
No 28
>PRK08582 hypothetical protein; Provisional
Probab=99.77 E-value=1.4e-18 Score=129.85 Aligned_cols=80 Identities=40% Similarity=0.572 Sum_probs=42.2
Q ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCC
Q ss_conf 04896658999981596699985142000000111101113557421003784579999986215504787520345432
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINP 359 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p 359 (576)
+++|+++.|+|+++++||+||+|.++++||||+||+||. ...++.+.|++||.|+|+|+.+|. +++|.||+|++.++|
T Consensus 3 ievG~iv~G~V~~I~~fGaFV~l~~g~~GLvHISeis~~-~V~~i~d~lkvGd~V~vKVi~id~-~gKI~LSiK~~~~~p 80 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN-YVKDINDHLSVGDEVEVKVLNVED-DGKIGLSIKKAKDRP 80 (139)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCC-CCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEHHHCCCCC
T ss_conf 447879999998996417899956996678873662566-568999957899999999998889-997051655545487
Q ss_pred CC
Q ss_conf 10
Q gi|254780456|r 360 WE 361 (576)
Q Consensus 360 ~~ 361 (576)
|.
T Consensus 81 ~~ 82 (139)
T PRK08582 81 RR 82 (139)
T ss_pred CC
T ss_conf 65
No 29
>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=99.76 E-value=1.7e-18 Score=129.36 Aligned_cols=72 Identities=60% Similarity=1.113 Sum_probs=67.3
Q ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 048966589999815966999851420000001111011135574210037845799999862155047875
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLG 351 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS 351 (576)
|++|++++|+|+++++||+||++++|++||+|+|||||..+..+|.+.|++||.++|+|+++|++++||+|.
T Consensus 1 Y~~G~~v~G~V~~It~fG~FV~i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~~rIsLG 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECCC
T ss_conf 988999999998994762399966993899997663165466796360389999999999995997995389
No 30
>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=99.75 E-value=3.3e-18 Score=127.58 Aligned_cols=73 Identities=22% Similarity=0.365 Sum_probs=35.8
Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHH
Q ss_conf 89879999999708908999617798499999747182121042011068987999999970576869987036
Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKA 531 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~ 531 (576)
+|++++|+|+++++||+||++. ..+++||+|.|++++.+..++.+.|++||.|+|+|+++|++++||.||+|+
T Consensus 2 VG~~v~G~V~~i~~fG~FV~l~-g~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~rI~LSiKa 74 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDID-GTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCEEEEEEEEEECEEEEEEEC-CCCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEEEC
T ss_conf 9899999999996417899967-898079988788175656898891689999999999998999999989841
No 31
>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=99.75 E-value=1.1e-17 Score=124.34 Aligned_cols=75 Identities=29% Similarity=0.357 Sum_probs=60.5
Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHH
Q ss_conf 789879999999708908999617798499999747182121042011068987999999970576869987036
Q gi|254780456|r 457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKA 531 (576)
Q Consensus 457 ~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~ 531 (576)
++|+++.|+|+++.+||+||++.+++|++||+|.|++|+.++.++.+.|++||.++|+|+++|++++||.||+|+
T Consensus 2 e~G~iv~G~V~~i~~~GafV~l~e~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~~i~LS~K~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEECC
T ss_conf 889999999999973469999733699199999799684511599995589999999999997899999822369
No 32
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.74 E-value=1.2e-17 Score=124.17 Aligned_cols=77 Identities=27% Similarity=0.346 Sum_probs=64.4
Q ss_pred HHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 0110047898799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 451 DSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 451 ~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
..++++++|+++.|+|.++.+||+||++. +|++||+|.|++++.++.++.+.|++||.|+|+|+++|++++||.||+
T Consensus 7 ~~~~~lk~G~iv~G~V~~i~~~G~FV~l~--~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~e~~ri~LSl 83 (83)
T cd04461 7 TNFSDLKPGMVVHGYVRNITPYGVFVEFL--GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred CCHHHCCCCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 76778799999999999992781999956--994899899996864226989945599999999999958988788759
No 33
>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=99.74 E-value=1.9e-17 Score=123.07 Aligned_cols=72 Identities=43% Similarity=0.831 Sum_probs=45.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEE-C-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECC
Q ss_conf 2233024678875314717774-4-8315788642024444433113326972589999874765279985215
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDL-S-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQ 267 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~-~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~ 267 (576)
++|++++|+|+++++||+||++ + +++||+|++++||.++.+|.+.|++||+++|+|+++|++++||.||+|+
T Consensus 1 kVG~~v~G~V~~i~~fG~FV~l~g~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~rI~LSiKa 74 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCCEEEEEEEEEECEEEEEEECCCCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEEEC
T ss_conf 99899999999996417899967898079988788175656898891689999999999998999999989841
No 34
>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=99.74 E-value=4.6e-18 Score=126.75 Aligned_cols=77 Identities=34% Similarity=0.549 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 10001122233024678875314717774-483157886420244444331133269725899998747652799852
Q gi|254780456|r 189 SEIVQKLEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGM 265 (576)
Q Consensus 189 ~~~~~~l~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lsl 265 (576)
...++++++|+++.|+|+++++||+||+| +|++||+|.+++||.++.+|++.|++||.++|+|+++|++++||.|||
T Consensus 6 ~~~~~~lk~G~iv~G~V~~i~~~G~FV~l~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~e~~ri~LSl 83 (83)
T cd04461 6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred CCCHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 576778799999999999992781999956994899899996864226989945599999999999958988788759
No 35
>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=99.73 E-value=2.1e-17 Score=122.76 Aligned_cols=73 Identities=42% Similarity=0.651 Sum_probs=53.1
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHH
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998703655
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALE 533 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~ 533 (576)
|++|+|+|+++.+||+||++. +++.||||.|++|+.+++++++.|++||.|+|+|+++|++++|+.||+|+++
T Consensus 1 G~iV~G~V~~i~~~G~fV~l~--~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~ri~LSiKalE 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG--DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCCEEEEEC--CCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCCEEEEEEEECC
T ss_conf 999999999997786899928--9969999989978211329254389999999999999788999986742459
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.73 E-value=3e-17 Score=121.83 Aligned_cols=76 Identities=33% Similarity=0.531 Sum_probs=56.3
Q ss_pred CCCEEEEEEEEECCCEEEEEEC--CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCC
Q ss_conf 8966589999815966999851--4200000011110111355742100378457999998621550478752034543
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVELQ--SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALIN 358 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l~--~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~ 358 (576)
+|+++.|+|+++.+||+||+|. +|++||||+||+|| ....++.+++++||.+.|+|+++|+++++|.||+|+..+.
T Consensus 8 ~g~~v~~~V~~i~~~Ga~v~l~ey~~~eG~i~isEis~-~~v~~i~d~~k~G~~v~~kVi~vd~~kg~IdLS~k~Vs~~ 85 (262)
T PRK03987 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVAS-GWVKNIRDYVKEGQKVVCKVIRVDPKKGHIDLSLKRVNEH 85 (262)
T ss_pred CCCEEEEEEEEEECCEEEEEECCCCCCCEEEEHHHCCH-HHHHCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCCHH
T ss_conf 99889999999956679999356599316788798346-7751999851589889999998838788787110449989
No 37
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.73 E-value=8.5e-18 Score=125.13 Aligned_cols=72 Identities=33% Similarity=0.624 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC---CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECC
Q ss_conf 22330246788753147177744---8315788642024444433113326972589999874765279985215
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS---GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQ 267 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~---g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~ 267 (576)
++|+++.|+|+++.+||+||++. |++||+|++++||.++.++++.|++||++.|+|+++|+++++|.||+|+
T Consensus 2 e~G~iv~G~V~~i~~~GafV~l~e~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~~i~LS~K~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEECC
T ss_conf 889999999999973469999733699199999799684511599995589999999999997899999822369
No 38
>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=99.72 E-value=3.5e-17 Score=121.43 Aligned_cols=70 Identities=23% Similarity=0.359 Sum_probs=58.3
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|++++|+|++++++|+||++ .++++||+|.|++|+.++.++++.|++||.|+|+|+++|++++|+.||+|
T Consensus 1 G~vv~G~V~~i~~~G~fV~~--~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~~~ri~LS~K 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSF--YNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEECCCEEEEE--CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 99999999999817189994--89969998989928320289899377999999999998089999999719
No 39
>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=99.72 E-value=1.4e-17 Score=123.82 Aligned_cols=71 Identities=27% Similarity=0.600 Sum_probs=45.2
Q ss_pred CCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCC
Q ss_conf 330246788753147177744-83157886420244444331133269725899998747652799852155
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQL 268 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l 268 (576)
|++|+|+|+++.+||+||+++ +++||+|++++||.++.++.+.|++||+++|+|+++|+++++|.||+|+|
T Consensus 1 G~iV~G~V~~i~~~G~fV~l~~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~ri~LSiKal 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCCEEEEEEEEC
T ss_conf 999999999997786899928996999998997821132925438999999999999978899998674245
No 40
>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=99.71 E-value=2.1e-17 Score=122.75 Aligned_cols=68 Identities=53% Similarity=0.948 Sum_probs=57.3
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEE
Q ss_conf 96658999981596699985142000000111101113557421003784579999986215504787
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISL 350 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~l 350 (576)
|++++|+|+++++||+||++.++++||+|+|||||.++..+|.+.|++||.|+|+|+++|++++||+|
T Consensus 1 G~~v~G~V~~i~~fG~FV~l~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~risL 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEECC
T ss_conf 99999999999131899997699659999488245666679768258999999999999798688638
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=99.71 E-value=6.5e-17 Score=119.76 Aligned_cols=69 Identities=22% Similarity=0.341 Sum_probs=53.9
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 98799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
|++++|+|+++++||+||++. .+++||+|.|++|+.++++|++.|++||+|+|+|+++|++++||.||+
T Consensus 1 G~iv~G~V~~i~~fG~fV~l~--~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~~~ri~LSl 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLS--DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEECCCEEEEEEC--CCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 999999999973842799957--990699878990865206988908999999999999948879988659
No 42
>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=99.70 E-value=3.6e-17 Score=121.35 Aligned_cols=69 Identities=29% Similarity=0.496 Sum_probs=44.2
Q ss_pred CCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 33024678875314717774-4831578864202444443311332697258999987476527998521
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
|++++|+|+++.+||+||+| +|++||+|.+++||.++.+|++.|++||.|+|+|+++|++++|+.||+|
T Consensus 1 G~vv~G~V~~i~~~G~fV~~~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~~~ri~LS~K 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9999999999981718999489969998989928320289899377999999999998089999999719
No 43
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.70 E-value=5.5e-17 Score=120.22 Aligned_cols=74 Identities=36% Similarity=0.637 Sum_probs=38.4
Q ss_pred CCEEEEEEEEECCCEEEEEEC---CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCC
Q ss_conf 966589999815966999851---4200000011110111355742100378457999998621550478752034543
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQ---SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALIN 358 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~---~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~ 358 (576)
|+++.|+|+++++||+||++. ++++||+|+||+||+.+..+|.+.|++||.|+|+|+++|. ++++||+|++.++
T Consensus 1 G~i~~G~V~~i~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~--~ki~LS~K~~~~~ 77 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQN--GKISLSMKDVDQD 77 (79)
T ss_pred CCEEEEEEEEEEEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEEC--CEEEEEEEECCCC
T ss_conf 9999999989975339999967889806789956815755558988936799999999999869--9888722613467
No 44
>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=99.69 E-value=4.9e-17 Score=120.51 Aligned_cols=69 Identities=35% Similarity=0.562 Sum_probs=33.3
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEE
Q ss_conf 9665899998159669998514200000011110111355742100378457999998621550478752
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGL 352 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~ 352 (576)
|++++|+|.++++||+||+++++++||+|.|++|| ....+|++.|++||.|+|+|+++|+++++++||+
T Consensus 1 G~iv~G~V~~i~~fG~fV~l~~~i~Glv~~s~lsd-~~v~~p~~~fk~G~~Vk~rVl~vD~~~~ri~LSl 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLAD-VRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCEEEEEEHHHHCC-CCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 99999999997384279995799069987899086-5206988908999999999999948879988659
No 45
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=1.1e-16 Score=118.37 Aligned_cols=83 Identities=25% Similarity=0.360 Sum_probs=75.1
Q ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHHHH
Q ss_conf 04789879999999708908999617798499999747182121042011068987999999970576869987036557
Q gi|254780456|r 455 SLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEI 534 (576)
Q Consensus 455 ~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~~ 534 (576)
.+++|++++|+|+.+++||+||.|. +|-.||||+|++++.|++++.+++++||.|.++|+++|. +++++||+|.+++
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~--~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELE--GGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred CCCCCCEEEEEEEEEEECCEEEEEC--CCCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECC-CCCCCEEHHHHHH
T ss_conf 7534646788897567433489823--997314883575443677399884278879999972146-8970335687664
Q ss_pred HHHHHH
Q ss_conf 777999
Q gi|254780456|r 535 AEEKGA 540 (576)
Q Consensus 535 ~~~~~~ 540 (576)
..++..
T Consensus 79 ~pe~~~ 84 (129)
T COG1098 79 EPEKQH 84 (129)
T ss_pred CCCCCC
T ss_conf 744334
No 46
>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=99.68 E-value=2.8e-16 Score=115.90 Aligned_cols=73 Identities=27% Similarity=0.387 Sum_probs=61.7
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 478987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
+++|++++|+|++++++|+||+++ .++.|++|+|+++++|++++.+.|++||.|+|+|+++|.+++||.||+|
T Consensus 1 lkvG~~l~G~Vt~V~~~g~fV~L~--~~~~Glvhisel~dd~~~~~~~~~~~g~~V~v~Vl~VD~~~krI~LSlr 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLG--NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEECCCEEEEEEC--CCCEEEEEHHHHCCCCCCCCHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 988989999999988887999908--9947999989930460138175168999999999999888998988619
No 47
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.67 E-value=2.9e-16 Score=115.85 Aligned_cols=69 Identities=29% Similarity=0.401 Sum_probs=40.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|++++|+|+++.+||+||++. +|++||+|.|++++.++.++++.|++||.++++|+++| +++|+.||+|
T Consensus 1 G~vv~G~V~~I~~fGaFV~l~--~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id-~~~ri~LS~K 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCEEECCC
T ss_conf 999999999998538999968--99889999698345655798891789999999999999-9996680159
No 48
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.67 E-value=1.3e-16 Score=118.04 Aligned_cols=73 Identities=40% Similarity=0.803 Sum_probs=47.8
Q ss_pred CCEEEEEEEEEECCCCEEEEC----CCEEEEEEEECCCC-CCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCC
Q ss_conf 330246788753147177744----83157886420244-4443311332697258999987476527998521555432
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS----GVDGLLHVTDIAWH-RILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNP 272 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~----g~~g~i~~~~ls~~-~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp 272 (576)
|++++|+|+++++||+||+|. +++||+|+|++||. ++.+|++.|++||+++++|+++|. +||+||+|++.+||
T Consensus 1 G~i~~G~V~~i~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~--~ki~LS~K~~~~~~ 78 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQN--GKISLSMKDVDQDT 78 (79)
T ss_pred CCEEEEEEEEEEEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEEC--CEEEEEEEECCCCC
T ss_conf 9999999989975339999967889806789956815755558988936799999999999869--98887226134679
No 49
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.67 E-value=9.1e-17 Score=118.89 Aligned_cols=68 Identities=44% Similarity=0.808 Sum_probs=39.5
Q ss_pred CCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 330246788753147177744-831578864202444443311332697258999987476527998521
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
|++++|+|+++++||+||+++ |++||+|+|++||.++.+|++.|++||+++++|+++| +++|++||+|
T Consensus 1 G~vv~G~V~~I~~fGaFV~l~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id-~~~ri~LS~K 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCEEECCC
T ss_conf 99999999999853899996899889999698345655798891789999999999999-9996680159
No 50
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=5.1e-17 Score=120.41 Aligned_cols=78 Identities=37% Similarity=0.705 Sum_probs=62.5
Q ss_pred CCCCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCC
Q ss_conf 122233024678875314717774-4831578864202444443311332697258999987476527998521555432
Q gi|254780456|r 194 KLEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNP 272 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp 272 (576)
++++|++++|+|++|++||+||+| +|-+||||+|++++..+.++.+.+++||+|.|+|+++|. +++++||+|.+.+.|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~p 80 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEP 80 (129)
T ss_pred CCCCCCEEEEEEEEEEECCEEEEECCCCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECC-CCCCCEEHHHHHHCC
T ss_conf 7534646788897567433489823997314883575443677399884278879999972146-897033568766474
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=99.66 E-value=1.5e-16 Score=117.56 Aligned_cols=72 Identities=21% Similarity=0.321 Sum_probs=41.3
Q ss_pred CCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 222330246788753147177744-831578864202444443311332697258999987476527998521
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
+++|++++|+|+++++||+||+++ +++|++|++|++|++..+|.+.|++||.++|+|+++|.+++||+||+|
T Consensus 1 lkvG~~l~G~Vt~V~~~g~fV~L~~~~~Glvhisel~dd~~~~~~~~~~~g~~V~v~Vl~VD~~~krI~LSlr 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9889899999999888879999089947999989930460138175168999999999999888998988619
No 52
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.66 E-value=1.4e-16 Score=117.78 Aligned_cols=67 Identities=60% Similarity=1.137 Sum_probs=41.7
Q ss_pred CCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEE
Q ss_conf 2330246788753147177744831578864202444443311332697258999987476527998
Q gi|254780456|r 197 EGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISL 263 (576)
Q Consensus 197 ~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l 263 (576)
.|++++|+|+++++||+||+++|++||+|++++||.++.+|.+.|++||+++|+|+++|++++||+|
T Consensus 1 eG~iv~g~V~~i~~fG~FV~l~gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~~k~rIsL 67 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECC
T ss_conf 9999999999995638899979989999843646666689889147999999999999999798649
No 53
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.66 E-value=1.7e-16 Score=117.30 Aligned_cols=68 Identities=25% Similarity=0.326 Sum_probs=34.8
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 9879999999708908999617798499999747182121042011068987999999970576869987
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
|++++|+|+++++||+||++. ++++||+|.|++++.+..++.+.|++||.|+|+|+++|++++||.||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~--~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~e~~ri~LS 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG--VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEECEEEEEEEC--CCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 999999999996528999914--99789998189767876798685799999999999998999988779
No 54
>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=99.65 E-value=5.3e-16 Score=114.25 Aligned_cols=68 Identities=28% Similarity=0.499 Sum_probs=58.4
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 9879999999708908999617798499999747182121042011068987999999970576869987
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
|+++.|+|++++++|+||+++ .+++|++|.|+||+.|++++.+.|++||.|+++|+++|++++||.||
T Consensus 1 G~~v~G~V~~i~~~G~FV~l~--~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~ri~LS 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLG--RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEECCCCEEEEEC--CCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 999899999803640799917--99679999599172356499891799999999999982875867359
No 55
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.65 E-value=5.7e-16 Score=114.06 Aligned_cols=67 Identities=49% Similarity=0.846 Sum_probs=38.2
Q ss_pred CCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 330246788753147177744-8315788642024444433113326972589999874765279985
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
|++++|+|+++++||+||+++ +++||+|++++||.++.+|++.|++||+++|+|+++|++++||+||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~e~~ri~LS 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEECEEEEEEECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 99999999999652899991499789998189767876798685799999999999998999988779
No 56
>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=99.65 E-value=2.8e-16 Score=115.98 Aligned_cols=68 Identities=50% Similarity=0.966 Sum_probs=30.8
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCC-CCCCCCEEECCCCEEEEEEEEECCCCCEEEE
Q ss_conf 22330246788753147177744-83157886420244-4443311332697258999987476527998
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWH-RILHPSKVLSIGQQVKVKIIRINQETHRISL 263 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~-~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l 263 (576)
++|++++|+|+++++||+||++. |++||+|+|+|||. +..+|++.|++||+++++|+++|++++||+|
T Consensus 2 ~~G~~v~G~V~~It~fG~FV~i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~~rIsL 71 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECC
T ss_conf 8899999999899476239996699389999766316546679636038999999999999599799538
No 57
>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=99.64 E-value=2.5e-16 Score=116.28 Aligned_cols=67 Identities=39% Similarity=0.604 Sum_probs=53.9
Q ss_pred CCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 330246788753147177744-8315788642024444433113326972589999874765279985
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
|++++|+|+++++||+||+++ +++|++|+++|||.++.+|++.|++||.|+++|+++|++++||.||
T Consensus 1 G~~v~G~V~~i~~~G~FV~l~~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~ri~LS 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEECCCCEEEEECCCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 99989999980364079991799679999599172356499891799999999999982875867359
No 58
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.63 E-value=2.7e-13 Score=97.85 Aligned_cols=213 Identities=24% Similarity=0.253 Sum_probs=151.8
Q ss_pred CCCCCEEEEEEEEECCCEEEEEECCCC-EEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCC
Q ss_conf 048966589999815966999851420-0000011110111355742100378457999998621550478752034543
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDYGVFVELQSGI-EGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALIN 358 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~G~~V~l~~~v-~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~ 358 (576)
..+|+.....|++..++|+|++=+.+= +-++|.++.- .+-..+||.|++-+. .|.+. ++..+.+ .
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~--------~~e~evGdev~vFiY-~D~~~-rl~aTt~----~ 68 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE--------EDELEVGDEVTVFIY-VDSED-RLIATTR----E 68 (287)
T ss_pred CCCCCEEEEEEEEEECEEEEEECCCCCEEEECCCCCCC--------CCCCCCCCEEEEEEE-ECCCC-CEEHEEE----C
T ss_conf 54440689999985221489966888607862566776--------785113768999999-88877-6301010----4
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEE-EEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 21000001222221369999985-01699970688413540055300122001234211123422688521565455320
Q gi|254780456|r 359 PWEEFSKSHPPGTEVEGEVKNKT-DFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISL 437 (576)
Q Consensus 359 p~~~~~~~~~~G~~v~g~V~~v~-~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~L 437 (576)
| ...+|.--.++|+.++ ..|+|++++-.-+.++|.+++.... .-=.++|+.+-|.+- +|..+ |+.-
T Consensus 69 p------~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~-----~~wpq~Gd~l~v~l~-~Dkk~-Ri~g 135 (287)
T COG2996 69 P------KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK-----SLWPQKGDKLLVYLY-VDKKG-RIWG 135 (287)
T ss_pred C------EEEECCEEEEEEEEECCCCCEEEECCCCCCEEEEHHHCCCCC-----CCCCCCCCEEEEEEE-ECCCC-CEEE
T ss_conf 1------374053237999987377515896598700361625364431-----237787989999999-85678-4777
Q ss_pred CHHHHHCCCCCCHHHHCCCC---CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEE
Q ss_conf 11322101110000110047---898799999997089089996177984999997471821210420110689879999
Q gi|254780456|r 438 GVKQLSGSAPDVVDSVSSLR---KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDAC 514 (576)
Q Consensus 438 S~K~l~~~~~~~~~~~~~~~---~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~ 514 (576)
+++- ....+ ....... .++.++|.|.+..+-|.||-. .++..||||.|+. ......|+.+.++
T Consensus 136 ~~a~--~~~l~--~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~--e~~~~GfIh~sEr--------~~~prlG~~l~~r 201 (287)
T COG2996 136 TLAI--EKILE--NLATPAYNNLKNQEVDATVYRLLESGTFVIT--ENGYLGFIHKSER--------FAEPRLGERLTAR 201 (287)
T ss_pred EECC--HHHHH--HCCCCCCHHHHCCEEEEEEEEEECCCEEEEE--CCCEEEEECCHHH--------CCCCCCCCEEEEE
T ss_conf 7331--55787--6177211145437610599998214239997--1876899860660--------0666677557889
Q ss_pred EEEECCCCCEEEEEEHHHHH
Q ss_conf 99970576869987036557
Q gi|254780456|r 515 VVNVSKKDGKVSLSIKALEI 534 (576)
Q Consensus 515 Vi~id~~~~ri~LS~k~~~~ 534 (576)
|+.+.. .+++-||++....
T Consensus 202 Vi~~re-Dg~lnLSl~p~~~ 220 (287)
T COG2996 202 VIGVRE-DGKLNLSLRPRAH 220 (287)
T ss_pred EEEECC-CCEEECCCCCCCH
T ss_conf 999824-8745022156317
No 59
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=99.63 E-value=2.9e-15 Score=109.74 Aligned_cols=73 Identities=36% Similarity=0.536 Sum_probs=49.0
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 478987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
.++|++++|+|.++.++|+||++. +++.||+|.|++++.+..++.+.|++||+++|+|+++|++++|+.||+|
T Consensus 2 ~~~G~iv~G~V~~i~~~G~fV~l~--~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~~~~i~lS~k 74 (74)
T pfam00575 2 PEEGDVVKGTVTRVTKGGAFVDLG--NGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERGRIILSIR 74 (74)
T ss_pred CCCCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 889999999999998775999978--9979999844613655567768305999999999999999999999839
No 60
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.63 E-value=1.4e-15 Score=111.70 Aligned_cols=68 Identities=25% Similarity=0.429 Sum_probs=43.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 98799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
|++++|+|+++.+||+||++. +|++||+|.|++++.++.++.+.|++||.++|+|+++| +++||.||+
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~--~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD-~~~ri~LSr 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEIL--PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCCCCC
T ss_conf 999999999997329999957--99624888689345654698890789999999999999-999720529
No 61
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.62 E-value=5.6e-16 Score=114.11 Aligned_cols=77 Identities=32% Similarity=0.656 Sum_probs=73.4
Q ss_pred CCCCCEEEEEEEEEECCCCEEEE---CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCC
Q ss_conf 22233024678875314717774---483157886420244444331133269725899998747652799852155543
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKN 271 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~---~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~d 271 (576)
-++|++|.|+|+++.+||+||++ +|++||+|++++||.|+.++.+.+++||.+.|+|+.+|+++++|.||+|+.+++
T Consensus 6 Pe~g~~v~~~V~~i~~~Ga~v~l~ey~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~kg~IdLS~k~Vs~~ 85 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPKKGHIDLSLKRVNEH 85 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCCHH
T ss_conf 99998899999999566799993565993167887983467751999851589889999998838788787110449989
No 62
>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=99.62 E-value=1.1e-15 Score=112.39 Aligned_cols=69 Identities=32% Similarity=0.618 Sum_probs=44.0
Q ss_pred CCCCEEEEEEEEEECCCCEEEECC--CEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 223302467887531471777448--3157886420244444331133269725899998747652799852
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLSG--VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGM 265 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~g--~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lsl 265 (576)
++|++++|+|+++++|||||++.| .+||+|+|+|||.|+.+|++.+++||++.++|+++| +++|+.||+
T Consensus 2 evg~i~~G~V~~i~~fGAFV~i~g~~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id-~~~ki~LSl 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKLSL 72 (73)
T ss_pred CCCCEEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCEEEEC
T ss_conf 78869999998997532399908988435599560541202899995579999999999886-899889841
No 63
>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=99.62 E-value=8.8e-16 Score=112.90 Aligned_cols=66 Identities=48% Similarity=0.992 Sum_probs=36.8
Q ss_pred CCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCC-CCCCCCEEECCCCEEEEEEEEECCCCCEEEE
Q ss_conf 330246788753147177744-83157886420244-4443311332697258999987476527998
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWH-RILHPSKVLSIGQQVKVKIIRINQETHRISL 263 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~-~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l 263 (576)
|++++|+|+++++||+||++. |++||+|++||||. ++.+|.+.|++||+++|+|+++|.+++||+|
T Consensus 1 G~~v~G~V~~i~~fG~FV~l~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~risL 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEECC
T ss_conf 99999999999131899997699659999488245666679768258999999999999798688638
No 64
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.61 E-value=6.6e-16 Score=113.67 Aligned_cols=66 Identities=41% Similarity=0.814 Sum_probs=36.4
Q ss_pred CCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 33024678875314717774-48315788642024444433113326972589999874765279985
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
|++++|+|+++++||+||++ +|++||+|+|++||+++.+|++.|++||+++|+|+++| +++||+||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD-~~~ri~LS 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCCCC
T ss_conf 99999999999732999995799624888689345654698890789999999999999-99972052
No 65
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=99.61 E-value=2.2e-15 Score=110.52 Aligned_cols=71 Identities=41% Similarity=0.816 Sum_probs=34.5
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 22330246788753147177744-831578864202444443311332697258999987476527998521
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
++|++++|+|.++.++|+||+++ +++||+|.+++||.+..+|.+.|++||+++|+|+++|++++++.||+|
T Consensus 3 ~~G~iv~G~V~~i~~~G~fV~l~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~~~~i~lS~k 74 (74)
T pfam00575 3 EEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERGRIILSIR 74 (74)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 899999999999987759999789979999844613655567768305999999999999999999999839
No 66
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.59 E-value=1.1e-14 Score=106.33 Aligned_cols=76 Identities=37% Similarity=0.594 Sum_probs=54.0
Q ss_pred CCCEEEEEEEEECCCEEEEEEC--CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCC
Q ss_conf 8966589999815966999851--4200000011110111355742100378457999998621550478752034543
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVELQ--SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALIN 358 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l~--~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~ 358 (576)
+|+++-|+|.++.+||+||.|. +|++||+|+||+| ..-..+..+.+++||.+-|+|+++|+.++.+.||+|+..++
T Consensus 11 eGEiVv~tV~~V~~~GA~v~L~EY~g~Eg~ihiSEva-s~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~ 88 (269)
T COG1093 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVA-SGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 (269)
T ss_pred CCCEEEEEEEEEECCCCEEEEECCCCEEEEEEHHHHH-HHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEHHHCCHH
T ss_conf 8868999999860464279842059962267789987-78998899986169869999988868777476254338787
No 67
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.58 E-value=7.6e-15 Score=107.23 Aligned_cols=66 Identities=30% Similarity=0.450 Sum_probs=38.1
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSL 527 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~L 527 (576)
|++++|+|+++++||+||++ .|++||||.|++|+.+..++.+.|++||.++|+|+++|++++||+|
T Consensus 2 G~iv~g~V~~i~~fG~FV~l---~gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~~k~rIsL 67 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCEEEEEEEEEECCEEEEEE---CCEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECC
T ss_conf 99999999999563889997---9989999843646666689889147999999999999999798649
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.58 E-value=9.4e-15 Score=106.69 Aligned_cols=79 Identities=20% Similarity=0.355 Sum_probs=73.1
Q ss_pred HHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHH
Q ss_conf 11004789879999999708908999617798499999747182121042011068987999999970576869987036
Q gi|254780456|r 452 SVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKA 531 (576)
Q Consensus 452 ~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~ 531 (576)
...+.++|++++|+|+++.+||+||++ .+|.+||+|+|+|++.++++.++.+++||.|+++++++|+ ++|+.||+|+
T Consensus 615 i~~~~evG~iy~g~V~~i~~fGafve~--~pg~~GLlHiSel~~~rv~~v~d~~~~Gd~i~Vk~~~id~-~Gri~Lsrk~ 691 (694)
T PRK11824 615 ITAEPEVGEIYEGKVVRIVDFGAFVEI--LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRKA 691 (694)
T ss_pred HCCCCCCCCEEEEEEEEEEECEEEEEE--CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEHHH
T ss_conf 457685897799999999844189996--7998068880024652346864511689889999998989-9986666477
Q ss_pred HH
Q ss_conf 55
Q gi|254780456|r 532 LE 533 (576)
Q Consensus 532 ~~ 533 (576)
+.
T Consensus 692 ~l 693 (694)
T PRK11824 692 VL 693 (694)
T ss_pred HH
T ss_conf 51
No 69
>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=99.57 E-value=8.4e-15 Score=106.98 Aligned_cols=71 Identities=25% Similarity=0.248 Sum_probs=52.9
Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 7898799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 457 ~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
++|++++|+|+++++|||||++. ..+.+||+|+|+|++.++.++++.+++||.|+++|+++| +++|+.||+
T Consensus 2 evg~i~~G~V~~i~~fGAFV~i~-g~~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id-~~~ki~LSl 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIP-GCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKLSL 72 (73)
T ss_pred CCCCEEEEEEEEEEECCEEEEEC-CCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCEEEEC
T ss_conf 78869999998997532399908-988435599560541202899995579999999999886-899889841
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.57 E-value=3.8e-15 Score=109.07 Aligned_cols=79 Identities=34% Similarity=0.477 Sum_probs=70.6
Q ss_pred CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHH
Q ss_conf 00012222213699999850169997068841354005530012200123421112342268852156545532011322
Q gi|254780456|r 363 FSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQL 442 (576)
Q Consensus 363 ~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l 442 (576)
+....++|.+.+|+|+++.++|+||++.+|.+|++|+|+++|. ...++.+.+++||.++|+++++|+ .+|+.||+|.+
T Consensus 615 i~~~~evG~iy~g~V~~i~~fGafve~~pg~~GLlHiSel~~~-rv~~v~d~~~~Gd~i~Vk~~~id~-~Gri~Lsrk~~ 692 (694)
T PRK11824 615 ITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIANE-RVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRKAV 692 (694)
T ss_pred HCCCCCCCCEEEEEEEEEEECEEEEEECCCCEEEEEHHHCCCC-CCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEHHHH
T ss_conf 4576858977999999998441899967998068880024652-346864511689889999998989-99866664775
Q ss_pred H
Q ss_conf 1
Q gi|254780456|r 443 S 443 (576)
Q Consensus 443 ~ 443 (576)
.
T Consensus 693 l 693 (694)
T PRK11824 693 L 693 (694)
T ss_pred H
T ss_conf 1
No 71
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.56 E-value=9.5e-13 Score=94.53 Aligned_cols=208 Identities=18% Similarity=0.242 Sum_probs=93.4
Q ss_pred HCCCEEEEEEEEEECCCEEEEECCC--HHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEECCCCCCCCCCCC
Q ss_conf 2897699999999679559997440--20000011234543334555553023111335432331122121112222212
Q gi|254780456|r 109 RAGERIEGVIFNQVKGGMTVDLNGE--VAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAE 186 (576)
Q Consensus 109 ~~g~~v~g~V~~~~k~G~~V~i~gi--~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~~~~ 186 (576)
..|+.....|.+..+.||++.-+.. .-|+|.+..... ...+|+.+.+-|- .|.+. ++.++-+
T Consensus 4 ~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-----e~evGdev~vFiY-~D~~~-rl~aTt~--------- 67 (287)
T COG2996 4 KIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-----ELEVGDEVTVFIY-VDSED-RLIATTR--------- 67 (287)
T ss_pred CCCCEEEEEEEEEECEEEEEECCCCCEEEECCCCCCCCC-----CCCCCCEEEEEEE-ECCCC-CEEHEEE---------
T ss_conf 444068999998522148996688860786256677678-----5113768999999-88877-6301010---------
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEE-CCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 11100011222330246788753-147177744-8315788642024444433113326972589999874765279985
Q gi|254780456|r 187 QRSEIVQKLEEGQVIEGTVKNIT-DYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 187 ~~~~~~~~l~~G~~v~g~V~~i~-~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
.-.+.+|.-=.+.|..+. +.|+|++.| .-+-++|.++++..+ +--.++||++-+++. +|... ||.-.
T Consensus 68 -----~p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~wpq~Gd~l~v~l~-~Dkk~-Ri~g~ 136 (287)
T COG2996 68 -----EPKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SLWPQKGDKLLVYLY-VDKKG-RIWGT 136 (287)
T ss_pred -----CCEEEECCEEEEEEEEECCCCCEEEECCCCCCEEEEHHHCCCCC----CCCCCCCCEEEEEEE-ECCCC-CEEEE
T ss_conf -----41374053237999987377515896598700361625364431----237787989999999-85678-47777
Q ss_pred ECCCCCCCCCCCCCCCC---CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEE
Q ss_conf 21555432100000004---896658999981596699985142000000111101113557421003784579999986
Q gi|254780456|r 265 MKQLEKNPWDDVQDKYV---EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEV 341 (576)
Q Consensus 265 lK~l~~dp~~~~~~~~~---~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~i 341 (576)
++ ...++........ .++.+.|+|-+....|.||-++++.-||||.||+. ...+.|+.++++|+.+
T Consensus 137 ~a--~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~---------~~prlG~~l~~rVi~~ 205 (287)
T COG2996 137 LA--IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF---------AEPRLGERLTARVIGV 205 (287)
T ss_pred EC--CHHHHHHCCCCCCHHHHCCEEEEEEEEEECCCEEEEECCCEEEEECCHHHC---------CCCCCCCEEEEEEEEE
T ss_conf 33--155787617721114543761059999821423999718768998606600---------6666775578899998
Q ss_pred ECCCCEEEEEEECC
Q ss_conf 21550478752034
Q gi|254780456|r 342 NPARKRISLGLKQA 355 (576)
Q Consensus 342 d~~~~~i~lS~k~~ 355 (576)
.+ .++|.||+++.
T Consensus 206 re-Dg~lnLSl~p~ 218 (287)
T COG2996 206 RE-DGKLNLSLRPR 218 (287)
T ss_pred CC-CCEEECCCCCC
T ss_conf 24-87450221563
No 72
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.55 E-value=3.8e-15 Score=109.04 Aligned_cols=67 Identities=48% Similarity=0.848 Sum_probs=62.8
Q ss_pred CCEEEEEEEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEECCC
Q ss_conf 9769999999967955999744020000011234543334555553023111335432331122121
Q gi|254780456|r 111 GERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRR 177 (576)
Q Consensus 111 g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k 177 (576)
|++++|+|++.++||++|++.|++||||+||++.++.+++..++|++++|+|+++|++++++++|||
T Consensus 1 g~~v~g~I~~~~kGG~~v~~~gv~~FiP~Sq~~~~~~~~~~~~vG~~i~~~Ii~~d~~~~~ivvSrk 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCCEEEEECCEEEEEECHHCCCCCCCCHHHHCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9999999999985719999999999988025255456896897899899999999278899999879
No 73
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.48 E-value=1.1e-13 Score=100.23 Aligned_cols=86 Identities=22% Similarity=0.268 Sum_probs=78.1
Q ss_pred HHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 00110047898799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 450 VDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 450 ~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
+..++++++|+++.|.|+++.++|+||+++ ...+|+||+|++++.|+.+|.+.+++|+.|+++|+++|..++||.||+
T Consensus 650 v~~i~dLk~Gm~leg~Vrnv~~fgafVdIg--v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm 727 (780)
T COG2183 650 VESITDLKPGMILEGTVRNVVDFGAFVDIG--VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM 727 (780)
T ss_pred HHHHHHCCCCCEEEEEEEEEEECCCEEEEC--CCCCEEEEHHHHHHHHCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEE
T ss_conf 341765067888889988754316468945--666606668985433307958840158779999999851457232476
Q ss_pred HHHHHHHH
Q ss_conf 36557777
Q gi|254780456|r 530 KALEIAEE 537 (576)
Q Consensus 530 k~~~~~~~ 537 (576)
+..+....
T Consensus 728 r~~~~~~~ 735 (780)
T COG2183 728 RLDEEEGK 735 (780)
T ss_pred ECCCCCCC
T ss_conf 34677665
No 74
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.48 E-value=6.5e-14 Score=101.61 Aligned_cols=77 Identities=34% Similarity=0.604 Sum_probs=67.2
Q ss_pred CCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHH
Q ss_conf 012222213699999850169997068841354005530012200123421112342268852156545532011322
Q gi|254780456|r 365 KSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQL 442 (576)
Q Consensus 365 ~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l 442 (576)
+++++|+++.|.|.++.++|+||+++-+.+|++|+|.+| +....+|.+.+++||.++++|+++|..++||.|||+.-
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls-~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~ 730 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS-DKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD 730 (780)
T ss_pred HHCCCCCEEEEEEEEEEECCCEEEECCCCCEEEEHHHHH-HHHCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEEECC
T ss_conf 650678888899887543164689456666066689854-33307958840158779999999851457232476346
No 75
>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=99.42 E-value=1.2e-12 Score=94.01 Aligned_cols=66 Identities=47% Similarity=0.700 Sum_probs=31.4
Q ss_pred CCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCC---CCCCCCCCCEEEEEEEEEECCCCEEEEEH
Q ss_conf 8779999999819989999479603678997505664---35563789879999999747998599968
Q gi|254780456|r 27 NCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKG---QYTPIKVGDEVEVYVERTENSFGEAVFSR 92 (576)
Q Consensus 27 G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~---~~~~~kvGd~i~v~V~~~~~~~g~i~lS~ 92 (576)
|++|+|+|++++++++|||+|++++|+||++|+++.. ..+.+++||+++|+|++.+++.|++.||+
T Consensus 1 G~iV~G~V~~i~~~gv~Vdig~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g~i~LS~ 69 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 998999999997886999968985026899994533238974712699999999999999999799850
No 76
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.42 E-value=2.4e-13 Score=98.14 Aligned_cols=72 Identities=18% Similarity=0.372 Sum_probs=66.3
Q ss_pred HCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 100478987999999970890899961779849999974718212104201106898799999997057686998
Q gi|254780456|r 453 VSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSL 527 (576)
Q Consensus 453 ~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~L 527 (576)
..+.++|++++|+|+++.+||+||++ .+|.+||+|+|+|++.++++.++.+++||.|+++++++|. ++|+.|
T Consensus 613 ~~~~evG~~y~g~V~~i~~fGafve~--~pg~~GLlHiSel~~~rv~~v~dv~~~Gd~i~Vk~~~id~-~Gri~L 684 (684)
T TIGR03591 613 TAEPEVGKIYEGKVVRIMDFGAFVEI--LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred CCCCCCCCEEEEEEEEEEECEEEEEE--CCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCCCC
T ss_conf 16685897799999999844089996--7998147870013653446864521689889999997889-998285
No 77
>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=99.42 E-value=4.3e-13 Score=96.62 Aligned_cols=70 Identities=26% Similarity=0.397 Sum_probs=41.4
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|++|+|+|.++.++|+||+++ .+.+|++|.+++++++..++.+.|++|+.++|+|+++|.+++++.||+|
T Consensus 1 G~iV~G~V~~i~~~gv~Vdig--~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g~i~LS~k 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG--YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEECCEEEEEEC--CCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 998999999997886999968--9850268999945332389747126999999999999999997998509
No 78
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.38 E-value=1.5e-12 Score=93.41 Aligned_cols=73 Identities=36% Similarity=0.503 Sum_probs=64.4
Q ss_pred CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 000122222136999998501699970688413540055300122001234211123422688521565455320
Q gi|254780456|r 363 FSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISL 437 (576)
Q Consensus 363 ~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~L 437 (576)
+....++|.+..|+|+++.++|+||++.+|.+|++|+|+++| .+..++.+.+++||.++++++++|+ .+|+.|
T Consensus 612 ~~~~~evG~~y~g~V~~i~~fGafve~~pg~~GLlHiSel~~-~rv~~v~dv~~~Gd~i~Vk~~~id~-~Gri~L 684 (684)
T TIGR03591 612 ITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIAN-ERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred HCCCCCCCCEEEEEEEEEEECEEEEEECCCCCEEEEEECCCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCCCC
T ss_conf 516685897799999999844089996799814787001365-3446864521689889999997889-998285
No 79
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=99.37 E-value=1.9e-12 Score=92.74 Aligned_cols=78 Identities=32% Similarity=0.590 Sum_probs=49.6
Q ss_pred CEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCC-----------CCCCEEECCCCEEEEEEEEECCCCC-----EEE
Q ss_conf 302467887531471777448315788642024444-----------4331133269725899998747652-----799
Q gi|254780456|r 199 QVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRI-----------LHPSKVLSIGQQVKVKIIRINQETH-----RIS 262 (576)
Q Consensus 199 ~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~-----------~~~~~~~~~G~~v~~~Vl~~d~~~~-----~i~ 262 (576)
++++|+|.++++||+||+++.++||+|+++|+++++ ....+.|++||.|++||+++|.+.+ +|.
T Consensus 1 Ev~eG~Vs~Vt~fG~FV~L~~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~Ig 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEECCEEEEECCCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEEE
T ss_conf 97999999588256699932810689936757843998124468985127869847999999999980620676764665
Q ss_pred EEECCCCCCCCCCC
Q ss_conf 85215554321000
Q gi|254780456|r 263 LGMKQLEKNPWDDV 276 (576)
Q Consensus 263 lslK~l~~dp~~~~ 276 (576)
||+||.-.-+|+.+
T Consensus 81 Ltmrqp~lGk~ew~ 94 (99)
T cd04460 81 LTMRQPGLGKLEWI 94 (99)
T ss_pred ECCCCCCCCCHHHH
T ss_conf 02247889874564
No 80
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.36 E-value=6.4e-13 Score=95.59 Aligned_cols=77 Identities=31% Similarity=0.667 Sum_probs=72.2
Q ss_pred CCCCCEEEEEEEEEECCCCEEEE---CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCC
Q ss_conf 22233024678875314717774---483157886420244444331133269725899998747652799852155543
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKN 271 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~---~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~d 271 (576)
-.+|++|-|+|+.|.+||+||.| +|++||+|+|++|-.++.++.+..++||++-|+||.+|+..+.|.||+|...++
T Consensus 9 PeeGEiVv~tV~~V~~~GA~v~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~ 88 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 (269)
T ss_pred CCCCCEEEEEEEEEECCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEHHHCCHH
T ss_conf 98886899999986046427984205996226778998778998899986169869999988868777476254338787
No 81
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=99.36 E-value=2.3e-12 Score=92.16 Aligned_cols=69 Identities=29% Similarity=0.445 Sum_probs=37.3
Q ss_pred CCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 21000000048966589999815966999851420000001111011135574210037845799999862155047875
Q gi|254780456|r 272 PWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLG 351 (576)
Q Consensus 272 p~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS 351 (576)
||-.+. ++++|+++.|+|+++++||+||++.++.+||+|+|++++ .|++||.+.++|++++ ++++|.|+
T Consensus 7 ~~C~~~-dlevG~~y~G~V~~v~~fGaFV~l~~~~~GLiHiS~l~~---------~~~vGD~V~VkV~~I~-~~Gki~L~ 75 (77)
T cd04473 7 PACTME-DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR---------DYEVGDEVIVQVTDIP-ENGNIDLI 75 (77)
T ss_pred CCCCCC-CCCCCCEEEEEEEEEEECCEEEECCCCCEEEEEEHHCCC---------CCCCCCEEEEEEEEEC-CCCCEEEE
T ss_conf 998730-352399999999889662889992699879689316668---------7899999999999999-99979318
No 82
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.34 E-value=1.1e-11 Score=88.15 Aligned_cols=72 Identities=31% Similarity=0.415 Sum_probs=50.5
Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 78987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 457 ~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
++|+++.|+|.++.++|+||+++ +++.||+|.+++++.+..++...|++|+.++|+|++++..++++.||+|
T Consensus 1 ~~G~iv~g~V~~v~~~g~~v~i~--~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~k 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG--NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 99989999999997873999976--9989999807505555478468363898999999999999999999859
No 83
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.32 E-value=1e-11 Score=88.34 Aligned_cols=71 Identities=20% Similarity=0.287 Sum_probs=56.1
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCH---HHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 47898799999997089089996177984999997471821210420---11068987999999970576869987
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDP---GRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~---~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
+++||++.|+|+++.+.|+||.++ ..++|+++.+++|+.++.+++ +.|.+|+.+.|+|+.+|++++|+.||
T Consensus 1 ikeGq~vRGyVk~v~~~GvFv~Ls--~~v~grv~~~nls~~~v~dp~~~~~~fp~GkLv~~kVlsvd~~~~~VELS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLS--SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEECCCCCEEEEEC--CCEEEEEEEECCCHHHHCCHHHHHCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 998879899999826873999956--87489999700362120682688614899989999999986776848609
No 84
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=99.31 E-value=1.4e-11 Score=87.48 Aligned_cols=76 Identities=22% Similarity=0.519 Sum_probs=40.2
Q ss_pred CCCCEEEEEEEEEECCCCEEEE---CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCC
Q ss_conf 2233024678875314717774---483157886420244444331133269725899998747652799852155543
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKN 271 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~---~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~d 271 (576)
++|++|-++|+.|.++|+||.+ ++++|++|.+++|..|+.++.+..++|+..-|+|+.+|++++.|-||+|..+++
T Consensus 16 e~~e~V~~~V~~i~~~gayV~LlEY~~~egmI~~sEls~rrir~I~k~ikvG~~~v~~VlRVD~~KGyIDLS~rrVs~e 94 (324)
T PTZ00248 16 EENDLVMVKVNRIEEMGVYVSLLEYDDIEGMILLSELSKRRIRSINKLVKVGRHEVVLVLRVDKDKGYIDLSKRRVTPE 94 (324)
T ss_pred CCCCEEEEEEEEEECCEEEEEEEEECCCCCEEEHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCEECHHHCCCHH
T ss_conf 9888899999998025689998400882221468886378886378871068778999999858778244415029988
No 85
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.30 E-value=2.1e-11 Score=86.45 Aligned_cols=67 Identities=18% Similarity=0.388 Sum_probs=62.5
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 987999999970890899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|++++|+|++..+.|++|.+ .|++||+|.||++..+.+++.++ +|++++++|+++|++++++.+|+|
T Consensus 1 g~~v~g~I~~~~kGG~~v~~---~gv~~FiP~Sq~~~~~~~~~~~~--vG~~i~~~Ii~~d~~~~~ivvSrk 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI---EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCCEEEEE---CCEEEEEECHHCCCCCCCCHHHH--CCCEEEEEEEEEECCCCEEEEECC
T ss_conf 99999999999857199999---99999988025255456896897--899899999999278899999879
No 86
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=99.30 E-value=5.7e-12 Score=89.80 Aligned_cols=63 Identities=29% Similarity=0.470 Sum_probs=24.0
Q ss_pred EEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 99999970890899961779849999974718212104201106898799999997057686998
Q gi|254780456|r 463 SCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSL 527 (576)
Q Consensus 463 ~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~L 527 (576)
+|+|.++.++|+||++. +|++||+|.|++++.+..++.+.|++||.|+|+|+++|++++|+.|
T Consensus 2 ~G~V~~i~~~G~fV~~~--~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~~~~~i~L 64 (65)
T cd00164 2 TGKVVSITKFGVFVELE--DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred EEEEEEEECCEEEEEEC--CCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEECCCCEEEC
T ss_conf 89999997845999989--8717889888916765359510985999999999999899998976
No 87
>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=99.29 E-value=1.1e-11 Score=88.09 Aligned_cols=70 Identities=30% Similarity=0.526 Sum_probs=60.1
Q ss_pred CCCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCC---EEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 222330246788753147177744-83157886420244444331---13326972589999874765279985
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPS---KVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~---~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
+++|+++.|.|+++.+.|+||.++ .++|+++.+++|+..+.+|. +.|.+|+.+.+||+++|++++++.||
T Consensus 1 ikeGq~vRGyVk~v~~~GvFv~Ls~~v~grv~~~nls~~~v~dp~~~~~~fp~GkLv~~kVlsvd~~~~~VELS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEECCCCCEEEEECCCEEEEEEEECCCHHHHCCHHHHHCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 99887989999982687399995687489999700362120682688614899989999999986776848609
No 88
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=99.28 E-value=1.7e-11 Score=86.90 Aligned_cols=63 Identities=41% Similarity=0.812 Sum_probs=32.5
Q ss_pred EEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 46788753147177744-8315788642024444433113326972589999874765279985
Q gi|254780456|r 202 EGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 202 ~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
+|+|+++.++|+||+++ |++||+|.++++|.+..+|.+.|++||.+.|+|+++|++++++.||
T Consensus 2 ~G~V~~i~~~G~fV~~~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~~~~~i~LS 65 (65)
T cd00164 2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred EEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEECCCCEEECC
T ss_conf 8999999784599998987178898889167653595109859999999999998999989769
No 89
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.27 E-value=1.8e-11 Score=86.74 Aligned_cols=71 Identities=42% Similarity=0.705 Sum_probs=40.9
Q ss_pred CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEE
Q ss_conf 896658999981596699985142000000111101113557421003784579999986215504787520
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLK 353 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k 353 (576)
+|+++.|+|+++.++|+||++++++.||+|.++++|. ...++.+.|++||.++|+|+.+++.++++.||+|
T Consensus 2 ~G~iv~g~V~~v~~~g~~v~i~~~~~g~l~~~~l~~~-~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~k 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCC-CCCCHHHEECCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 9989999999997873999976998999980750555-5478468363898999999999999999999859
No 90
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=99.26 E-value=2.2e-11 Score=86.29 Aligned_cols=73 Identities=22% Similarity=0.269 Sum_probs=63.6
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHH-HHCC----------CHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 47898799999997089089996177984999997471821-2104----------201106898799999997057686
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRD-RVDQ----------DPGRFSKGQIVDACVVNVSKKDGK 524 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~-~~~~----------~~~~~~vG~~v~~~Vi~id~~~~r 524 (576)
-++|+...|.|++|+.||+||+|.+ ..++||||+|.|.++ |.-+ -...|+.||.|+++|+++|.+.++
T Consensus 670 ~~iG~~f~G~Is~VT~FG~FVeL~~-~~ieGLVhI~~L~dDYY~Fd~~~~~L~G~R~gk~frLGD~v~V~V~~ad~~~~~ 748 (755)
T TIGR02063 670 EKIGEEFEGVISGVTSFGLFVELEN-NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK 748 (755)
T ss_pred HCCCCEEEEEEEEEEEEEEEEEECC-CEEEEEEECCCCCCCCCEECCCCCEEEEECCCCEEECCCEEEEEEEEECCCCCE
T ss_conf 5079688779975662013897367-411102632789885630752207886432687372487489999996103366
Q ss_pred EEEEE
Q ss_conf 99870
Q gi|254780456|r 525 VSLSI 529 (576)
Q Consensus 525 i~LS~ 529 (576)
|.+.+
T Consensus 749 idF~L 753 (755)
T TIGR02063 749 IDFEL 753 (755)
T ss_pred EEEEE
T ss_conf 98997
No 91
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=99.24 E-value=4.2e-11 Score=84.57 Aligned_cols=65 Identities=26% Similarity=0.416 Sum_probs=38.9
Q ss_pred HCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 1004789879999999708908999617798499999747182121042011068987999999970576869987
Q gi|254780456|r 453 VSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 453 ~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
++++++|++++|+|+++.+||+||++. ++.+||+|+|+++.. |++|+.|.++|+++| +++||.|+
T Consensus 11 ~~dlevG~~y~G~V~~v~~fGaFV~l~--~~~~GLiHiS~l~~~--------~~vGD~V~VkV~~I~-~~Gki~L~ 75 (77)
T cd04473 11 MEDLEVGKLYKGKVNGVAKYGVFVDLN--DHVRGLIHRSNLLRD--------YEVGDEVIVQVTDIP-ENGNIDLI 75 (77)
T ss_pred CCCCCCCCEEEEEEEEEEECCEEEECC--CCCEEEEEEHHCCCC--------CCCCCEEEEEEEEEC-CCCCEEEE
T ss_conf 303523999999998896628899926--998796893166687--------899999999999999-99979318
No 92
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=99.24 E-value=3.6e-11 Score=84.96 Aligned_cols=68 Identities=26% Similarity=0.407 Sum_probs=30.3
Q ss_pred EEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHH-----------CCCHHHCCCCCEEEEEEEEECCCCC-----E
Q ss_conf 79999999708908999617798499999747182121-----------0420110689879999999705768-----6
Q gi|254780456|r 461 VVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRV-----------DQDPGRFSKGQIVDACVVNVSKKDG-----K 524 (576)
Q Consensus 461 iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~-----------~~~~~~~~vG~~v~~~Vi~id~~~~-----r 524 (576)
+++|.|+++++||+||++. .++||+|+|+|.+++. +.....|+.||.|+++|+.+|.+.+ +
T Consensus 2 v~eG~Vs~Vt~fG~FV~L~---~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~ 78 (99)
T cd04460 2 VVEGEVVEVVDFGAFVRIG---PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred EEEEEEEEEEECCEEEEEC---CCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCE
T ss_conf 7999999588256699932---8106899367578439981244689851278698479999999999806206767646
Q ss_pred EEEEEHH
Q ss_conf 9987036
Q gi|254780456|r 525 VSLSIKA 531 (576)
Q Consensus 525 i~LS~k~ 531 (576)
|.||+|+
T Consensus 79 IgLtmrq 85 (99)
T cd04460 79 IGLTMRQ 85 (99)
T ss_pred EEECCCC
T ss_conf 6502247
No 93
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.23 E-value=2.1e-11 Score=86.35 Aligned_cols=62 Identities=21% Similarity=0.457 Sum_probs=44.4
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCCC--CCCCCCCCCCCEECCCCEEEEEEEEEECCC
Q ss_conf 966589999815966999851420000001111--011135574210037845799999862155
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI--SWTKKNIHPSKILSVGQQVEVVILEVNPAR 345 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sel--s~~~~~~~~~~~~~~G~~v~~~Vl~id~~~ 345 (576)
|++++|+|+++.++|++|+|++++.|+||+||+ +| ....+|.+.|++||.|+|+|+++...+
T Consensus 1 G~vv~g~V~sik~~~l~V~L~d~~~GrVhiSei~D~~-~~~k~P~~~~k~Gq~V~~rViG~~d~k 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW-PDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCC-CCCCCHHHHCCCCCEEEEEEEEEECCC
T ss_conf 9779999999946708999689957789845521355-555694685689999999999765462
No 94
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=3.7e-11 Score=84.89 Aligned_cols=103 Identities=22% Similarity=0.403 Sum_probs=80.4
Q ss_pred ECCCCCCCCCCCHHH--HHCCCCCCH-HHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHH
Q ss_conf 215654553201132--210111000-01100478987999999970890899961779849999974718212104201
Q gi|254780456|r 427 DIDVGKERISLGVKQ--LSGSAPDVV-DSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPG 503 (576)
Q Consensus 427 ~id~~~~~i~LS~K~--l~~~~~~~~-~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~ 503 (576)
.++ +++++..+... ....+...+ ....++++|+++.|+|+++.+||+||.+. +|-+|++|+|+++..++...++
T Consensus 586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~--~gkdgl~hiS~~~~~rv~kv~d 662 (692)
T COG1185 586 DIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVED 662 (692)
T ss_pred EEC-CCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEC--CCCCEEEEEHHHHHHHHHCCCC
T ss_conf 845-8985899956568889999999998743101528998899986412589833--8962068743533455532045
Q ss_pred HCCCCCEEEEEEEEECCCCCEEEEEEHHHH
Q ss_conf 106898799999997057686998703655
Q gi|254780456|r 504 RFSKGQIVDACVVNVSKKDGKVSLSIKALE 533 (576)
Q Consensus 504 ~~~vG~~v~~~Vi~id~~~~ri~LS~k~~~ 533 (576)
.+++||.+.++++++| +++|+.||++..+
T Consensus 663 vlk~Gd~v~Vkv~~iD-~~Gri~ls~~~~~ 691 (692)
T COG1185 663 VLKEGDEVKVKVIEID-KQGRIRLSIKAVL 691 (692)
T ss_pred EEECCCEEEEEEEEEC-CCCCCCCEEHHCC
T ss_conf 3544865999996336-6677032112104
No 95
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=99.21 E-value=5.8e-11 Score=83.73 Aligned_cols=72 Identities=29% Similarity=0.480 Sum_probs=63.0
Q ss_pred CCCCCEEEEEEEEEEEEEEEEECC-CCEEEEEHHHHHCCCCCHH----------HHHHHCCCCCCEEEEEECCCCCCCCC
Q ss_conf 222213699999850169997068-8413540055300122001----------23421112342268852156545532
Q gi|254780456|r 368 PPGTEVEGEVKNKTDFGLFIGLDE-HLDGMIHLSDLDWNRPGEK----------VIAEYAKGDIVKAVVLDIDVGKERIS 436 (576)
Q Consensus 368 ~~G~~v~g~V~~v~~~g~~V~l~~-~i~g~i~~~dls~~~~~~~----------~~~~~k~G~~i~~~Vl~id~~~~~i~ 436 (576)
++|+.++|.|++||.||+||+|+. .++|+||++.|.+|...-+ -...|+.||.|+++|..+|...++|.
T Consensus 671 ~iG~~f~G~Is~VT~FG~FVeL~~~~ieGLVhI~~L~dDYY~Fd~~~~~L~G~R~gk~frLGD~v~V~V~~ad~~~~~id 750 (755)
T TIGR02063 671 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKID 750 (755)
T ss_pred CCCCEEEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCEECCCCCEEEEECCCCEEECCCEEEEEEEEECCCCCEEE
T ss_conf 07968877997566201389736741110263278988563075220788643268737248748999999610336698
Q ss_pred CCH
Q ss_conf 011
Q gi|254780456|r 437 LGV 439 (576)
Q Consensus 437 LS~ 439 (576)
+.+
T Consensus 751 F~L 753 (755)
T TIGR02063 751 FEL 753 (755)
T ss_pred EEE
T ss_conf 997
No 96
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.20 E-value=2.8e-11 Score=85.61 Aligned_cols=100 Identities=29% Similarity=0.428 Sum_probs=76.6
Q ss_pred EEECCCCEEEEEEECCC--CCCC---CCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHH
Q ss_conf 86215504787520345--4321---000001222221369999985016999706884135400553001220012342
Q gi|254780456|r 340 EVNPARKRISLGLKQAL--INPW---EEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAE 414 (576)
Q Consensus 340 ~id~~~~~i~lS~k~~~--~~p~---~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~ 414 (576)
.++ +.+.+..+..... ..+. ..+.+...+|.+..|+|+++.++|+||++.+|-+|++|+|+++|. ......+.
T Consensus 586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~-rv~kv~dv 663 (692)
T COG1185 586 DIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE-RVEKVEDV 663 (692)
T ss_pred EEC-CCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEECCCCCEEEEEHHHHHH-HHHCCCCE
T ss_conf 845-8985899956568889999999998743101528998899986412589833896206874353345-55320453
Q ss_pred HCCCCCCEEEEEECCCCCCCCCCCHHHH
Q ss_conf 1112342268852156545532011322
Q gi|254780456|r 415 YAKGDIVKAVVLDIDVGKERISLGVKQL 442 (576)
Q Consensus 415 ~k~G~~i~~~Vl~id~~~~~i~LS~K~l 442 (576)
++.||.+.++++.+|. .+++.||++..
T Consensus 664 lk~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 664 LKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred EECCCEEEEEEEEECC-CCCCCCEEHHC
T ss_conf 5448659999963366-67703211210
No 97
>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=99.16 E-value=1.5e-10 Score=81.28 Aligned_cols=70 Identities=26% Similarity=0.420 Sum_probs=35.6
Q ss_pred CCCCCEEEEEEEEEEC-CCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 2223302467887531-47177744-831578864202444443311332697258999987476527998521
Q gi|254780456|r 195 LEEGQVIEGTVKNITD-YGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~-~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
|+.|+++.|.|.++.+ .|++|+++ |..|.+|++|+++++.++|.+.|++||.|+|+|++ ..++.+.||++
T Consensus 1 L~~G~i~~G~V~kV~p~~Gl~Vqlp~g~~G~V~itdl~D~y~~~Pl~~f~~~qiVrc~VLs--~~~g~~~LSlR 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS--KKDGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEE--CCCCEEEEEEC
T ss_conf 9887474039999728985699848996668999971474544967765789789999995--36998998749
No 98
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.13 E-value=3.2e-10 Score=79.22 Aligned_cols=33 Identities=42% Similarity=0.930 Sum_probs=13.4
Q ss_pred CCEEEEEEEEECCCEEEEEECC-CCEEEEECCCC
Q ss_conf 9665899998159669998514-20000001111
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQS-GIEGLAHISQI 315 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~-~v~G~i~~sel 315 (576)
|+.+.|.|+.+.++|+||+|.+ +++||+|.+++
T Consensus 2 G~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l 35 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTL 35 (83)
T ss_pred CCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCC
T ss_conf 9999999998983069999828873999982214
No 99
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.11 E-value=2.7e-10 Score=79.64 Aligned_cols=70 Identities=27% Similarity=0.291 Sum_probs=32.2
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH--HCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 987999999970890899961779849999974718212--104201106898799999997057686998703
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR--VDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~--~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
|+.+.|+|.++.+.+++|.+. ++|+|.||..++|++. ..++.+.|++|+-++|+|+.+|.+++++.||.|
T Consensus 1 G~~v~gfV~n~~~~~~wv~iS--p~V~gri~~l~lSdd~s~l~~~e~~FpvG~avk~~V~~vD~e~~~l~LS~r 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS--PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEECCCCEEEEEEC--CCEEEEEEHHHHCCCHHHHCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEC
T ss_conf 987999999725984999988--881899970542688568538887299984599999998287788999803
No 100
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.11 E-value=5.5e-10 Score=77.81 Aligned_cols=70 Identities=20% Similarity=0.261 Sum_probs=29.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH-H----------CCCHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 987999999970890899961779849999974718212-1----------04201106898799999997057686998
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR-V----------DQDPGRFSKGQIVDACVVNVSKKDGKVSL 527 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~-~----------~~~~~~~~vG~~v~~~Vi~id~~~~ri~L 527 (576)
|++++|.|++++++|+||++.+ .+++||+|.++|++++ . ......|+.||.|+++|.++|+.+++|.|
T Consensus 2 G~~f~g~I~~v~~~GiFV~l~~-~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~I~f 80 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDN-LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCEEEEEEEEEEEEEEEEEEEC-CCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCEEEE
T ss_conf 9999999998983069999828-873999982214567224474021898134775997899999999999430398989
Q ss_pred EE
Q ss_conf 70
Q gi|254780456|r 528 SI 529 (576)
Q Consensus 528 S~ 529 (576)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
T ss_conf 97
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=99.10 E-value=1.6e-10 Score=81.04 Aligned_cols=58 Identities=24% Similarity=0.321 Sum_probs=24.1
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHH--HHCCCHHHCCCCCEEEEEEEEE
Q ss_conf 98799999997089089996177984999997471821--2104201106898799999997
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRD--RVDQDPGRFSKGQIVDACVVNV 518 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~--~~~~~~~~~~vG~~v~~~Vi~i 518 (576)
|++++|+|++++++|++|.++ .++.|+||+||+.+. ..++|.+.|++||.|+|+|+.+
T Consensus 1 G~vv~g~V~sik~~~l~V~L~--d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG~ 60 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA--DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGG 60 (70)
T ss_pred CCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEEE
T ss_conf 977999999994670899968--995778984552135555569468568999999999976
No 102
>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=99.09 E-value=8.6e-10 Score=76.63 Aligned_cols=71 Identities=23% Similarity=0.407 Sum_probs=53.0
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCC-CCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEE
Q ss_conf 966589999815966999851420000001111011-13557421003784579999986215504787520
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWT-KKNIHPSKILSVGQQVEVVILEVNPARKRISLGLK 353 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~-~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k 353 (576)
|+.+.|.|.++.+.++||.+.+++.|.||..++|.+ ....+|++.|++|+.++|+|+++|.+++++.||++
T Consensus 1 G~~v~gfV~n~~~~~~wv~iSp~V~gri~~l~lSdd~s~l~~~e~~FpvG~avk~~V~~vD~e~~~l~LS~r 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCCCHHHHCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEC
T ss_conf 987999999725984999988881899970542688568538887299984599999998287788999803
No 103
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=99.06 E-value=5.9e-11 Score=83.67 Aligned_cols=81 Identities=27% Similarity=0.444 Sum_probs=71.8
Q ss_pred CCCC-CCCEEEEEEEEECCCEEEEEEC--CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf 0004-8966589999815966999851--420000001111011135574210037845799999862155047875203
Q gi|254780456|r 278 DKYV-EGSKVSGVVTNLTDYGVFVELQ--SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 278 ~~~~-~G~~v~g~V~~v~~~G~~V~l~--~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
++|| +|+++-++|.++.++|+||.|- ++++|+||.||+| .+...+..+.+++|+..-|.|+++|++++.|.||+|+
T Consensus 12 ~~~Pe~~e~V~~~V~~i~~~gayV~LlEY~~~egmI~~sEls-~rrir~I~k~ikvG~~~v~~VlRVD~~KGyIDLS~rr 90 (324)
T PTZ00248 12 NKYPEENDLVMVKVNRIEEMGVYVSLLEYDDIEGMILLSELS-KRRIRSINKLVKVGRHEVVLVLRVDKDKGYIDLSKRR 90 (324)
T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCCEEEHHHHH-HHHHHHHHHHHCCCCEEEEEEEEECCCCCCEECHHHC
T ss_conf 569998888999999980256899984008822214688863-7888637887106877899999985877824441502
Q ss_pred CCCCC
Q ss_conf 45432
Q gi|254780456|r 355 ALINP 359 (576)
Q Consensus 355 ~~~~p 359 (576)
..+.-
T Consensus 91 Vs~ed 95 (324)
T PTZ00248 91 VTPED 95 (324)
T ss_pred CCHHH
T ss_conf 99889
No 104
>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=99.06 E-value=7.6e-10 Score=76.96 Aligned_cols=71 Identities=31% Similarity=0.454 Sum_probs=44.8
Q ss_pred CCCCCEEEEEEEEEECC-EEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 47898799999997089-0899961779849999974718212104201106898799999997057686998703
Q gi|254780456|r 456 LRKNDVVSCEVISVSEG-GIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~-G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
+++|+++.|.|.++.|. |++|.++ .+..|.+|.+++++.+.++|.+.|++||.|+|+|+. .+++.+.||+|
T Consensus 1 L~~G~i~~G~V~kV~p~~Gl~Vqlp--~g~~G~V~itdl~D~y~~~Pl~~f~~~qiVrc~VLs--~~~g~~~LSlR 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLP--FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS--KKDGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEECCCCCEEEECC--CCCEEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEE--CCCCEEEEEEC
T ss_conf 9887474039999728985699848--996668999971474544967765789789999995--36998998749
No 105
>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=99.00 E-value=3.3e-09 Score=73.08 Aligned_cols=73 Identities=22% Similarity=0.342 Sum_probs=40.3
Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHH-------------------CCCHHHCCCCCEEEEEEEEE
Q ss_conf 89879999999708908999617798499999747182121-------------------04201106898799999997
Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRV-------------------DQDPGRFSKGQIVDACVVNV 518 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~-------------------~~~~~~~~vG~~v~~~Vi~i 518 (576)
+|+.+-|.|++|.++++.|.++ +++.|++|+.++|+.+. .++++.|++||.++|+|+..
T Consensus 3 ~G~lvLG~V~~I~~~~l~isLP--~~L~G~V~it~ISd~~t~~le~~~~~~~~~~~~~e~~~L~~lF~vGq~vr~~V~s~ 80 (100)
T cd05693 3 EGMLVLGQVKEITKLDLVISLP--NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCEEEEEEEEECCCCEEEECC--CCCEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCEEEEEEEEC
T ss_conf 8989999998984663899858--98589988788529999999998730023676323458788476898999999984
Q ss_pred CCC---CCEEEEEEHHH
Q ss_conf 057---68699870365
Q gi|254780456|r 519 SKK---DGKVSLSIKAL 532 (576)
Q Consensus 519 d~~---~~ri~LS~k~~ 532 (576)
+.. ++||.||++..
T Consensus 81 ~~~~~~~krI~LSl~P~ 97 (100)
T cd05693 81 DKSKSGKKRIELSLEPE 97 (100)
T ss_pred CCCCCCCEEEEEECCHH
T ss_conf 58877854899982879
No 106
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.97 E-value=9.3e-10 Score=76.42 Aligned_cols=37 Identities=32% Similarity=0.592 Sum_probs=18.9
Q ss_pred CCCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCC
Q ss_conf 2233024678875314717774-483157886420244
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWH 232 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~ 232 (576)
.+|+.+-|+|+.|.++++.+.+ ++++|++|++++|+.
T Consensus 2 ~~G~lvLG~V~~I~~~~l~isLP~~L~G~V~it~ISd~ 39 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA 39 (100)
T ss_pred CCCCEEEEEEEEECCCCEEEECCCCCEEEEEHHHHHHH
T ss_conf 88989999998984663899858985899887885299
No 107
>PRK11642 exoribonuclease R; Provisional
Probab=98.92 E-value=5e-09 Score=71.98 Aligned_cols=74 Identities=23% Similarity=0.218 Sum_probs=63.3
Q ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH-HC----------CCHHHCCCCCEEEEEEEEECCCCC
Q ss_conf 0478987999999970890899961779849999974718212-10----------420110689879999999705768
Q gi|254780456|r 455 SLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR-VD----------QDPGRFSKGQIVDACVVNVSKKDG 523 (576)
Q Consensus 455 ~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~-~~----------~~~~~~~vG~~v~~~Vi~id~~~~ 523 (576)
.-.+|+.+.|.|+.|++||+||++.+ .+++||||+|.|.+++ .- .-...|..||.|+++|.++|..++
T Consensus 640 ~~~iGe~f~G~IsgVt~fG~FVeL~~-~~vEGLVhvs~L~dD~Y~yd~~~~~LvG~rtg~~y~lGD~V~V~v~~Vd~~~~ 718 (813)
T PRK11642 640 LDQVGNVFKGVIASVTGFGFFVRLDD-LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDER 718 (813)
T ss_pred HHHCCCEEEEEEEEEEEEEEEEEECC-CCEEEEEECCCCCCCEEEECCCCCEEEEEECCCEEECCCEEEEEEEEECHHHC
T ss_conf 97449978899960761008999548-86378888012888318983357889865079788269979999999742137
Q ss_pred EEEEEE
Q ss_conf 699870
Q gi|254780456|r 524 KVSLSI 529 (576)
Q Consensus 524 ri~LS~ 529 (576)
+|-|.+
T Consensus 719 qIDfeL 724 (813)
T PRK11642 719 KIDFSL 724 (813)
T ss_pred EEEEEE
T ss_conf 355898
No 108
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.91 E-value=5.3e-09 Score=71.86 Aligned_cols=69 Identities=33% Similarity=0.477 Sum_probs=48.6
Q ss_pred CCEEE-EEEEEEEC-CEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 98799-99999708-9089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 459 NDVVS-CEVISVSE-GGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 459 G~iv~-g~V~~v~~-~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
|.+++ ++|+++.+ .|+++++. .|+.||+|+|++++++++..+..|++|.+.+|||+..++-.+...||+
T Consensus 1 G~i~~~~~V~~v~~~~G~~~~l~--~g~~gfvhiS~lsD~kv~~~~~~fk~Gs~H~~RVig~s~~D~l~~lSL 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELK--DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CCCCCEEEEEEECCCCCEEEEEC--CCCEEEEEEHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEECC
T ss_conf 96233405999858853799969--996899996012666423665786479988899983474341488419
No 109
>PRK11642 exoribonuclease R; Provisional
Probab=98.91 E-value=7.1e-09 Score=71.05 Aligned_cols=73 Identities=30% Similarity=0.558 Sum_probs=62.2
Q ss_pred CCCCCEEEEEEEEEEEEEEEEECC-CCEEEEEHHHHHCCCC----------CHHHHHHHCCCCCCEEEEEECCCCCCCCC
Q ss_conf 222213699999850169997068-8413540055300122----------00123421112342268852156545532
Q gi|254780456|r 368 PPGTEVEGEVKNKTDFGLFIGLDE-HLDGMIHLSDLDWNRP----------GEKVIAEYAKGDIVKAVVLDIDVGKERIS 436 (576)
Q Consensus 368 ~~G~~v~g~V~~v~~~g~~V~l~~-~i~g~i~~~dls~~~~----------~~~~~~~~k~G~~i~~~Vl~id~~~~~i~ 436 (576)
.+|+.+.|.|+.|++||+||+|.+ +++|+||++.|.+|.+ ++.....|+.||.|+++|..+|...++|.
T Consensus 642 ~iGe~f~G~IsgVt~fG~FVeL~~~~vEGLVhvs~L~dD~Y~yd~~~~~LvG~rtg~~y~lGD~V~V~v~~Vd~~~~qID 721 (813)
T PRK11642 642 QVGNVFKGVIASVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID 721 (813)
T ss_pred HCCCEEEEEEEEEEEEEEEEEECCCCEEEEEECCCCCCCEEEECCCCCEEEEEECCCEEECCCEEEEEEEEECHHHCEEE
T ss_conf 44997889996076100899954886378888012888318983357889865079788269979999999742137355
Q ss_pred CCHH
Q ss_conf 0113
Q gi|254780456|r 437 LGVK 440 (576)
Q Consensus 437 LS~K 440 (576)
+.+=
T Consensus 722 feLv 725 (813)
T PRK11642 722 FSLI 725 (813)
T ss_pred EEEE
T ss_conf 8982
No 110
>KOG1067 consensus
Probab=98.90 E-value=2e-09 Score=74.46 Aligned_cols=78 Identities=17% Similarity=0.273 Sum_probs=69.8
Q ss_pred HCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHH
Q ss_conf 10047898799999997089089996177984999997471821210420110689879999999705768699870365
Q gi|254780456|r 453 VSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKAL 532 (576)
Q Consensus 453 ~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~ 532 (576)
..++..|-+++++|+++.++|+||.+ +++..|++|.||++.++++.+++.+.+||.|.++.++.|+..++..+|.+.+
T Consensus 663 ~~~l~~g~vyt~tIte~rd~G~~V~l--~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ralL 740 (760)
T KOG1067 663 VQDLEFGGVYTATITEIRDTGVMVEL--YPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALL 740 (760)
T ss_pred CCCEEEEEEEEEEEEEECCCCEEEEE--CCCCHHHCCCHHCCCCCCCCHHHHHHHCCEEEEEEEEECCCCCEEEHHHHHC
T ss_conf 35258601777888664156359995--6874100000011512005857887520406889986657666210126526
No 111
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.85 E-value=9e-09 Score=70.43 Aligned_cols=64 Identities=27% Similarity=0.393 Sum_probs=30.4
Q ss_pred EEEEEECC-CEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEE
Q ss_conf 99998159-669998514200000011110111355742100378457999998621550478752
Q gi|254780456|r 288 GVVTNLTD-YGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGL 352 (576)
Q Consensus 288 g~V~~v~~-~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~ 352 (576)
++|+++.+ .|+++++++++.||+|+|.+| +.+...+...|++|..++|||++.++-.+...||+
T Consensus 7 ~~V~~v~~~~G~~~~l~~g~~gfvhiS~ls-D~kv~~~~~~fk~Gs~H~~RVig~s~~D~l~~lSL 71 (71)
T cd05696 7 VKVTKVEPDLGAVFELKDGLLGFVHISHLS-DDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred EEEEEECCCCCEEEEECCCCEEEEEEHHCC-CCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEECC
T ss_conf 059998588537999699968999960126-66423665786479988899983474341488419
No 112
>KOG1067 consensus
Probab=98.78 E-value=1.1e-08 Score=69.98 Aligned_cols=80 Identities=18% Similarity=0.183 Sum_probs=68.2
Q ss_pred CCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCC
Q ss_conf 12222213699999850169997068841354005530012200123421112342268852156545532011322101
Q gi|254780456|r 366 SHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGS 445 (576)
Q Consensus 366 ~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~ 445 (576)
.+..|-+.+|+|+++.++|+||++.++..|++|.++|+ .++..+|.+.+++||++.++.++.|+..+. .+|.|++..+
T Consensus 665 ~l~~g~vyt~tIte~rd~G~~V~l~p~~~~Llh~sqL~-~e~iakpsd~levGq~I~vk~ie~d~~g~~-~ls~ralLp~ 742 (760)
T KOG1067 665 DLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLD-QEKIAKPSDLLEVGQEIQVKYIERDPRGGI-MLSSRALLPD 742 (760)
T ss_pred CEEEEEEEEEEEEEECCCCEEEEECCCCHHHCCCHHCC-CCCCCCHHHHHHHCCEEEEEEEEECCCCCE-EEHHHHHCCC
T ss_conf 25860177788866415635999568741000000115-120058578875204068899866576662-1012652689
Q ss_pred CC
Q ss_conf 11
Q gi|254780456|r 446 AP 447 (576)
Q Consensus 446 ~~ 447 (576)
|.
T Consensus 743 p~ 744 (760)
T KOG1067 743 PA 744 (760)
T ss_pred CC
T ss_conf 54
No 113
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.65 E-value=8.7e-08 Score=64.49 Aligned_cols=66 Identities=20% Similarity=0.306 Sum_probs=30.9
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 9879999999708908999617798499999747182121042011068987999999970576869987
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
|++|++.|.++.+.|++++|.+ .+.|.+..-|+++.. ...+.|++||.++|+|+.+||..++|.||
T Consensus 1 GmlV~a~V~kV~~~Gl~~~fl~--~F~G~Vd~~HL~~~~--~~~~~Y~~~~~v~ArIL~Vdp~tK~V~Ls 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLS--SFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEECCCCEEEEEEC--CEEEEEEHHHCCCCC--CCCCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 9559999999817948999651--289998876768776--87000467988999999998874788539
No 114
>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=98.65 E-value=2.6e-07 Score=61.62 Aligned_cols=68 Identities=25% Similarity=0.429 Sum_probs=38.0
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECC-CEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEHHH
Q ss_conf 3898779999999819989999479-6036789975056643556378987999999974799859996878
Q gi|254780456|r 24 LAENCVTKGIVVGLEKDTVVVDVGL-KFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDK 94 (576)
Q Consensus 24 ~~~G~iv~G~V~~i~~~~v~vdig~-k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g~i~lS~~k 94 (576)
+.+|.++.|.|.+++|+|+++|+|. ...||+|..|..+ ...+++|+.+.|.|++.+...+.+.||.++
T Consensus 2 l~~g~~l~a~V~SvEDHGyild~Gi~~~~gFl~~k~~~~---~~~l~~G~v~~c~V~~v~~~g~vv~ls~~~ 70 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN---FSKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCEEEEEEEEEECCEEEEECCCCCCEEEEEHHHCCC---CCCCCCCCEEEEEEEEEECCCEEEEEECCH
T ss_conf 667829999985671441899847777266730133475---563348878999999992896099996685
No 115
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.64 E-value=1.1e-07 Score=63.97 Aligned_cols=72 Identities=33% Similarity=0.661 Sum_probs=38.4
Q ss_pred CCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCC----------CC-CCEEECCCCEEEEEEEEECCCC-----C
Q ss_conf 223302467887531471777448315788642024444----------43-3113326972589999874765-----2
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRI----------LH-PSKVLSIGQQVKVKIIRINQET-----H 259 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~----------~~-~~~~~~~G~~v~~~Vl~~d~~~-----~ 259 (576)
..|.+|.|.|..+.++|+||.+|-.+||+|.+++.+++. .. -...+++|+.|++||++..... .
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~ 159 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRES 159 (183)
T ss_pred CCCCEEEEEEEEEEECCEEEEECCCCCCCCHHHCCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEECCCCCCCCC
T ss_conf 35638999999996144699963622211386665753252755541240365158841988999999961467765421
Q ss_pred EEEEEECC
Q ss_conf 79985215
Q gi|254780456|r 260 RISLGMKQ 267 (576)
Q Consensus 260 ~i~lslK~ 267 (576)
+|.|++|+
T Consensus 160 ~I~lTmrq 167 (183)
T COG1095 160 KIGLTMRQ 167 (183)
T ss_pred EEEEEECC
T ss_conf 69999536
No 116
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.63 E-value=2.8e-07 Score=61.35 Aligned_cols=65 Identities=20% Similarity=0.435 Sum_probs=45.4
Q ss_pred CCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 33024678875314717774-48315788642024444433113326972589999874765279985
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
|++|+++|+++.++|+.++| +.++|.+..-+++... ...+.|++||+++||||.+||.+++|.||
T Consensus 1 GmlV~a~V~kV~~~Gl~~~fl~~F~G~Vd~~HL~~~~--~~~~~Y~~~~~v~ArIL~Vdp~tK~V~Ls 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEECCCCEEEEEECCEEEEEEHHHCCCCC--CCCCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 9559999999817948999651289998876768776--87000467988999999998874788539
No 117
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.61 E-value=1.7e-07 Score=62.67 Aligned_cols=34 Identities=41% Similarity=0.739 Sum_probs=16.0
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHC
Q ss_conf 22136999998501699970688413540055300
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDW 404 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~ 404 (576)
|++|.|.|.++.++|+||.++ -.+||+|.+++.+
T Consensus 82 gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~d 115 (183)
T COG1095 82 GEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMD 115 (183)
T ss_pred CCEEEEEEEEEEECCEEEEEC-CCCCCCCHHHCCC
T ss_conf 638999999996144699963-6222113866657
No 118
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.55 E-value=1.1e-05 Score=51.64 Aligned_cols=199 Identities=13% Similarity=0.157 Sum_probs=126.2
Q ss_pred CEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCC
Q ss_conf 10037845799999862155047875203454321000001222221369999985016999706884135400553001
Q gi|254780456|r 326 KILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWN 405 (576)
Q Consensus 326 ~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~ 405 (576)
..|..|+.+-+.+.++-....++ ++..++... + .-++|++|=|.|+.++..+-+|+++....|++|.+++.|.
T Consensus 26 Gty~~~~~i~As~~G~v~~~~k~-v~ViPl~gr----Y--~P~~GD~VIG~V~~v~~~~W~VDI~s~~~a~L~~s~~~~r 98 (232)
T PRK04163 26 GTYVEGGKIYSSVVGLVEIKDDK-VRVIPLEGK----Y--IPKKGDLVIGKVTDVGFSGWEVDINSPYKAILPVSEVLGR 98 (232)
T ss_pred CEEEECCEEEEEEEEEEEEECCE-EEEEECCCC----C--CCCCCCEEEEEEEEECCCEEEEECCCCCEEEECHHHCCCC
T ss_conf 85998999999998889997999-999989851----0--5876998999999831871799869960558524445665
Q ss_pred CC---CHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCC
Q ss_conf 22---001234211123422688521565455320113221011100001100478987999999970890899961779
Q gi|254780456|r 406 RP---GEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHK 482 (576)
Q Consensus 406 ~~---~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~ 482 (576)
.. ..+....|.+||.+-|+|..++... .+.||+|. ..+-.++- |.+.++.+.-
T Consensus 99 ~~~~~~~~mr~~l~~GDlI~ArV~~v~~~~-~~~Lt~k~---------~~lGkL~~-----G~li~V~p~~--------- 154 (232)
T PRK04163 99 PVDVESTDLRKYLDIGDYIIAKVKDVDETK-DVVLTLKG---------RGLGKLEG-----GTIVEIKPSK--------- 154 (232)
T ss_pred CCCCCHHHHHHHCCCCCEEEEEEEEECCCC-CEEEEECC---------CCCCCCCC-----CEEEEECHHH---------
T ss_conf 555643567751788988999999966899-78999548---------98855469-----8899973121---------
Q ss_pred CEEEEEEH--HHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHH-HHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 84999997--471821210420110689879999999705768699870365-577779999984034457779999999
Q gi|254780456|r 483 GINSFIRR--SDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKAL-EIAEEKGAVAQFGSSDSGASLGDILGM 559 (576)
Q Consensus 483 gv~G~i~~--s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~-~~~~~~~~~~~~~~~~~~~tlg~~~~~ 559 (576)
+.-++-+ |.++. ..+...|.|+ + -.++||.++.... .+..-.++++....++-...|.|-++.
T Consensus 155 -VpRvIGk~gsmi~~-----------ik~~t~~~I~-V-G~NG~IWI~g~~~~~~~~a~~aI~~Ie~eah~~gLtd~i~~ 220 (232)
T PRK04163 155 -VPRVIGKKGSMINM-----------LKEETGCDII-V-GQNGRIWIKGKNEEDEELAIEAIKKIEREAHTSGLTDRVKE 220 (232)
T ss_pred -CCEEECCCCHHHHH-----------HHHHHCCEEE-E-CCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf -87145588359999-----------7652195899-9-17978999769888999999999999986300358999999
Q ss_pred HHHHHHCCCC
Q ss_conf 9987431112
Q gi|254780456|r 560 ALKNRGNDAG 569 (576)
Q Consensus 560 ~lk~~~~~~~ 569 (576)
.|++..++.+
T Consensus 221 ~l~~~~~~~~ 230 (232)
T PRK04163 221 FLEEEKGERD 230 (232)
T ss_pred HHHHHHCCCC
T ss_conf 9987434245
No 119
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=98.55 E-value=3.2e-07 Score=61.07 Aligned_cols=73 Identities=38% Similarity=0.736 Sum_probs=54.0
Q ss_pred CCCCCEEEEEEEEEECCCCEEE-ECCCEEEEEEEECCCCCCC-CC-------------CEEECCCCEEEEEEEEEC----
Q ss_conf 2223302467887531471777-4483157886420244444-33-------------113326972589999874----
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVD-LSGVDGLLHVTDIAWHRIL-HP-------------SKVLSIGQQVKVKIIRIN---- 255 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~-~~g~~g~i~~~~ls~~~~~-~~-------------~~~~~~G~~v~~~Vl~~d---- 255 (576)
-.-+.+|+|.|..+..||+||+ +|=++|++|.+++.+++.. +| ...|.+|+.|+|||.++.
T Consensus 79 P~l~EiVeGev~~~~efG~fV~LlGp~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~slk~~ 158 (184)
T TIGR00448 79 PELGEIVEGEVIEIVEFGAFVSLLGPFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVALSLKDR 158 (184)
T ss_pred CCCEEEEEEEEEEEEECCCEEEEECCCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEEEECCC
T ss_conf 35216786589989852742675223132344100113563662656604567401217351016756678888764041
Q ss_pred -C-CCCEEEEEECC
Q ss_conf -7-65279985215
Q gi|254780456|r 256 -Q-ETHRISLGMKQ 267 (576)
Q Consensus 256 -~-~~~~i~lslK~ 267 (576)
+ +..++.|+++|
T Consensus 159 ~pk~~~k~~LtmRq 172 (184)
T TIGR00448 159 RPKEGSKIGLTMRQ 172 (184)
T ss_pred CCCCCCEEEEECCC
T ss_conf 37888511001157
No 120
>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=98.54 E-value=4.2e-07 Score=60.35 Aligned_cols=68 Identities=26% Similarity=0.381 Sum_probs=51.5
Q ss_pred CCCCCEEEEEEEEECCCEEEEEEC-CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf 048966589999815966999851-420000001111011135574210037845799999862155047875203
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDYGVFVELQ-SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~G~~V~l~-~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
+.+|.++.|.|.+++|||+.++++ ++++||+|..++.. ...+++|+.+.|.|..++...+.+.||..+
T Consensus 2 l~~g~~l~a~V~SvEDHGyild~Gi~~~~gFl~~k~~~~-------~~~l~~G~v~~c~V~~v~~~g~vv~ls~~~ 70 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN-------FSKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCEEEEEEEEEECCEEEEECCCCCCEEEEEHHHCCC-------CCCCCCCCEEEEEEEEEECCCEEEEEECCH
T ss_conf 667829999985671441899847777266730133475-------563348878999999992896099996685
No 121
>PRK05054 exoribonuclease II; Provisional
Probab=98.50 E-value=5.5e-07 Score=59.64 Aligned_cols=72 Identities=21% Similarity=0.376 Sum_probs=57.6
Q ss_pred CCCCC--EEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHH---HH--CC-------CHHHCCCCCEEEEEEEEECCC
Q ss_conf 47898--799999997089089996177984999997471821---21--04-------201106898799999997057
Q gi|254780456|r 456 LRKND--VVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRD---RV--DQ-------DPGRFSKGQIVDACVVNVSKK 521 (576)
Q Consensus 456 ~~~G~--iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~---~~--~~-------~~~~~~vG~~v~~~Vi~id~~ 521 (576)
-.+|+ +..|.|++++++|+||.+.+ .+++||||.+.+.+. +. .. -...|+.||.|+++|.++|.+
T Consensus 557 ~~iG~~~~f~g~Is~vt~fG~fV~L~~-~~~eG~V~~~~l~~~~~~~~~~~~~~~~~~~~~~~yrlGd~v~V~v~~vd~~ 635 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLLE-NGAIAFIPAPFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRME 635 (644)
T ss_pred HHCCCCCEEEEEEEEEEECCEEEEEEC-CCEEEEEEEEECCCCCCEEEECCHHHHEECCCCEEEECCCEEEEEEEEEECH
T ss_conf 744898727899975981778999866-8508999811325677338982022103405868997899999999998000
Q ss_pred CCEEEEE
Q ss_conf 6869987
Q gi|254780456|r 522 DGKVSLS 528 (576)
Q Consensus 522 ~~ri~LS 528 (576)
+++|.+-
T Consensus 636 ~r~I~~~ 642 (644)
T PRK05054 636 TRSIIAR 642 (644)
T ss_pred HCEEEEE
T ss_conf 1848769
No 122
>PRK05054 exoribonuclease II; Provisional
Probab=98.48 E-value=7.8e-07 Score=58.69 Aligned_cols=70 Identities=19% Similarity=0.212 Sum_probs=53.9
Q ss_pred CCCC--CEEEEEEEEEEEEEEEEE-CCCCEEEEEHHHHHCC--CCC---H------HHHHHHCCCCCCEEEEEECCCCCC
Q ss_conf 2222--136999998501699970-6884135400553001--220---0------123421112342268852156545
Q gi|254780456|r 368 PPGT--EVEGEVKNKTDFGLFIGL-DEHLDGMIHLSDLDWN--RPG---E------KVIAEYAKGDIVKAVVLDIDVGKE 433 (576)
Q Consensus 368 ~~G~--~v~g~V~~v~~~g~~V~l-~~~i~g~i~~~dls~~--~~~---~------~~~~~~k~G~~i~~~Vl~id~~~~ 433 (576)
.+|+ .+.|.|+.++++|+||++ ..+++||||.+.+.++ ... + .-...|+.||.|+++|..+|.+.+
T Consensus 558 ~iG~~~~f~g~Is~vt~fG~fV~L~~~~~eG~V~~~~l~~~~~~~~~~~~~~~~~~~~~~~yrlGd~v~V~v~~vd~~~r 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAIAFIPAPFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred HCCCCCEEEEEEEEEEECCEEEEEECCCEEEEEEEEECCCCCCEEEECCHHHHEECCCCEEEECCCEEEEEEEEEECHHC
T ss_conf 44898727899975981778999866850899981132567733898202210340586899789999999999800018
Q ss_pred CCCC
Q ss_conf 5320
Q gi|254780456|r 434 RISL 437 (576)
Q Consensus 434 ~i~L 437 (576)
+|.+
T Consensus 638 ~I~~ 641 (644)
T PRK05054 638 SIIA 641 (644)
T ss_pred EEEE
T ss_conf 4876
No 123
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.46 E-value=7.4e-07 Score=58.84 Aligned_cols=32 Identities=44% Similarity=0.910 Sum_probs=11.8
Q ss_pred CCEEEEEEEEEECCCCEEEECCCEEEEEEEEC
Q ss_conf 33024678875314717774483157886420
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLSGVDGLLHVTDI 229 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~l 229 (576)
|.++.|.|.+++++|+||++|-+++|+|.+++
T Consensus 82 ~EVv~g~V~~~~~~G~fv~~Gp~d~~vh~sqi 113 (182)
T PRK08563 82 QEVVEGEVVEVVEFGAFVRIGPVDGLLHISQI 113 (182)
T ss_pred CCEEEEEEEEEECCEEEEEEECCCEEEEHHHC
T ss_conf 84899999999667699998466117609994
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=98.44 E-value=1.7e-06 Score=56.59 Aligned_cols=63 Identities=27% Similarity=0.518 Sum_probs=42.0
Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCC--CEEEEE
Q ss_conf 8987799999998199899994796036789975056643556378987999999974799--859996
Q gi|254780456|r 25 AENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSF--GEAVFS 91 (576)
Q Consensus 25 ~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~--g~i~lS 91 (576)
++|+++.|+|.++++..++||+| +.+|++|.+|.. +.+.|++||.++|+|..++... -++.||
T Consensus 2 k~geiv~G~V~r~~~~~v~vdlg-~~eailp~~eqi---p~E~~~~Gdrik~~i~~V~~~~kgp~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQI---PGESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEECCCEEEEEC-CCEEECCHHHCC---CCCCCCCCCEEEEEEEEEEECCCCCEEEEE
T ss_conf 87888999999980897999989-948973789957---886639999899999998746998889983
No 125
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.43 E-value=1.7e-06 Score=56.58 Aligned_cols=71 Identities=28% Similarity=0.526 Sum_probs=33.4
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCC----------CHHHHHHHCCCCCCEEEEEECC-----CCCCC
Q ss_conf 22136999998501699970688413540055300122----------0012342111234226885215-----65455
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRP----------GEKVIAEYAKGDIVKAVVLDID-----VGKER 434 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~----------~~~~~~~~k~G~~i~~~Vl~id-----~~~~~ 434 (576)
|+++.|.|++++++|+||++++ +++|+|.+++.++.. .++....++.|+.|++||..+. +...+
T Consensus 82 ~EVv~g~V~~~~~~G~fv~~Gp-~d~~vh~sqi~dd~~~fD~~~~~~ig~~s~~~i~~Gd~VR~RIv~vs~~~~~~~~~k 160 (182)
T PRK08563 82 QEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDEKNGALIGKESKRTLKVGDVVRARIVAVSLNEREPRDSK 160 (182)
T ss_pred CCEEEEEEEEEECCEEEEEEEC-CCEEEEHHHCCCCCCEECCCCCEEEEECCCEEECCCCEEEEEEEEEECCCCCCCCCE
T ss_conf 8489999999966769999846-611760999477762383656519990686498289989999999771888877662
Q ss_pred CCCCHHH
Q ss_conf 3201132
Q gi|254780456|r 435 ISLGVKQ 441 (576)
Q Consensus 435 i~LS~K~ 441 (576)
|.||||+
T Consensus 161 IglTmrq 167 (182)
T PRK08563 161 IGLTMRQ 167 (182)
T ss_pred EEEEECC
T ss_conf 6689538
No 126
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=98.41 E-value=3e-06 Score=55.16 Aligned_cols=34 Identities=18% Similarity=0.391 Sum_probs=15.5
Q ss_pred CCCEEEEEEEEEECCCCEEEECCCEEEEEEEECC
Q ss_conf 2330246788753147177744831578864202
Q gi|254780456|r 197 EGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIA 230 (576)
Q Consensus 197 ~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls 230 (576)
.|++++|.|.++.++|+|+++|-+++|+|.+.++
T Consensus 81 ~~EVvdg~V~~v~~~G~fv~~GPl~~fv~~s~i~ 114 (170)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLKIFVSRTAIP 114 (170)
T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCC
T ss_conf 7989999999996407999912808998989999
No 127
>KOG2916 consensus
Probab=98.40 E-value=8.6e-07 Score=58.45 Aligned_cols=74 Identities=22% Similarity=0.534 Sum_probs=33.4
Q ss_pred CCCCEEEEEEEEEECCCCEEEE---CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCC
Q ss_conf 2233024678875314717774---4831578864202444443311332697258999987476527998521555
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLE 269 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~---~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~ 269 (576)
.++++|-+.|..|.+-|++|.+ ++++|++-.++||..|+-.+.+..++|..=.|.|+.+|.+++-|.||.+..+
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CCCCEEEEEEEEEHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEECHHCCCC
T ss_conf 75327998753702062167621027811110035777888898999984077534899997177870662131388
No 128
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=98.39 E-value=7.6e-06 Score=52.70 Aligned_cols=207 Identities=21% Similarity=0.297 Sum_probs=117.0
Q ss_pred EEEEECCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC-CEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99996795599974402000001123454333455555302311133543233-11221211122222121110001122
Q gi|254780456|r 118 IFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRG-NIVVSRRAVLEESRAEQRSEIVQKLE 196 (576)
Q Consensus 118 V~~~~k~G~~V~i~gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~Ii~~d~~~~-~ivvS~k~~l~~~~~~~~~~~~~~l~ 196 (576)
++.+++++-.|.+....-+|+++--... -+-....+++..++.+.++.++.+ -.++| ....+.+++
T Consensus 55 pc~~c~gkG~V~v~~~c~~c~G~gkv~~-c~~cG~~~~~~~~~lc~~c~~~~~~vy~l~------------~~c~~~Dve 121 (715)
T COG1107 55 PCPKCRGKGTVTVYDTCPECGGTGKVLT-CDICGDIIVPWEEGLCPECRRKPKIVYVLD------------NSCTMEDVE 121 (715)
T ss_pred CCCEECCCEEEEEEEECCCCCCCEEEEE-ECCCCCEECCCCCCCCHHHHHCCCEEEEEC------------CCCCHHHCC
T ss_conf 7771105516898862566798103776-044454625763334746760776169963------------556620034
Q ss_pred CCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCC
Q ss_conf 2330246788753147177744-831578864202444443311332697258999987476527998521555432100
Q gi|254780456|r 197 EGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDD 275 (576)
Q Consensus 197 ~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~ 275 (576)
.|....|.|.++..||+||+++ .+.|++|.++++.. .-|.+|+++-+.|..+.++++.+.+-...+. +|..
T Consensus 122 ~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~--~Y~~ 193 (715)
T COG1107 122 AGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD--RYRE 193 (715)
T ss_pred CCEEEECCCCCHHHHCCEEECCHHHHCCCCCCCCCCC------CCCCCCCEEEEEEECCCCCCCCCCEEECCCC--CCHH
T ss_conf 6405403102143406524337354334440124788------7778787489984215777775420665875--2101
Q ss_pred --CCCCC----------CCCCEE--EEEEEEECC-CEE-EEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEE
Q ss_conf --00000----------489665--899998159-669-99851420000001111011135574210037845799999
Q gi|254780456|r 276 --VQDKY----------VEGSKV--SGVVTNLTD-YGV-FVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVIL 339 (576)
Q Consensus 276 --~~~~~----------~~G~~v--~g~V~~v~~-~G~-~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl 339 (576)
++..+ ..|+.+ .|.|+.+.- .|- +..+.++ +|+++..-+-.......|. ..+|+.|.+ +=
T Consensus 194 ~~~~ke~~r~~i~did~~ig~tV~I~GeV~qikqT~GPTVFtltDe-tg~i~aAAFe~aGvRAyP~--ievGdiV~V-iG 269 (715)
T COG1107 194 VQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLTDE-TGAIWAAAFEEAGVRAYPE--IEVGDIVEV-IG 269 (715)
T ss_pred HHHHHHCCCCCHHHHHHHCCCEEEEEEEEEEEEECCCCEEEEEECC-CCCEEHHHHCCCCCCCCCC--CCCCCEEEE-EE
T ss_conf 1122104531077777534866999778999997589879998068-8844266643577434899--877856999-87
Q ss_pred EEECCCCEEE
Q ss_conf 8621550478
Q gi|254780456|r 340 EVNPARKRIS 349 (576)
Q Consensus 340 ~id~~~~~i~ 349 (576)
.++...+++-
T Consensus 270 ~V~~r~g~lQ 279 (715)
T COG1107 270 EVTRRDGRLQ 279 (715)
T ss_pred EEEECCCCEE
T ss_conf 7750478278
No 129
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.32 E-value=1.7e-05 Score=50.54 Aligned_cols=32 Identities=38% Similarity=0.607 Sum_probs=13.0
Q ss_pred CCCEEEEEEEEEECCCEEEEECCCHHHHHCCC
Q ss_conf 89769999999967955999744020000011
Q gi|254780456|r 110 AGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQ 141 (576)
Q Consensus 110 ~g~~v~g~V~~~~k~G~~V~i~gi~~FlP~s~ 141 (576)
.|++|.|.|.....+.++|++++..|+||.++
T Consensus 135 ~Geiv~G~V~r~~~~~i~Vdlg~~ea~Lp~~e 166 (428)
T PRK09202 135 VGEIITGTVKRVERGNIIVDLGRAEAILPRDE 166 (428)
T ss_pred CCCEEEEEEEEECCCCEEEEECCEEEECCHHH
T ss_conf 29889999999727838999788257564787
No 130
>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=98.32 E-value=6.1e-06 Score=53.28 Aligned_cols=71 Identities=24% Similarity=0.257 Sum_probs=34.0
Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH----HCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf 78987999999970890899961779849999974718212----104201106898799999997057686998703
Q gi|254780456|r 457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR----VDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 (576)
Q Consensus 457 ~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~----~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k 530 (576)
++|++|-|+|.++...+.+|++. ....|++|.|++...+ ..+.+++|.+|+.|-|+|.++| ..+.+.|++|
T Consensus 5 ~~GD~ViG~V~~i~~~~w~vdi~--s~~~a~L~ls~v~~~~~~~d~~~mr~~l~iGDli~a~V~~v~-~~~~v~L~~r 79 (86)
T cd05789 5 EVGDVVIGRVTEVGFKRWKVDIN--SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD-SDGSVSLHTR 79 (86)
T ss_pred CCCCEEEEEEEEEECCCEEEECC--CCEEEEEEHHHCCCCCCCHHHHHHHHHCCCCCEEEEEEEEEC-CCCCEEEEEC
T ss_conf 88999999999980881899749--960779874544677763146778865668989999999988-9997999965
No 131
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=98.31 E-value=2e-06 Score=56.16 Aligned_cols=32 Identities=13% Similarity=0.265 Sum_probs=14.6
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHH
Q ss_conf 221369999985016999706884135400553
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDL 402 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dl 402 (576)
|++++|.|++++++|+|++++ .+++|+|.+.+
T Consensus 82 ~EVvdg~V~~v~~~G~fv~~G-Pl~~fv~~s~i 113 (170)
T PTZ00162 82 DEVLDAIVTDVNKLGFFAQAG-PLKIFVSRTAI 113 (170)
T ss_pred CCEEEEEEEEEECCEEEEEEC-CEEEEEEHHHC
T ss_conf 989999999996407999912-80899898999
No 132
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=98.30 E-value=1.4e-06 Score=57.11 Aligned_cols=71 Identities=30% Similarity=0.472 Sum_probs=38.9
Q ss_pred CCCEEEEEEEEEEEEEEEE-ECCCCEEEEEHHHHHCCCC------------C-HHHHHHHCCCCCCEEEEEECC-----C
Q ss_conf 2213699999850169997-0688413540055300122------------0-012342111234226885215-----6
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIG-LDEHLDGMIHLSDLDWNRP------------G-EKVIAEYAKGDIVKAVVLDID-----V 430 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~-l~~~i~g~i~~~dls~~~~------------~-~~~~~~~k~G~~i~~~Vl~id-----~ 430 (576)
+++|+|-|..++.+|+||+ || -++|++|.|++.++.- . +.....|.+|+.|+|||..+. +
T Consensus 82 ~EiVeGev~~~~efG~fV~LlG-p~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~slk~~~p 160 (184)
T TIGR00448 82 GEIVEGEVIEIVEFGAFVSLLG-PFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVALSLKDRRP 160 (184)
T ss_pred EEEEEEEEEEEEECCCEEEEEC-CCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEEEECCCCC
T ss_conf 1678658998985274267522-313234410011356366265660456740121735101675667888876404137
Q ss_pred -CCCCCCCCHHH
Q ss_conf -54553201132
Q gi|254780456|r 431 -GKERISLGVKQ 441 (576)
Q Consensus 431 -~~~~i~LS~K~ 441 (576)
+..++.|++||
T Consensus 161 k~~~k~~LtmRq 172 (184)
T TIGR00448 161 KEGSKIGLTMRQ 172 (184)
T ss_pred CCCCEEEEECCC
T ss_conf 888511001157
No 133
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=98.29 E-value=1.9e-05 Score=50.28 Aligned_cols=64 Identities=23% Similarity=0.373 Sum_probs=42.6
Q ss_pred CCCCEEEEEEEEECCC-EEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCC---EEEEEE
Q ss_conf 4896658999981596-69998514200000011110111355742100378457999998621550---478752
Q gi|254780456|r 281 VEGSKVSGVVTNLTDY-GVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK---RISLGL 352 (576)
Q Consensus 281 ~~G~~v~g~V~~v~~~-G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~---~i~lS~ 352 (576)
.+|+++.|+|.++... .++|+++ +++|++|.+|. -|.+.|++|+.++|.|.++....+ +|.||-
T Consensus 137 r~GeiV~G~V~r~~~~~~~~vdlg-~~ea~Lp~~eq-------ip~E~y~~Gdrik~~i~~V~~~~~~gpqI~lSR 204 (375)
T PRK12328 137 KVGSVVFGTVVRVDNEENTFIEID-EIRAILPMKNR-------IKGEKFKVGDVVKAVLRRVKIDKKNGIKLELSR 204 (375)
T ss_pred HCCCEEEEEEEEEECCCCEEEECC-CCEEEECHHHC-------CCCCCCCCCCEEEEEEEEEECCCCCCCEEEEEC
T ss_conf 429489999999965884899739-81798027763-------886558999869999999872789995899967
No 134
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.28 E-value=1.7e-05 Score=50.64 Aligned_cols=57 Identities=26% Similarity=0.405 Sum_probs=30.3
Q ss_pred CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCC
Q ss_conf 89665899998159669998514200000011110111355742100378457999998621550
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK 346 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~ 346 (576)
+|+++.|+|.++...+++|+++ +++|++|.+|. -|.+.|++||.++|.|.+++...+
T Consensus 134 ~GeiV~G~V~r~~~~~~~Vdlg-~~ea~LP~~eq-------ip~E~~~~Gdrika~i~~V~~~~k 190 (353)
T PRK12327 134 EGDIVTGTVQRDDNRFVYVNLG-KIEAVLPPAEQ-------IPGETYKHGDRIKVYVVKVEKTTK 190 (353)
T ss_pred CCCEEEEEEEEECCCCEEEEEC-CEEEECCHHHC-------CCCCCCCCCCEEEEEEEEEEECCC
T ss_conf 3966999999975885899978-82464687986-------998777999979999999997599
No 135
>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=98.23 E-value=1.1e-05 Score=51.73 Aligned_cols=56 Identities=20% Similarity=0.364 Sum_probs=24.4
Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCC
Q ss_conf 89879999999708908999617798499999747182121042011068987999999970576
Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKD 522 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~ 522 (576)
+|+++.|.|.++....++|++ ++++|++|.++.. +.+.|++|+.|+|.|.+++...
T Consensus 3 ~geiv~G~V~r~~~~~v~vdl---g~~eailp~~eqi------p~E~~~~Gdrik~~i~~V~~~~ 58 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDL---GKVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTS 58 (67)
T ss_pred CCCEEEEEEEEEECCCEEEEE---CCCEEECCHHHCC------CCCCCCCCCEEEEEEEEEEECC
T ss_conf 788899999998089799998---9948973789957------8866399998999999987469
No 136
>KOG1856 consensus
Probab=98.23 E-value=2.5e-06 Score=55.59 Aligned_cols=82 Identities=26% Similarity=0.352 Sum_probs=69.1
Q ss_pred CCCCCCCEEEEEEEEEECC-EEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEHHH
Q ss_conf 0047898799999997089-089996177984999997471821210420110689879999999705768699870365
Q gi|254780456|r 454 SSLRKNDVVSCEVISVSEG-GIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKAL 532 (576)
Q Consensus 454 ~~~~~G~iv~g~V~~v~~~-G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k~~ 532 (576)
+.+..|.+|.+.|.+++.. |..|.+-..+|+.||||.+.+|+.-+.+|...+++|++|.|+|+.+|.++=.+-||+|..
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 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred HHHCCCCEEEEEEEEEEECCCCEEEEEECCCCCEEEECCCCCHHHCCCHHHHHCCCCEEEEEEEEEEHHHHHHHHHHHHH
T ss_conf 67356756777556787156531578742787315443336734215877751147627999653328545531100148
Q ss_pred HHH
Q ss_conf 577
Q gi|254780456|r 533 EIA 535 (576)
Q Consensus 533 ~~~ 535 (576)
...
T Consensus 1061 dlk 1063 (1299)
T KOG1856 1061 DLK 1063 (1299)
T ss_pred HHH
T ss_conf 765
No 137
>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=98.22 E-value=4.9e-06 Score=53.88 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=12.5
Q ss_pred CCCEEEEEEEEEECCCCEEEECC-CEEEEEEEECC
Q ss_conf 23302467887531471777448-31578864202
Q gi|254780456|r 197 EGQVIEGTVKNITDYGVFVDLSG-VDGLLHVTDIA 230 (576)
Q Consensus 197 ~G~~v~g~V~~i~~~g~~V~~~g-~~g~i~~~~ls 230 (576)
+||+|-|+|..+...+-+|++|+ ..|++|.+++.
T Consensus 6 ~GD~ViG~V~~i~~~~w~vdi~s~~~a~L~ls~v~ 40 (86)
T cd05789 6 VGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVN 40 (86)
T ss_pred CCCEEEEEEEEEECCCEEEECCCCEEEEEEHHHCC
T ss_conf 89999999999808818997499607798745446
No 138
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation 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 Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=98.19 E-value=2.3e-06 Score=55.84 Aligned_cols=107 Identities=28% Similarity=0.435 Sum_probs=60.1
Q ss_pred CCCCCCEEECCCCEEEEEEEEECCCCCEEEE-EECCCCCC-----CCCCCCCCC--CCCCEEEEEEEE--ECCCE----E
Q ss_conf 4443311332697258999987476527998-52155543-----210000000--489665899998--15966----9
Q gi|254780456|r 233 RILHPSKVLSIGQQVKVKIIRINQETHRISL-GMKQLEKN-----PWDDVQDKY--VEGSKVSGVVTN--LTDYG----V 298 (576)
Q Consensus 233 ~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l-slK~l~~d-----p~~~~~~~~--~~G~~v~g~V~~--v~~~G----~ 298 (576)
+-.+|. +++||.+..-+-.-+- +|+.. ++||.... --..+.+.| ++|+++.|+|.+ +...+ +
T Consensus 92 ~~~~p~--~~iGd~~~~~~~~~~F--gR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~ 167 (366)
T TIGR01953 92 REIDPD--VQIGDEVKKEINPENF--GRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGL 167 (366)
T ss_pred HHCCCC--CCCCCEEEEECCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEE
T ss_conf 210779--6215378874276664--478999999999888899998767766433318089999999752578752107
Q ss_pred EEEE-CCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCC----EEEEE
Q ss_conf 9985-14200000011110111355742100378457999998621550----47875
Q gi|254780456|r 299 FVEL-QSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK----RISLG 351 (576)
Q Consensus 299 ~V~l-~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~----~i~lS 351 (576)
+|+| + .++|+||.+|+ .|.+.|+.|+.|+|+|.+|.+..+ +|.||
T Consensus 168 ~v~l~g-~~e~~lp~~e~-------iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lS 217 (366)
T TIGR01953 168 IVELAG-KTEAILPKKEQ-------IPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILS 217 (366)
T ss_pred EEEECC-CEEEECCHHHC-------CCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEE
T ss_conf 999857-50252135337-------888752358889999999998688966899997
No 139
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation 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 Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=98.18 E-value=2.1e-05 Score=50.00 Aligned_cols=111 Identities=21% Similarity=0.338 Sum_probs=61.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCEEECCCCCC-CCCCCCCCCCCCCC--CCCCCEEEEEEEE--EECCC----CEEEE-
Q ss_conf 334555553023111335432331122121112-22221211100011--2223302467887--53147----17774-
Q gi|254780456|r 148 RDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL-EESRAEQRSEIVQK--LEEGQVIEGTVKN--ITDYG----VFVDL- 217 (576)
Q Consensus 148 ~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l-~~~~~~~~~~~~~~--l~~G~~v~g~V~~--i~~~g----~~V~~- 217 (576)
.++..-+|..+..-+---+=.+.-+ -..|+++ +..+...+...++. -++|++|.|+|.. +...+ ++|++
T Consensus 94 ~~p~~~iGd~~~~~~~~~~FgR~a~-~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~ 172 (366)
T TIGR01953 94 IDPDVQIGDEVKKEINPENFGRIAA-QAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGLIVELA 172 (366)
T ss_pred CCCCCCCCCEEEEECCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEEEEEEC
T ss_conf 0779621537887427666447899-999999988889999876776643331808999999975257875210799985
Q ss_pred CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCC----CEEEEEE
Q ss_conf 48315788642024444433113326972589999874765----2799852
Q gi|254780456|r 218 SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQET----HRISLGM 265 (576)
Q Consensus 218 ~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~----~~i~lsl 265 (576)
|.++|++|.+++ -|.|.|+.|+++++.|..+.+.. -+|.||.
T Consensus 173 g~~e~~lp~~e~------iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSR 218 (366)
T TIGR01953 173 GKTEAILPKKEQ------IPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSR 218 (366)
T ss_pred CCEEEECCHHHC------CCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEC
T ss_conf 750252135337------8887523588899999999986889668999970
No 140
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=98.18 E-value=2.2e-06 Score=55.97 Aligned_cols=109 Identities=17% Similarity=0.253 Sum_probs=64.7
Q ss_pred CCCCCCCCEEEECCCCCCCCCCCEE-ECCCCCC-CCCCCCCCCCCCCC--CCCCCEEEEEEEEEECCC-CEEEECCCEEE
Q ss_conf 3455555302311133543233112-2121112-22221211100011--222330246788753147-17774483157
Q gi|254780456|r 149 DVTPLMHEPQLFEILKMDKRRGNIV-VSRRAVL-EESRAEQRSEIVQK--LEEGQVIEGTVKNITDYG-VFVDLSGVDGL 223 (576)
Q Consensus 149 d~~~~vG~~i~~~Ii~~d~~~~~iv-vS~k~~l-~~~~~~~~~~~~~~--l~~G~~v~g~V~~i~~~g-~~V~~~g~~g~ 223 (576)
++...+|..+...+..-+ =+|+. -..|+++ +.-+...+...++. -++|+++.|+|..+...| ++|++|+++|+
T Consensus 88 ~~~~~iGd~i~~~i~~~~--FgRiAaq~AKQvi~QkireaEr~~i~~efk~r~GeiV~G~V~r~~~~~~~~vdlg~~ea~ 165 (375)
T PRK12328 88 DPDVEIGDELSYELSLEN--MGRTAANTLFKELEYHIQRLLEDSIFEKYKEKVGSVVFGTVVRVDNEENTFIEIDEIRAI 165 (375)
T ss_pred CCCCCCCCEEEEECCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCEEEECCCCEEE
T ss_conf 899841788998428445--418999999999999999999999999998642948999999996588489973981798
Q ss_pred EEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCC---CEEEEEE
Q ss_conf 88642024444433113326972589999874765---2799852
Q gi|254780456|r 224 LHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQET---HRISLGM 265 (576)
Q Consensus 224 i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~---~~i~lsl 265 (576)
+|.++. -|.+.|+.||.++|.|..+..+. .+|.||.
T Consensus 166 Lp~~eq------ip~E~y~~Gdrik~~i~~V~~~~~~gpqI~lSR 204 (375)
T PRK12328 166 LPMKNR------IKGEKFKVGDVVKAVLRRVKIDKKNGIKLELSR 204 (375)
T ss_pred ECHHHC------CCCCCCCCCCEEEEEEEEEECCCCCCCEEEEEC
T ss_conf 027763------886558999869999999872789995899967
No 141
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.17 E-value=4.5e-05 Score=48.05 Aligned_cols=105 Identities=20% Similarity=0.286 Sum_probs=75.9
Q ss_pred EECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCC--CCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC
Q ss_conf 33269725899998747652799852155543210000000--4896658999981596699985142000000111101
Q gi|254780456|r 240 VLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKY--VEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW 317 (576)
Q Consensus 240 ~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~--~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~ 317 (576)
.|..|+++.+.+.++-...++. +++.++.. .| ++||.+-|+|+.+...+-+|+++....|++|.|++.|
T Consensus 27 ty~~~~~i~As~~G~v~~~~k~-v~ViPl~g--------rY~P~~GD~VIG~V~~v~~~~W~VDI~s~~~a~L~~s~~~~ 97 (232)
T PRK04163 27 TYVEGGKIYSSVVGLVEIKDDK-VRVIPLEG--------KYIPKKGDLVIGKVTDVGFSGWEVDINSPYKAILPVSEVLG 97 (232)
T ss_pred EEEECCEEEEEEEEEEEEECCE-EEEEECCC--------CCCCCCCCEEEEEEEEECCCEEEEECCCCCEEEECHHHCCC
T ss_conf 5998999999998889997999-99998985--------10587699899999983187179986996055852444566
Q ss_pred CC---CCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf 11---35574210037845799999862155047875203
Q gi|254780456|r 318 TK---KNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 318 ~~---~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
-. ...+..++|.+||.+-|+|..+++.. .+.|++|.
T Consensus 98 r~~~~~~~~mr~~l~~GDlI~ArV~~v~~~~-~~~Lt~k~ 136 (232)
T PRK04163 98 RPVDVESTDLRKYLDIGDYIIAKVKDVDETK-DVVLTLKG 136 (232)
T ss_pred CCCCCCHHHHHHHCCCCCEEEEEEEEECCCC-CEEEEECC
T ss_conf 5555643567751788988999999966899-78999548
No 142
>KOG1856 consensus
Probab=98.15 E-value=2.3e-06 Score=55.89 Aligned_cols=77 Identities=25% Similarity=0.419 Sum_probs=60.7
Q ss_pred CCCCCCCEEEEEEEEECCCE---EEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf 00048966589999815966---999851420000001111011135574210037845799999862155047875203
Q gi|254780456|r 278 DKYVEGSKVSGVVTNLTDYG---VFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 278 ~~~~~G~~v~g~V~~v~~~G---~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
+.|-.|.++.++|++++..- +-|.+..|++||||.+++| +....+|...+++||.+.|+|+.+|.++=.+.||++.
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S-d~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS-DRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred HHHCCCCEEEEEEEEEEECCCCEEEEEECCCCCEEEECCCCC-HHHCCCHHHHHCCCCEEEEEEEEEEHHHHHHHHHHHH
T ss_conf 673567567775567871565315787427873154433367-3421587775114762799965332854553110014
Q ss_pred C
Q ss_conf 4
Q gi|254780456|r 355 A 355 (576)
Q Consensus 355 ~ 355 (576)
+
T Consensus 1060 s 1060 (1299)
T KOG1856 1060 S 1060 (1299)
T ss_pred H
T ss_conf 8
No 143
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.13 E-value=1.2e-06 Score=57.58 Aligned_cols=64 Identities=23% Similarity=0.487 Sum_probs=36.1
Q ss_pred CCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCC--EEEEEE
Q ss_conf 2233024678875314717774483157886420244444331133269725899998747652--799852
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETH--RISLGM 265 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~--~i~lsl 265 (576)
++|+++.|+|..+...+++|++|+++|++|.++. -|.+.|++||.++|.|..+....+ +|.||.
T Consensus 133 r~GeiV~G~V~r~~~~~~~Vdlg~~ea~LP~~eq------ip~E~~~~Gdrika~i~~V~~~~kgp~I~lSR 198 (353)
T PRK12327 133 REGDIVTGTVQRDDNRFVYVNLGKIEAVLPPAEQ------IPGETYKHGDRIKVYVVKVEKTTKGPQIFVSR 198 (353)
T ss_pred HCCCEEEEEEEEECCCCEEEEECCEEEECCHHHC------CCCCCCCCCCEEEEEEEEEEECCCCCEEEEEC
T ss_conf 4396699999997588589997882464687986------99877799997999999999759974799964
No 144
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.05 E-value=2e-06 Score=56.16 Aligned_cols=64 Identities=25% Similarity=0.458 Sum_probs=34.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCC--EEEEEE
Q ss_conf 2233024678875314717774483157886420244444331133269725899998747652--799852
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETH--RISLGM 265 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~--~i~lsl 265 (576)
++|+++.|+|+++....++|++|+++|++|.++. -|.+.|++|+.++|.|..+..+.+ +|.||.
T Consensus 134 r~Geiv~G~V~r~~~~~i~Vdlg~~ea~Lp~~e~------ip~E~~~~Gdrik~~i~~V~~~~kg~qi~lSR 199 (428)
T PRK09202 134 RVGEIITGTVKRVERGNIIVDLGRAEAILPRDEQ------IPRENFRPGDRVRAYVYEVRKEARGPQIILSR 199 (428)
T ss_pred HCCCEEEEEEEEECCCCEEEEECCEEEECCHHHC------CCCCCCCCCCEEEEEEEEHHCCCCCCEEEEEC
T ss_conf 3298899999997278389997882575647876------99866799987999872021258985799954
No 145
>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=98.04 E-value=1.9e-05 Score=50.31 Aligned_cols=72 Identities=25% Similarity=0.311 Sum_probs=45.1
Q ss_pred CCCCCEEEEEEEEECCC--EEEEEECCCCEEEEECCCCCCCC--CCCCCCCEECCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 04896658999981596--69998514200000011110111--35574210037845799999862155047875
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDY--GVFVELQSGIEGLAHISQISWTK--KNIHPSKILSVGQQVEVVILEVNPARKRISLG 351 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~--G~~V~l~~~v~G~i~~sels~~~--~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS 351 (576)
-.+|+++.|+|.++.+. ++||+++.+-.||+|.+++.+.. ...+..+.+++||.+-|.|+.--...+--.||
T Consensus 5 ~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~Kgp~lT 80 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLT 80 (88)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCCCCEEE
T ss_conf 6112489999988666874899965898689999034572351357887783779999999997668799786088
No 146
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=98.03 E-value=8.5e-05 Score=46.35 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=36.8
Q ss_pred CCCCEEEEEEEEECCCEEEEEECCC-----CEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEEC-CC--CEEEEE
Q ss_conf 4896658999981596699985142-----00000011110111355742100378457999998621-55--047875
Q gi|254780456|r 281 VEGSKVSGVVTNLTDYGVFVELQSG-----IEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNP-AR--KRISLG 351 (576)
Q Consensus 281 ~~G~~v~g~V~~v~~~G~~V~l~~~-----v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~-~~--~~i~lS 351 (576)
++|+++.|+|.++...+++|.++.+ ++|++|.+|. -|.+.|++|+.++|.|.++.. .+ -+|.||
T Consensus 152 k~GeIVtG~V~Rve~~~viv~l~~~lG~~~~EAiLP~~Eq-------IP~E~yr~Gdrira~i~~V~~~~~kGpqIiLS 223 (457)
T PRK12329 152 LEDPVLTARVLRFERQSVIMAVSSGFGRPEVEAELPKREQ-------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVS 223 (457)
T ss_pred HCCCEEEEEEEEEECCCEEEEECCCCCCCCEEEEECHHHC-------CCCCCCCCCCEEEEEEEEEECCCCCCCEEEEE
T ss_conf 5596799999998169779996477776423697278886-------99987899998999999976467888569995
No 147
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.99 E-value=1.6e-05 Score=50.77 Aligned_cols=70 Identities=36% Similarity=0.425 Sum_probs=42.3
Q ss_pred HHCCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEEEE
Q ss_conf 4021463898779999999819989999479603678997505664355637898799999997479985999
Q gi|254780456|r 18 SFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVF 90 (576)
Q Consensus 18 ~~~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g~i~l 90 (576)
+-+..+++.|....|+|.+++..|+|++++....|.++.+++.. ...+.+|+.+-+.+..+....|.+.+
T Consensus 114 ~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~---~~~~~vgdeiiV~v~~vr~~~geidf 183 (715)
T COG1107 114 SCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG---DPDYAVGDEIIVQVSDVRPEKGEIDF 183 (715)
T ss_pred CCCHHHCCCCEEEECCCCCHHHHCCEEECCHHHHCCCCCCCCCC---CCCCCCCCEEEEEEECCCCCCCCCCE
T ss_conf 56620034640540310214340652433735433444012478---87778787489984215777775420
No 148
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.90 E-value=9.3e-05 Score=46.13 Aligned_cols=60 Identities=20% Similarity=0.406 Sum_probs=28.0
Q ss_pred CCCCCEEEEEEEEEECCCCEEEEC------------CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEE
Q ss_conf 222330246788753147177744------------831578864202444443311332697258999987
Q gi|254780456|r 195 LEEGQVIEGTVKNITDYGVFVDLS------------GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRI 254 (576)
Q Consensus 195 l~~G~~v~g~V~~i~~~g~~V~~~------------g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~ 254 (576)
.++|++|-|.|..+.+.-+.|.+- .+.|.+|++++......++.+.|.+||.++|+|++.
T Consensus 62 p~vGdiVig~V~~v~~~~a~v~I~~v~g~~~~~l~~~~~g~i~i~~v~~~~~~~~~d~fr~gDIVrAkVis~ 133 (187)
T PRK09521 62 LKKGDIVYGRVVDVKEQRALVRIVSIEGRGNRELATSKLGGIHISQVSDGYVEDLTDAFKIGDIVRAKVIST 133 (187)
T ss_pred CCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf 898999999999954767999999986868862565448888854378667452675248786899999735
No 149
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.88 E-value=0.00027 Score=43.30 Aligned_cols=70 Identities=24% Similarity=0.308 Sum_probs=48.7
Q ss_pred CCCCCEEEEEEEEECCCEEEEEECC-----------CCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEE
Q ss_conf 0489665899998159669998514-----------20000001111011135574210037845799999862155047
Q gi|254780456|r 280 YVEGSKVSGVVTNLTDYGVFVELQS-----------GIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRI 348 (576)
Q Consensus 280 ~~~G~~v~g~V~~v~~~G~~V~l~~-----------~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i 348 (576)
.++|+++-|+|+++.+.-+.|++-. ...|.+|++++. .....++.+.|++||.|.++|++..+ .+
T Consensus 62 p~vGdiVig~V~~v~~~~a~v~I~~v~g~~~~~l~~~~~g~i~i~~v~-~~~~~~~~d~fr~gDIVrAkVis~~~---~~ 137 (187)
T PRK09521 62 LKKGDIVYGRVVDVKEQRALVRIVSIEGRGNRELATSKLGGIHISQVS-DGYVEDLTDAFKIGDIVRAKVISTTD---PI 137 (187)
T ss_pred CCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEEEEECCCC-HHHHHHHHHHCCCCCEEEEEEEECCC---CE
T ss_conf 898999999999954767999999986868862565448888854378-66745267524878689999973598---46
Q ss_pred EEEEE
Q ss_conf 87520
Q gi|254780456|r 349 SLGLK 353 (576)
Q Consensus 349 ~lS~k 353 (576)
.||.+
T Consensus 138 ~Lst~ 142 (187)
T PRK09521 138 QLSTK 142 (187)
T ss_pred EEEEC
T ss_conf 99953
No 150
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.88 E-value=6.9e-05 Score=46.91 Aligned_cols=74 Identities=20% Similarity=0.285 Sum_probs=61.8
Q ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHH-----------CCCHHHCCCCCEEEEEEEEECCCCC
Q ss_conf 04789879999999708908999617798499999747182121-----------0420110689879999999705768
Q gi|254780456|r 455 SLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRV-----------DQDPGRFSKGQIVDACVVNVSKKDG 523 (576)
Q Consensus 455 ~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~-----------~~~~~~~~vG~~v~~~Vi~id~~~~ 523 (576)
.-.+|+...|.|.+++.+|+||.+.+ .+++|++|.+.+...+- ......|..|+.|+++++++|...+
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~-~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~ 697 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPE-LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER 697 (706)
T ss_pred HHCCCCEEEEEEEEEECCCEEEEECC-CCEEEEEECCCCCCCEEECCHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCC
T ss_conf 86158768899998732757999627-54033476355886103023011232035566542338869999998705656
Q ss_pred EEEEEE
Q ss_conf 699870
Q gi|254780456|r 524 KVSLSI 529 (576)
Q Consensus 524 ri~LS~ 529 (576)
++.+++
T Consensus 698 ~i~~~~ 703 (706)
T COG0557 698 KIDFEL 703 (706)
T ss_pred CEEEEE
T ss_conf 135885
No 151
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.88 E-value=0.00012 Score=45.46 Aligned_cols=72 Identities=36% Similarity=0.585 Sum_probs=55.8
Q ss_pred CCCCCEEEEEEEEEEEEEEEEECC-CCEEEEEHHHHHCCC----------CCHHHHHHHCCCCCCEEEEEECCCCCCCCC
Q ss_conf 222213699999850169997068-841354005530012----------200123421112342268852156545532
Q gi|254780456|r 368 PPGTEVEGEVKNKTDFGLFIGLDE-HLDGMIHLSDLDWNR----------PGEKVIAEYAKGDIVKAVVLDIDVGKERIS 436 (576)
Q Consensus 368 ~~G~~v~g~V~~v~~~g~~V~l~~-~i~g~i~~~dls~~~----------~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~ 436 (576)
.+|+...|.|..++.+|+||.+.. +++|++|.+.+..+. ..+.....|..|+.+++++.+++...+.+.
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 CCCCEEEEEEEEEECCCEEEEECCCCEEEEEECCCCCCCEEECCHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCEE
T ss_conf 15876889999873275799962754033476355886103023011232035566542338869999998705656135
Q ss_pred CCH
Q ss_conf 011
Q gi|254780456|r 437 LGV 439 (576)
Q Consensus 437 LS~ 439 (576)
+++
T Consensus 701 ~~~ 703 (706)
T COG0557 701 FEL 703 (706)
T ss_pred EEE
T ss_conf 885
No 152
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.85 E-value=0.00022 Score=43.82 Aligned_cols=64 Identities=17% Similarity=0.233 Sum_probs=36.8
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC-C-----CEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECC-C-C-CEEEEEE
Q ss_conf 22330246788753147177744-8-----3157886420244444331133269725899998747-6-5-2799852
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS-G-----VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQ-E-T-HRISLGM 265 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~-g-----~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~-~-~-~~i~lsl 265 (576)
++|+++.|+|+.+...+++|+++ + ++|++|.++. -|.+.|++|+.++|.|..+.. . + .+|.||.
T Consensus 152 k~GeIVtG~V~Rve~~~viv~l~~~lG~~~~EAiLP~~Eq------IP~E~yr~Gdrira~i~~V~~~~~kGpqIiLSR 224 (457)
T PRK12329 152 LEDPVLTARVLRFERQSVIMAVSSGFGRPEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 224 (457)
T ss_pred HCCCEEEEEEEEEECCCEEEEECCCCCCCCEEEEECHHHC------CCCCCCCCCCEEEEEEEEEECCCCCCCEEEEEC
T ss_conf 5596799999998169779996477776423697278886------999878999989999999764678885699954
No 153
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.81 E-value=0.002 Score=38.04 Aligned_cols=162 Identities=16% Similarity=0.220 Sum_probs=95.8
Q ss_pred CCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCC---CCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHC
Q ss_conf 222213699999850169997068841354005530012---20012342111234226885215654553201132210
Q gi|254780456|r 368 PPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNR---PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSG 444 (576)
Q Consensus 368 ~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~---~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~ 444 (576)
.+|++|=|.|..+...+-.|+++....+++|++++.|.. ...+....|++||.+-|+|..+|++. ...|++|.
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~-~~~L~~k~--- 138 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDG-EVELTLKD--- 138 (239)
T ss_pred CCCCEEEEEEEEECCCCEEEECCCCCCEEEEHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCC-CEEEEEEC---
T ss_conf 88999999999971563389728953237426662002255422345222676878999999726777-53799606---
Q ss_pred CCCCCHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 11100001100478987999999970890899961779849999974718212104201106898799999997057686
Q gi|254780456|r 445 SAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGK 524 (576)
Q Consensus 445 ~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~r 524 (576)
..+..++.|+++. +.+.- +|. -+... ...-.. ......|.|+ + --+++
T Consensus 139 ------~~~GkL~~G~iv~-----i~p~k--------------VpR-vig~~--~sm~~~--l~~~~~~~I~-V-G~NG~ 186 (239)
T COG1097 139 ------EGLGKLKNGQIVK-----IPPSK--------------VPR-VIGKK--GSMLNM--LKEKTGCEII-V-GQNGR 186 (239)
T ss_pred ------CCCCCCCCCEEEE-----ECHHH--------------CCE-EECCC--CCHHHH--HHHCCCEEEE-E-ECCCE
T ss_conf ------6773024888999-----76022--------------524-76688--647887--6540576899-9-66988
Q ss_pred EEEEEHHH-HHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99870365-577779999984034457779999999998743
Q gi|254780456|r 525 VSLSIKAL-EIAEEKGAVAQFGSSDSGASLGDILGMALKNRG 565 (576)
Q Consensus 525 i~LS~k~~-~~~~~~~~~~~~~~~~~~~tlg~~~~~~lk~~~ 565 (576)
|.++.+.. .+.--.+++.+...+....-+.|..+..+++..
T Consensus 187 IWV~~~~~~~e~~~~~aI~~ie~ea~~~gltdr~~~~i~~~~ 228 (239)
T COG1097 187 IWVDGENESLEELAIEAIRKIEREAHTSGLTDRIKEFLKKLL 228 (239)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 996278863279999999987554335667999999999987
No 154
>KOG2916 consensus
Probab=97.76 E-value=1.5e-05 Score=50.98 Aligned_cols=81 Identities=26% Similarity=0.416 Sum_probs=66.0
Q ss_pred CCCC-CCCEEEEEEEEECCCEEEEEEC--CCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf 0004-8966589999815966999851--420000001111011135574210037845799999862155047875203
Q gi|254780456|r 278 DKYV-EGSKVSGVVTNLTDYGVFVELQ--SGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 278 ~~~~-~G~~v~g~V~~v~~~G~~V~l~--~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
++|| +++++-+.|..+.+-|++|.|- ++++|.|-.|||| -+++.+.++..++|..=-|.|+.+|++++-|.||.++
T Consensus 11 ~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS-rRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916 11 NKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS-RRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred CCCCCCCCEEEEEEEEEHHCCCEEEEEECCCCCCCHHHHHHH-HHHHHHHHHHHHCCCCCEEEEEEECCCCCCEECHHCC
T ss_conf 159975327998753702062167621027811110035777-8888989999840775348999971778706621313
Q ss_pred CCCCC
Q ss_conf 45432
Q gi|254780456|r 355 ALINP 359 (576)
Q Consensus 355 ~~~~p 359 (576)
..++-
T Consensus 90 Vs~ed 94 (304)
T KOG2916 90 VSPED 94 (304)
T ss_pred CCHHH
T ss_conf 88778
No 155
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.76 E-value=0.00015 Score=44.81 Aligned_cols=72 Identities=21% Similarity=0.345 Sum_probs=47.8
Q ss_pred CCCCCCCCEEEEEEEEEECCCCEEEECC-----------CEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCE
Q ss_conf 0112223302467887531471777448-----------31578864202444443311332697258999987476527
Q gi|254780456|r 192 VQKLEEGQVIEGTVKNITDYGVFVDLSG-----------VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHR 260 (576)
Q Consensus 192 ~~~l~~G~~v~g~V~~i~~~g~~V~~~g-----------~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~ 260 (576)
...++.|++|-|.|..+....+.|.+-+ ..|-+|.++++...+.+.++.|++||.++|+|++.- -.
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~ 135 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP 135 (188)
T ss_pred CCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECC---CC
T ss_conf 776898879999995326608999999994333367887402589782023111020134464617999998617---87
Q ss_pred EEEEEC
Q ss_conf 998521
Q gi|254780456|r 261 ISLGMK 266 (576)
Q Consensus 261 i~lslK 266 (576)
+.||.+
T Consensus 136 ~~Lst~ 141 (188)
T COG1096 136 IQLSTK 141 (188)
T ss_pred EEEEEC
T ss_conf 189852
No 156
>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=97.75 E-value=0.00027 Score=43.32 Aligned_cols=60 Identities=15% Similarity=0.168 Sum_probs=22.0
Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEEC
Q ss_conf 89879999999708908999617798499999747182121042011068987999999970
Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVS 519 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id 519 (576)
+|++|.|+|.++......|++... -.+.+|.+.....-..+..+.|.+|+.|.|+|+.++
T Consensus 6 vGDvVigrV~~v~~~~w~vdI~~~--~~a~l~~~~~~~~D~~~m~~~f~~GDlI~A~V~~~~ 65 (82)
T cd04454 6 VGDIVIGIVTEVNSRFWKVDILSR--GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLG 65 (82)
T ss_pred CCCEEEEEEEEECCCEEEEEECCC--EEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEEC
T ss_conf 999999999997078189996863--288973021677306679874587768999999976
No 157
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase ..
Probab=97.74 E-value=1.1e-05 Score=51.81 Aligned_cols=73 Identities=22% Similarity=0.331 Sum_probs=62.2
Q ss_pred HCCCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCH----HHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 1004789879999999708908999617798499999747182----121042011068987999999970576869987
Q gi|254780456|r 453 VSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSR----DRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLS 528 (576)
Q Consensus 453 ~~~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~----~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS 528 (576)
...-++|+-+-|+|.+...||+||.+. +|-+|++|+|++-. .+++...+.+.+|+++.+.|.++| ++++++|-
T Consensus 648 P~~P~vG~~~lGtvvk~~~fGafvsll--PG~dGl~his~~r~l~~G~~~~~v~~v~~~G~k~~ve~~~~d-~rGkl~l~ 724 (725)
T TIGR02696 648 PTLPEVGERFLGTVVKTTAFGAFVSLL--PGKDGLLHISEIRKLAGGKRVEKVEDVLSVGQKIQVEIADID-DRGKLSLV 724 (725)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCEEEEC--CCCCCEEEHHHHHHHHCCCCHHHHHHHHHCCCCEEEEEEECC-CCCCEEEC
T ss_conf 888740013420331002334146740--688750316556763157203557888722430133111112-57745621
No 158
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.73 E-value=0.0011 Score=39.54 Aligned_cols=105 Identities=19% Similarity=0.233 Sum_probs=68.4
Q ss_pred ECCCCEEEEEEEEECC-CCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCC
Q ss_conf 3269725899998747-652799852155543210000000489665899998159669998514200000011110111
Q gi|254780456|r 241 LSIGQQVKVKIIRINQ-ETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTK 319 (576)
Q Consensus 241 ~~~G~~v~~~Vl~~d~-~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~ 319 (576)
|-.|+.+.+.+.+.-. ..+.+ .+-++.. + .+ =.+||++=|+|..+...+-.|+++.-..+++|.|++-|-+
T Consensus 30 y~~~~~iyssv~G~~~~~~~~v--~VIpl~g-~--Yi---P~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~ 101 (239)
T COG1097 30 YFEGGKIYSSVVGLLDVKGKLV--RVIPLEG-R--YI---PEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRK 101 (239)
T ss_pred EECCCEEEEEEEEEEEEECCEE--EEEECCC-C--CC---CCCCCEEEEEEEEECCCCEEEECCCCCCEEEEHHHHHCCC
T ss_conf 8619879999875789908868--9986787-5--24---8889999999999715633897289532374266620022
Q ss_pred ---CCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEEC
Q ss_conf ---35574210037845799999862155047875203
Q gi|254780456|r 320 ---KNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQ 354 (576)
Q Consensus 320 ---~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~ 354 (576)
...++..+|++||.|-|+|..+|+. ....|++|.
T Consensus 102 ~~~~~~~~r~~l~vGD~v~AkV~~vd~~-~~~~L~~k~ 138 (239)
T COG1097 102 FENAEKDLRPFLNVGDLVYAKVVDVDRD-GEVELTLKD 138 (239)
T ss_pred CCCCCCCCCCCCCCCCEEEEEEEECCCC-CCEEEEEEC
T ss_conf 5542234522267687899999972677-753799606
No 159
>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=97.72 E-value=0.00018 Score=44.44 Aligned_cols=16 Identities=31% Similarity=0.443 Sum_probs=5.0
Q ss_pred EEEEECCCEEEEEEHH
Q ss_conf 9999479603678997
Q gi|254780456|r 42 VVVDVGLKFEGRIPRR 57 (576)
Q Consensus 42 v~vdig~k~~G~i~~~ 57 (576)
+|||+|....||+|.+
T Consensus 25 AFVdiG~~k~gfL~~~ 40 (88)
T cd04453 25 AFVDIGLGKNGFLHLS 40 (88)
T ss_pred EEEECCCCCCEEEECH
T ss_conf 9996589868999903
No 160
>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=97.71 E-value=0.00016 Score=44.73 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=6.6
Q ss_pred CCEEEEEEEEEECCEEEEEEC
Q ss_conf 877999999981998999947
Q gi|254780456|r 27 NCVTKGIVVGLEKDTVVVDVG 47 (576)
Q Consensus 27 G~iv~G~V~~i~~~~v~vdig 47 (576)
|++|.|+|.++..+...+|++
T Consensus 7 GDvVigrV~~v~~~~w~vdI~ 27 (82)
T cd04454 7 GDIVIGIVTEVNSRFWKVDIL 27 (82)
T ss_pred CCEEEEEEEEECCCEEEEEEC
T ss_conf 999999999970781899968
No 161
>PRK11712 ribonuclease G; Provisional
Probab=97.65 E-value=0.00045 Score=41.95 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=32.6
Q ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHC
Q ss_conf 63898779999999819--989999479603678997505
Q gi|254780456|r 23 DLAENCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFM 60 (576)
Q Consensus 23 ~~~~G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~ 60 (576)
.-..|.|..|+|.++.+ +.+|||+|..-.||+|.+|+.
T Consensus 35 ~~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~ 74 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIV 74 (489)
T ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCC
T ss_conf 7766766999994306887769998479874287855438
No 162
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.64 E-value=0.00026 Score=43.41 Aligned_cols=96 Identities=16% Similarity=0.223 Sum_probs=52.7
Q ss_pred ECCCCEEEEEEEEE-CCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECC--C--------CEEE
Q ss_conf 32697258999987-47652799852155543210000000489665899998159669998514--2--------0000
Q gi|254780456|r 241 LSIGQQVKVKIIRI-NQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQS--G--------IEGL 309 (576)
Q Consensus 241 ~~~G~~v~~~Vl~~-d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~--~--------v~G~ 309 (576)
+..|..+.+-+.+. ..+......|++.-. ......+.|+++-|.|+++....+.|++.. + ..|-
T Consensus 27 ~~~~g~i~A~~~G~~~~d~~n~~~~V~p~~-----~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ 101 (188)
T COG1096 27 YEEGGEIRAAATGVVRRDDKNRVISVKPGK-----KTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAAD 101 (188)
T ss_pred EEECCEEEEEECCCEEECCCCEEEEECCCC-----CCCCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCEEE
T ss_conf 867999998503538861364499952477-----777768988799999953266089999999943333678874025
Q ss_pred EECCCCCCCCCCCCCCCEECCCCEEEEEEEEEE
Q ss_conf 001111011135574210037845799999862
Q gi|254780456|r 310 AHISQISWTKKNIHPSKILSVGQQVEVVILEVN 342 (576)
Q Consensus 310 i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id 342 (576)
+|+|+.+ +....+..+.|++||.|.++|++.-
T Consensus 102 ihvs~~~-~~~~~~~~d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 102 IHVSQVR-DGYVEKLSDAFRIGDIVRARVISTG 133 (188)
T ss_pred EEEEECC-CCCCCCCCCCCCCCCEEEEEEEECC
T ss_conf 8978202-3111020134464617999998617
No 163
>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=97.55 E-value=0.0005 Score=41.69 Aligned_cols=70 Identities=19% Similarity=0.219 Sum_probs=0.0
Q ss_pred CCCCEEEEEEEEECCCEEEEEE--------CCCCEEEEECCCC-CCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 4896658999981596699985--------1420000001111-011135574210037845799999862155047875
Q gi|254780456|r 281 VEGSKVSGVVTNLTDYGVFVEL--------QSGIEGLAHISQI-SWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLG 351 (576)
Q Consensus 281 ~~G~~v~g~V~~v~~~G~~V~l--------~~~v~G~i~~sel-s~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS 351 (576)
++|+++.|+|+++.+..++|++ .+...|.||.+++ +.........+.|++||.|.++|++.. +.+...||
T Consensus 5 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~l~~~f~g~Ir~~dVr~te~d~v~m~~~FrpGDIVrA~Vislg-d~~~y~LS 83 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG-DASSYYLS 83 (92)
T ss_pred CCCCEEEEEEEEECCCEEEEEEEEECCEECCCEEEEEEEHHHCCCCCCCCEEHHHCCCCCCEEEEEEEECC-CCCEEEEE
T ss_conf 89999999999971137899999999998376257887924434355530434135499989999999747-87249998
No 164
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase ..
Probab=97.48 E-value=6.3e-05 Score=47.15 Aligned_cols=69 Identities=30% Similarity=0.482 Sum_probs=57.1
Q ss_pred CCCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHC---CCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 2222136999998501699970688413540055300---122001234211123422688521565455320
Q gi|254780456|r 368 PPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDW---NRPGEKVIAEYAKGDIVKAVVLDIDVGKERISL 437 (576)
Q Consensus 368 ~~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~---~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~L 437 (576)
.+|+..-|+|.+.+.+|+||++-+|-+|++|++++.. -...+...+.+.+|+++.+-|..+|. +++++|
T Consensus 652 ~vG~~~lGtvvk~~~fGafvsllPG~dGl~his~~r~l~~G~~~~~v~~v~~~G~k~~ve~~~~d~-rGkl~l 723 (725)
T TIGR02696 652 EVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISEIRKLAGGKRVEKVEDVLSVGQKIQVEIADIDD-RGKLSL 723 (725)
T ss_pred CCHHHHHHHHHHCCCCCCEEEECCCCCCEEEHHHHHHHHCCCCHHHHHHHHHCCCCEEEEEEECCC-CCCEEE
T ss_conf 400134203310023341467406887503165567631572035578887224301331111125-774562
No 165
>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=97.36 E-value=0.0004 Score=42.26 Aligned_cols=69 Identities=19% Similarity=0.347 Sum_probs=32.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCC--HHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 9879999999708908999617798499999747182121042--0110689879999999705768699870
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQD--PGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~--~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
|++|+++|.+.++.|+-|.+.. ..+.||+|..++|+.....+ -..+++|+.+ .+++-....++++.|+.
T Consensus 1 Gq~VdvkVlkkt~~GLeV~ilp-~~~~afLPt~HLSDhv~N~~LL~~~lq~GD~i-~~vmCls~~~~~iil~r 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILP-EEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTI-PNLMCLSNYKGRIILTK 71 (72)
T ss_pred CCEEEEEEEEECCCCCEEEECC-CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCH-HCEEEEECCCCCEEEEC
T ss_conf 9606889998628872789768-88542144532233322458999988447861-02578862788288845
No 166
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.36 E-value=0.0018 Score=38.28 Aligned_cols=61 Identities=23% Similarity=0.378 Sum_probs=49.1
Q ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHCCCC------------CCCCCCCCCEEEEEEEEEEC
Q ss_conf 63898779999999819--989999479603678997505664------------35563789879999999747
Q gi|254780456|r 23 DLAENCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFMGKG------------QYTPIKVGDEVEVYVERTEN 83 (576)
Q Consensus 23 ~~~~G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~~~~------------~~~~~kvGd~i~v~V~~~~~ 83 (576)
.-..|.|..|+|.+|.+ ..+|||+|..-.||+|.+|+..++ ..+.++.||.|-|-|.+-.-
T Consensus 35 ~q~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~~ey~~~~~~~~grp~I~dvLkeGQeILVQV~KEp~ 109 (1063)
T PRK10811 35 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEER 109 (1063)
T ss_pred CCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCCHHHCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCC
T ss_conf 534054268999785688605777238975542168882865426553435687878836799989999966787
No 167
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.31 E-value=0.00068 Score=40.89 Aligned_cols=35 Identities=23% Similarity=0.296 Sum_probs=22.3
Q ss_pred HCCCEEEEEEEEEECC--CEEEEEC-CCHHHHHCCCCC
Q ss_conf 2897699999999679--5599974-402000001123
Q gi|254780456|r 109 RAGERIEGVIFNQVKG--GMTVDLN-GEVAFLPRSQID 143 (576)
Q Consensus 109 ~~g~~v~g~V~~~~k~--G~~V~i~-gi~~FlP~s~~~ 143 (576)
..|.+-.|+|++...+ ..||+|| +-.||||++.+.
T Consensus 37 ~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~ 74 (1063)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA 74 (1063)
T ss_pred CCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCC
T ss_conf 40542689997856886057772389755421688828
No 168
>PRK11712 ribonuclease G; Provisional
Probab=97.26 E-value=0.0017 Score=38.53 Aligned_cols=66 Identities=23% Similarity=0.365 Sum_probs=48.5
Q ss_pred CCCCCCEEEEEEEEEEC--CCCEEEEC-CCEEEEEEEECCC-C-----------CCCCCCEEECCCCEEEEEEEEECCCC
Q ss_conf 12223302467887531--47177744-8315788642024-4-----------44433113326972589999874765
Q gi|254780456|r 194 KLEEGQVIEGTVKNITD--YGVFVDLS-GVDGLLHVTDIAW-H-----------RILHPSKVLSIGQQVKVKIIRINQET 258 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~--~g~~V~~~-g~~g~i~~~~ls~-~-----------~~~~~~~~~~~G~~v~~~Vl~~d~~~ 258 (576)
.-.+|.++.|+|.++.+ .++||++| +-.||+|.+|+.. . ...++.+.++.||.+-+.|..--..+
T Consensus 35 ~~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~~~~~~~~~~~~~~~~~~~I~~~l~~Gq~ilVQV~Ke~~~~ 114 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGT 114 (489)
T ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCCCCHHCCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCCCC
T ss_conf 77667669999943068877699984798742878554385211133322356664676774679998999996268789
Q ss_pred C
Q ss_conf 2
Q gi|254780456|r 259 H 259 (576)
Q Consensus 259 ~ 259 (576)
+
T Consensus 115 K 115 (489)
T PRK11712 115 K 115 (489)
T ss_pred C
T ss_conf 8
No 169
>pfam10246 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. that are highly conserved from worms to humans. The structure has previously been referred to as MRP-S18 but the current numbering fits the preferred nomenclature from these authors.
Probab=97.26 E-value=0.0016 Score=38.71 Aligned_cols=73 Identities=23% Similarity=0.272 Sum_probs=55.5
Q ss_pred CHHHHHHHHHHHHH-CCCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEE
Q ss_conf 10688999988540-214638987799999998199899994796036789975056643556378987999999974
Q gi|254780456|r 6 PSREDFATLLEESF-TKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTE 82 (576)
Q Consensus 6 ~~~~~f~~ll~~~~-~~~~~~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~ 82 (576)
..++.|+.||..|- ..---..|.++.|+|..+-++-+|+|+|+|+...+..- ....+.|+.|..|.+++...+
T Consensus 2 ~~~~sFasLLR~S~fi~lG~~~gk~v~G~I~hvv~dDLYIDfG~KFhcVc~rP----~~~~~~y~~G~rV~lrLkdlE 75 (105)
T pfam10246 2 HPEKSFASLLRNSKFVQLGDAEGKLVIGKIFHIVEDDLYIDFGGKFHCVCKRP----AVNGEKYQRGSRVRLRLKDLE 75 (105)
T ss_pred CCHHHHHHHHHCCCHHHCCCCCCCEEEEEEEEEECCCEEEEECCEEEEEECCC----CCCHHHCCCCCEEEEEECCHH
T ss_conf 75221999973591210578557788999999706725998377167887376----647100577888999966875
No 170
>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=97.21 E-value=0.00045 Score=41.98 Aligned_cols=69 Identities=22% Similarity=0.241 Sum_probs=39.7
Q ss_pred CCCEEEEEEEEEEEEEEEEE-CCCCEEEEEHHHHHCCCCCHHHH-HHHCCCCCCEEEEEECCCCCCCCCCCH
Q ss_conf 22136999998501699970-68841354005530012200123-421112342268852156545532011
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGL-DEHLDGMIHLSDLDWNRPGEKVI-AEYAKGDIVKAVVLDIDVGKERISLGV 439 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l-~~~i~g~i~~~dls~~~~~~~~~-~~~k~G~~i~~~Vl~id~~~~~i~LS~ 439 (576)
|..|+++|.+.++.|+-|.+ +..+.||+|...+||...+...+ .-++.||.+. +++.+....+++.|+.
T Consensus 1 Gq~VdvkVlkkt~~GLeV~ilp~~~~afLPt~HLSDhv~N~~LL~~~lq~GD~i~-~vmCls~~~~~iil~r 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIP-NLMCLSNYKGRIILTK 71 (72)
T ss_pred CCEEEEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHH-CEEEEECCCCCEEEEC
T ss_conf 9606889998628872789768885421445322333224589999884478610-2578862788288845
No 171
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.11 E-value=0.0023 Score=37.68 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=15.8
Q ss_pred CCEEEEEEEEEECCCCEEEECCCEEEEEEEEC
Q ss_conf 33024678875314717774483157886420
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLSGVDGLLHVTDI 229 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~g~~g~i~~~~l 229 (576)
|+++.|.|+++.+.|.|.+.|-+..|+....+
T Consensus 2 GEVvDavVt~Vnk~G~Fa~~GPl~~fvS~~~i 33 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEVGPLSIFISRHLI 33 (88)
T ss_pred CCEEEEEEEEECCEEEEEEECCEEEEEECCCC
T ss_conf 95799999998347899980475899991118
No 172
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=97.04 E-value=0.0021 Score=37.97 Aligned_cols=13 Identities=38% Similarity=0.376 Sum_probs=4.3
Q ss_pred CCEEEEEEEEECC
Q ss_conf 9665899998159
Q gi|254780456|r 283 GSKVSGVVTNLTD 295 (576)
Q Consensus 283 G~~v~g~V~~v~~ 295 (576)
|+++.|+|++++.
T Consensus 5 GdiV~arVtrv~~ 17 (72)
T pfam10447 5 GDIVLARVTRVTP 17 (72)
T ss_pred CCEEEEEEEEECH
T ss_conf 9999999999750
No 173
>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=96.56 E-value=0.016 Score=32.62 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=11.1
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEH
Q ss_conf 221369999985016999706884135400
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHL 399 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~ 399 (576)
|++++|.|+++++.|.|.+.+ .++.|+..
T Consensus 2 GEVvDavVt~Vnk~G~Fa~~G-Pl~~fvS~ 30 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEVG-PLSIFISR 30 (88)
T ss_pred CCEEEEEEEEECCEEEEEEEC-CEEEEEEC
T ss_conf 957999999983478999804-75899991
No 174
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=96.55 E-value=0.0011 Score=39.53 Aligned_cols=99 Identities=17% Similarity=0.151 Sum_probs=59.9
Q ss_pred CCCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHCCCCCCCC-----CCC-------CCEEEEEEEEEECCCCE
Q ss_conf 463898779999999819--9899994796036789975056643556-----378-------98799999997479985
Q gi|254780456|r 22 KDLAENCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFMGKGQYTP-----IKV-------GDEVEVYVERTENSFGE 87 (576)
Q Consensus 22 ~~~~~G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~~~~~~~~-----~kv-------Gd~i~v~V~~~~~~~g~ 87 (576)
..-.+|.|..|.|.+|.+ +.+|||+|....||+|.+|+........ +.. +... .-.....+...
T Consensus 23 ~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~~~~~~d~~NA~~~a~~~~~--~~~~~~~kp~~ 100 (464)
T TIGR00757 23 SRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLEQLVDTDDDNAEAEAAPAEA--KREAGQEKPEE 100 (464)
T ss_pred HHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCCCCCHHHH--HHHHHCCCCHH
T ss_conf 1011002320202022037644774206883556303320332456888862021257677882332--20100136213
Q ss_pred EE-EEHHHHH-HHHHHHHHHHHHHCCCEEEEEEEEEE
Q ss_conf 99-9687875-55758999998528976999999996
Q gi|254780456|r 88 AV-FSRDKAL-REGVWEKIEAKFRAGERIEGVIFNQV 122 (576)
Q Consensus 88 i~-lS~~k~~-~~~~~~~i~~a~~~g~~v~g~V~~~~ 122 (576)
.. -|...+. ....-..|.+.+.+|+.|-+.|.+.-
T Consensus 101 ~~QS~~~~~~~~~~~~~~I~e~L~~gq~vlVQV~Kep 137 (464)
T TIGR00757 101 IIQSSGDELERRQSKTASISELLRPGQSVLVQVVKEP 137 (464)
T ss_pred HHCCCHHHHHHHHCCCCCHHHHHCCCCEEEEEEEECC
T ss_conf 2025302455431354352666128885899988526
No 175
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=96.47 E-value=0.025 Score=31.36 Aligned_cols=60 Identities=20% Similarity=0.235 Sum_probs=41.4
Q ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHCCC-------CCCCCCCCCCEEEEEEEEEE
Q ss_conf 63898779999999819--98999947960367899750566-------43556378987999999974
Q gi|254780456|r 23 DLAENCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFMGK-------GQYTPIKVGDEVEVYVERTE 82 (576)
Q Consensus 23 ~~~~G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~~~-------~~~~~~kvGd~i~v~V~~~~ 82 (576)
...+|.+..|.|.+|.+ ..+|||+|..-.||+|.+|..+. .....++.|+.+-+-|.+..
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred EEEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCHHHHHCCCCCCEEEECCCCEEEEEEEEEC
T ss_conf 763067168886231766322205516876606884105534420002350055417862899998625
No 176
>KOG3409 consensus
Probab=96.47 E-value=0.018 Score=32.29 Aligned_cols=14 Identities=43% Similarity=0.669 Sum_probs=5.0
Q ss_pred HHCCCCCCEEEEEE
Q ss_conf 21112342268852
Q gi|254780456|r 414 EYAKGDIVKAVVLD 427 (576)
Q Consensus 414 ~~k~G~~i~~~Vl~ 427 (576)
.|++||.+.++|++
T Consensus 122 sFrPgDiVlAkVis 135 (193)
T KOG3409 122 SFRPGDIVLAKVIS 135 (193)
T ss_pred CCCCCCEEEEEEEE
T ss_conf 36988688888851
No 177
>KOG3409 consensus
Probab=95.88 E-value=0.038 Score=30.26 Aligned_cols=59 Identities=19% Similarity=0.233 Sum_probs=23.5
Q ss_pred CCCEEEEEEEEECCCEEEEEE--------CCCCEEEEECCCCCCC-CCCCCCCCEECCCCEEEEEEEE
Q ss_conf 896658999981596699985--------1420000001111011-1355742100378457999998
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVEL--------QSGIEGLAHISQISWT-KKNIHPSKILSVGQQVEVVILE 340 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l--------~~~v~G~i~~sels~~-~~~~~~~~~~~~G~~v~~~Vl~ 340 (576)
+|+++.++|.++....+-|+| .+...|+||..++--+ +....+-+.|++||.|-++|++
T Consensus 68 ~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis 135 (193)
T KOG3409 68 VGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVIS 135 (193)
T ss_pred CCCEEEEEEEEECCCEEEEEEEEECCEEHHHHHCCEEEHHHCCCCCCCHHHHHHCCCCCCEEEEEEEE
T ss_conf 57679999876244135678999867970011211433543564440112163436988688888851
No 178
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=95.81 E-value=0.0051 Score=35.56 Aligned_cols=39 Identities=28% Similarity=0.529 Sum_probs=23.9
Q ss_pred CCCCCCEEEEEEEEEEC--CCCEEEEC-CCEEEEEEEECCCC
Q ss_conf 12223302467887531--47177744-83157886420244
Q gi|254780456|r 194 KLEEGQVIEGTVKNITD--YGVFVDLS-GVDGLLHVTDIAWH 232 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~--~g~~V~~~-g~~g~i~~~~ls~~ 232 (576)
.-.+|+++.|.|++|.+ -++||++| .-.||+|.+|+.|.
T Consensus 24 ~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~ 65 (464)
T TIGR00757 24 RQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGEN 65 (464)
T ss_pred HCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCC
T ss_conf 011002320202022037644774206883556303320332
No 179
>KOG4078 consensus
Probab=95.58 E-value=0.032 Score=30.74 Aligned_cols=51 Identities=22% Similarity=0.339 Sum_probs=24.2
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEEC
Q ss_conf 22136999998501699970688413540055300122001234211123422688521
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDI 428 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~i 428 (576)
|..|-|+|-.+....++++++....+.|..-.+ ..+.|..|-.|..+++..
T Consensus 83 gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~--------n~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078 83 GKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPAL--------NGEAYQKGARVRLRLIDL 133 (173)
T ss_pred CCEEEEEEEEEECCCEEEECCCEEEEEECCCCC--------CHHHHHCCCEEEEEECCH
T ss_conf 858876520110442389618748888737675--------877750576699997276
No 180
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=95.52 E-value=0.035 Score=30.51 Aligned_cols=73 Identities=22% Similarity=0.319 Sum_probs=54.5
Q ss_pred CCCCCCCCEEEEEEEEEECC--CCEEEEC-CCEEEEEEEECCCCCCCC-----CCEEECCCCEEEEEEEEECCCCCEEEE
Q ss_conf 01122233024678875314--7177744-831578864202444443-----311332697258999987476527998
Q gi|254780456|r 192 VQKLEEGQVIEGTVKNITDY--GVFVDLS-GVDGLLHVTDIAWHRILH-----PSKVLSIGQQVKVKIIRINQETHRISL 263 (576)
Q Consensus 192 ~~~l~~G~~v~g~V~~i~~~--g~~V~~~-g~~g~i~~~~ls~~~~~~-----~~~~~~~G~~v~~~Vl~~d~~~~~i~l 263 (576)
.....+|+++.|+|.++.+. .+||++| +-.||+|.+++.+ +... .+..++.||.+-+.|+.-...++--.|
T Consensus 32 ~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~l 110 (487)
T COG1530 32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARL 110 (487)
T ss_pred CCEEEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCH-HHHHCCCCCCEEEECCCCEEEEEEEEECCCCCCCCC
T ss_conf 7376306716888623176632220551687660688410553-442000235005541786289999862576603421
Q ss_pred EE
Q ss_conf 52
Q gi|254780456|r 264 GM 265 (576)
Q Consensus 264 sl 265 (576)
|-
T Consensus 111 T~ 112 (487)
T COG1530 111 TT 112 (487)
T ss_pred EE
T ss_conf 24
No 181
>KOG3298 consensus
Probab=94.89 E-value=0.14 Score=26.84 Aligned_cols=25 Identities=28% Similarity=0.627 Sum_probs=10.7
Q ss_pred CCEEEEEEEEEECCCCEEEECCCEE
Q ss_conf 3302467887531471777448315
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDLSGVDG 222 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~~g~~g 222 (576)
|+++.|+|+++...|+|.+.|-++-
T Consensus 82 GEVvdgvV~~Vnk~G~F~~~GPl~~ 106 (170)
T KOG3298 82 GEVVDGVVTKVNKMGVFARSGPLEV 106 (170)
T ss_pred CCEEEEEEEEEEEEEEEEECCCEEE
T ss_conf 7688899999842448996056675
No 182
>KOG3298 consensus
Probab=94.69 E-value=0.17 Score=26.29 Aligned_cols=27 Identities=26% Similarity=0.446 Sum_probs=17.4
Q ss_pred CCCEEEEEEEEEEEEEEEEECCCCEEEE
Q ss_conf 2213699999850169997068841354
Q gi|254780456|r 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMI 397 (576)
Q Consensus 370 G~~v~g~V~~v~~~g~~V~l~~~i~g~i 397 (576)
|++++|.|+.+++.|+|++.++ ++.|+
T Consensus 82 GEVvdgvV~~Vnk~G~F~~~GP-l~~f~ 108 (170)
T KOG3298 82 GEVVDGVVTKVNKMGVFARSGP-LEVFY 108 (170)
T ss_pred CCEEEEEEEEEEEEEEEEECCC-EEEEE
T ss_conf 7688899999842448996056-67532
No 183
>CHL00010 infA translation initiation factor 1
Probab=94.51 E-value=0.23 Score=25.61 Aligned_cols=65 Identities=28% Similarity=0.360 Sum_probs=38.0
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECC
Q ss_conf 58999981596699-98514200000011110111355742100378457999998621550478752034
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQA 355 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~ 355 (576)
+.|.|+.+.+.+.| |+|.+|..-+.|+| .+-..+--+ .-+||.|++.+-..|..+++|..-+|..
T Consensus 9 ~eG~V~e~Lpn~~F~V~Leng~~Vla~~s----GKmR~~~Ir-il~GD~V~VE~SpYDltkGRI~~R~k~~ 74 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGDLVLGYIS----GKIRRNSIR-ILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEEC----CHHEECEEE-ECCCCEEEEEECCCCCCCEEEEEEECCC
T ss_conf 98999998699889999789999999998----052003189-7489989999875678857899990456
No 184
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=94.31 E-value=0.24 Score=25.40 Aligned_cols=65 Identities=22% Similarity=0.336 Sum_probs=41.6
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECC
Q ss_conf 58999981596699-98514200000011110111355742100378457999998621550478752034
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQA 355 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~ 355 (576)
+.|+|+.+.+.+.| |+|++|..-+.|+| .+-..+--+ .-+||.|+|.+-..|..+.+|..-.|..
T Consensus 9 ~eG~V~e~lpn~~FrV~LeNg~~Vla~~s----GKmR~~~Ir-Il~GD~V~VElSpYDltkGRIvyR~k~~ 74 (87)
T PRK12442 9 LDGIVDEVLPDSRYRVTLENGVEVGAYAS----GRMRKHRIR-ILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEEE----CCEEEEEEE-ECCCCEEEEEECCCCCCCEEEEEEECCC
T ss_conf 87899998799879999779989999985----501330277-7689989999887778874899884788
No 185
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus 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 cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process.
Probab=94.21 E-value=0.029 Score=30.99 Aligned_cols=74 Identities=20% Similarity=0.274 Sum_probs=61.3
Q ss_pred CCCCC--CEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCH--HHHC-----------CCHHHCCCCCEEEEEEEEEC
Q ss_conf 04789--879999999708908999617798499999747182--1210-----------42011068987999999970
Q gi|254780456|r 455 SLRKN--DVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSR--DRVD-----------QDPGRFSKGQIVDACVVNVS 519 (576)
Q Consensus 455 ~~~~G--~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~--~~~~-----------~~~~~~~vG~~v~~~Vi~id 519 (576)
.-++| ....|.+..++.+|+|+.+.+ .++.|++|.+.+.+ ++.. .....|++|+.+.+++.+++
T Consensus 595 ~~~~g~~~~f~g~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~ 673 (684)
T TIGR00358 595 LDKVGTDEEFSGEISSVTGFGLFVRLDD-NGIDGLVPVSTLPNNKDYYRFDKEKLALIGKGTGKVYRLGDRLEVKLTEVN 673 (684)
T ss_pred HHHCCCCCCHHHHHHHHHCCCEEEEEEC-CCCCEEEEECCCCCCCHHEEECCCCCEEEECCCCCEEEECCEEEEEEEHHH
T ss_conf 7541675300122212202640687503-563103541222243112034213226876156735751541477520121
Q ss_pred CCCCEEEEEE
Q ss_conf 5768699870
Q gi|254780456|r 520 KKDGKVSLSI 529 (576)
Q Consensus 520 ~~~~ri~LS~ 529 (576)
...+++.+++
T Consensus 674 ~~~~~~~~~~ 683 (684)
T TIGR00358 674 LDERSIDFEL 683 (684)
T ss_pred HHHHHHCEEC
T ss_conf 2233000001
No 186
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=93.43 E-value=0.4 Score=24.08 Aligned_cols=60 Identities=32% Similarity=0.377 Sum_probs=30.9
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEE
Q ss_conf 58999981596699-985142000000111101113557421003784579999986215504787
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISL 350 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~l 350 (576)
+.|.|+...+.+.| |+|.+|..-+.|.| . +...-.=..-+||.|++.+-..|..+++|..
T Consensus 9 ~~G~V~e~lpn~~F~V~Leng~~v~a~~s----G-KmR~~~Iril~GD~V~vE~spYDltkGRIv~ 69 (72)
T PRK00276 9 MEGTVLETLPNAMFRVELENGHEVLAHIS----G-KMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEEC----H-HEEEEEEEECCCCEEEEEECCCCCCCEEEEE
T ss_conf 99999998599889999789999999974----1-3110169975899899998866799578999
No 187
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus 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 cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process.
Probab=93.32 E-value=0.071 Score=28.65 Aligned_cols=53 Identities=25% Similarity=0.191 Sum_probs=33.7
Q ss_pred CCCCEEEEEEEEEECCEEEEEE--CCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEEC
Q ss_conf 8987799999998199899994--7960367899750566435563789879999999747
Q gi|254780456|r 25 AENCVTKGIVVGLEKDTVVVDV--GLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTEN 83 (576)
Q Consensus 25 ~~G~iv~G~V~~i~~~~v~vdi--g~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~ 83 (576)
..-..++|.+..-.+.+.|+.. +.+..-++|..++.. .--||.+.+.......
T Consensus 14 ~~~~~~~g~~~~~~~~~gf~~~~~~~~~~~~~~~~~~~~------~~~gd~~~~~~~~~~~ 68 (684)
T TIGR00358 14 EKLDLVKGVVKGHNKGFGFLRPDDGDKKDYFIPPPQLKG------ALHGDLVLACPLGKPE 68 (684)
T ss_pred HHHHHHCCEEEECCCCCEEEEECCCCCCEEEECCHHHHH------HHCCCEEEEEECCCCC
T ss_conf 123322100220456530133316775236645334312------1045424675336664
No 188
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=92.46 E-value=0.5 Score=23.50 Aligned_cols=58 Identities=36% Similarity=0.473 Sum_probs=26.0
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEE
Q ss_conf 58999981596699-9851420000001111011135574210037845799999862155047
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRI 348 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i 348 (576)
++|+|+...+.+.| |+|++|..-+.|.| .+-..+ .=..-+||.|++.+-..|..+.+|
T Consensus 3 ~~G~V~e~lpn~~F~V~Leng~~v~a~~s----GKmr~~-~Iril~GD~V~VE~SpYDltkGRI 61 (64)
T cd04451 3 MEGVVTEALPNAMFRVELENGHEVLAHIS----GKMRMN-YIRILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEEC----CHHEEE-EEEECCCCEEEEEECCCCCCCEEE
T ss_conf 88999998799889999789989999972----330412-698458998999988667885789
No 189
>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=91.55 E-value=0.75 Score=22.44 Aligned_cols=67 Identities=22% Similarity=0.232 Sum_probs=34.8
Q ss_pred CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC-CCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEE
Q ss_conf 896658999981596699985142000000111101-11355742100378457999998621550478752
Q gi|254780456|r 282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW-TKKNIHPSKILSVGQQVEVVILEVNPARKRISLGL 352 (576)
Q Consensus 282 ~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~-~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~ 352 (576)
+||.+-|.|+........|+|++...+++|.--+.- ++++ .| .+++|+.|-|||...+++ ....|||
T Consensus 6 ~gD~VIGiV~~~~~d~y~vdi~~~~~a~L~~laFegATKkn-rP--~L~~GdlVYaRV~~a~~~-~e~EL~C 73 (86)
T cd05790 6 KGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRN-RP--NLNVGDLVYARVVKANRD-MEPELSC 73 (86)
T ss_pred CCCEEEEEEEEECCCEEEEECCCCCCEEECCCEECCCCCCC-CC--CCCCCCEEEEEEEECCCC-CCEEEEE
T ss_conf 99989999944327668997679866485001017876556-88--788788999999874899-9704898
No 190
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 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 (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=90.72 E-value=0.78 Score=22.34 Aligned_cols=59 Identities=37% Similarity=0.429 Sum_probs=29.4
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEE
Q ss_conf 58999981596699-98514200000011110111355742100378457999998621550478
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRIS 349 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~ 349 (576)
+.|.|+...+.+.| |.|+++..-..|+| .+-..+.-++ =+||.|++.+-..|-.++||.
T Consensus 7 ~~G~v~e~l~n~~f~V~LeN~~~v~a~iS----Gk~r~~~iri-LpGD~V~ve~SpYdl~~GRI~ 66 (69)
T TIGR00008 7 VEGKVVESLPNAMFRVELENGHEVLAHIS----GKIRKNYIRI-LPGDKVKVELSPYDLTRGRII 66 (69)
T ss_pred ECCEEEECCCCCEEEEEECCCCEEEEEEC----CEEECCEEEE-CCCCEEEEEECCCCCCCCCEE
T ss_conf 42389854369826999479978989971----0341351755-479878998713648775087
No 191
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase 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.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=89.58 E-value=0.38 Score=24.26 Aligned_cols=71 Identities=20% Similarity=0.425 Sum_probs=57.3
Q ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHC------------CCHHHCCCCCEEEEEEEEECCCC
Q ss_conf 047898799999997089089996177984999997471821210------------42011068987999999970576
Q gi|254780456|r 455 SLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVD------------QDPGRFSKGQIVDACVVNVSKKD 522 (576)
Q Consensus 455 ~~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~------------~~~~~~~vG~~v~~~Vi~id~~~ 522 (576)
+.-...-..+.|..|.-.|+=|+|.+ +|-..|||..-|.+.+-+ +-.-.||+||.|++++.+|..++
T Consensus 579 k~~~~~~F~AEi~Dv~R~G~Rv~Lle-NGA~~FIPA~~Lh~~keel~~n~e~G~v~Ikge~~YKi~D~~~v~LtEv~~~t 657 (664)
T TIGR02062 579 KEAKNTRFEAEIVDVSRAGMRVRLLE-NGASAFIPAAFLHDNKEELVCNQEEGTVYIKGEVVYKIGDVIEVVLTEVREET 657 (664)
T ss_pred CCCCCCCEEEEEEEECCCCCEEEEEC-CCCCHHCCHHHHCCCCCEEEEECCCCEEEEEEEEEEEEEEEEEEEEEEEECCC
T ss_conf 33368612446887247874343120-56311114344303321366506876388710789866106999984540134
Q ss_pred CEEE
Q ss_conf 8699
Q gi|254780456|r 523 GKVS 526 (576)
Q Consensus 523 ~ri~ 526 (576)
|.|+
T Consensus 658 RSiv 661 (664)
T TIGR02062 658 RSIV 661 (664)
T ss_pred CCEE
T ss_conf 5011
No 192
>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=88.74 E-value=1.3 Score=21.01 Aligned_cols=64 Identities=20% Similarity=0.346 Sum_probs=26.1
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 966589999815966999851420000001111011135574210037845799999862155047875
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLG 351 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS 351 (576)
|+.++-.|..+++.|-.+=-+..+.|+.-.. | +.-...+.+.+||++++.|+.+|.-+-++.+|
T Consensus 1 G~~l~lvVq~v~edGsv~Fs~g~v~gltv~A--s---rYH~~g~~l~pGqK~k~viLHVD~lk~~VhVS 64 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLA--S---RYHKEGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CCEEEEEEEEECCCCCEEEECCCCCCEEEEE--E---EEEECCEECCCCCEEEEEEEEEEEEEEEEEEE
T ss_conf 9579999987304874898379868829997--8---87627704288866789999987477789982
No 193
>KOG1004 consensus
Probab=84.81 E-value=2.1 Score=19.69 Aligned_cols=61 Identities=16% Similarity=0.198 Sum_probs=31.9
Q ss_pred CCCCEEEEEEEEEEEEEEEEECCCCEEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf 222136999998501699970688413540055300122001234211123422688521565
Q gi|254780456|r 369 PGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVG 431 (576)
Q Consensus 369 ~G~~v~g~V~~v~~~g~~V~l~~~i~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~ 431 (576)
+|+.|=|.|+.-......|++++.-.+.++..-+. .-.+...-.+++|+.+-|+|...+++
T Consensus 65 ~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe--~AtkrNrPnl~vGdliyakv~~a~~~ 125 (230)
T KOG1004 65 KGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE--GATKRNRPNLQVGDLIYAKVVDANKD 125 (230)
T ss_pred CCCEEEEEEEECCCCEEEEECCCCCEEEEEECCCC--CCCCCCCCCCCCCCEEEEEEEECCCC
T ss_conf 89989999985046517996389866533100236--85435788643165789998706777
No 194
>KOG1999 consensus
Probab=83.70 E-value=2.4 Score=19.40 Aligned_cols=32 Identities=16% Similarity=0.403 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCEEEEEEEEECC-CEEEEEECCC
Q ss_conf 0000000489665899998159-6699985142
Q gi|254780456|r 274 DDVQDKYVEGSKVSGVVTNLTD-YGVFVELQSG 305 (576)
Q Consensus 274 ~~~~~~~~~G~~v~g~V~~v~~-~G~~V~l~~~ 305 (576)
-.+.+-|++|+.++..--+.+. .|++|.+..+
T Consensus 454 ~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999 454 SELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred HHHHHHCCCCCEEEEEECCCCCCCCEEEEEECC
T ss_conf 766542357875789731202775359998377
No 195
>PRK12366 replication factor A; Reviewed
Probab=82.15 E-value=2.7 Score=19.03 Aligned_cols=74 Identities=12% Similarity=0.160 Sum_probs=35.6
Q ss_pred HHHHHHCCCCCCEEEEEECCCCCCCCCCCH--HH-HHCCCCCC-------HHHHCCCCCC--CEEEEEEEEEECCEEEEE
Q ss_conf 123421112342268852156545532011--32-21011100-------0011004789--879999999708908999
Q gi|254780456|r 410 KVIAEYAKGDIVKAVVLDIDVGKERISLGV--KQ-LSGSAPDV-------VDSVSSLRKN--DVVSCEVISVSEGGIEVS 477 (576)
Q Consensus 410 ~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~--K~-l~~~~~~~-------~~~~~~~~~G--~iv~g~V~~v~~~G~~V~ 477 (576)
++...+++|+.+++.=-.+......+.||+ .. ...+|... -+......-+ .-|.|+|+.+.+..++..
T Consensus 455 ~a~~~i~eGDviki~~a~vke~~~y~eL~ig~~~rI~~npeg~~v~i~t~kk~i~~~~~d~~veV~Gtiv~v~~~~l~~~ 534 (649)
T PRK12366 455 DAEIEIKEGDVIKIIHGYAKESGDYLDLSIGRFGRILVNPEGIKVSIKVPRKIIADLEDGRSTEIRGTVVDYRKQKIILT 534 (649)
T ss_pred CCCCCCCCCCEEEEECCEEECCCCEEEEEECCCCEEEECCCCCEEEEECCCEEEEECCCCCEEEEEEEEEEEECCCEEEE
T ss_conf 34574468978999525670058707999547514886886644788613112210358864799999999816847897
Q ss_pred ECCCCC
Q ss_conf 617798
Q gi|254780456|r 478 LIDHKG 483 (576)
Q Consensus 478 l~~~~g 483 (576)
+-.+|+
T Consensus 535 ~CP~C~ 540 (649)
T PRK12366 535 LCPNCR 540 (649)
T ss_pred ECCCCC
T ss_conf 286667
No 196
>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=81.29 E-value=2.8 Score=19.02 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=4.0
Q ss_pred HCCCCCEEEEEE
Q ss_conf 106898799999
Q gi|254780456|r 504 RFSKGQIVDACV 515 (576)
Q Consensus 504 ~~~vG~~v~~~V 515 (576)
++++||.+.+.+
T Consensus 45 KL~vGq~~~v~l 56 (69)
T cd05701 45 KLSVGQCLDVTL 56 (69)
T ss_pred EEECCCEEEEEE
T ss_conf 153365499998
No 197
>TIGR02142 modC_ABC molybdate ABC transporter, ATP-binding protein; InterPro: IPR011868 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulphate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulphate transporter rather than by a specific molybdate transporter.; GO: 0005524 ATP binding, 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=79.31 E-value=2.9 Score=18.85 Aligned_cols=56 Identities=23% Similarity=0.468 Sum_probs=31.5
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEECC-CEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEE
Q ss_conf 3210000000489665899998159-6699-9851420000001111011135574210037845799999862
Q gi|254780456|r 271 NPWDDVQDKYVEGSKVSGVVTNLTD-YGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVN 342 (576)
Q Consensus 271 dp~~~~~~~~~~G~~v~g~V~~v~~-~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id 342 (576)
.||....+ .|.++.++|.+.++ ||++ +.++++ |.+-+++. .=.+|+....+|-.-|
T Consensus 226 ~p~~~~~~---~g~~~~~~v~~~~~~ygL~~l~l~e~--~~l~V~~~-----------~~~~G~~~R~~v~A~D 283 (361)
T TIGR02142 226 PPWLEREE---AGSVLEGVVAEHDQHYGLTALRLGED--GHLWVPEK-----------KGPVGARLRLRVPARD 283 (361)
T ss_pred CCCCCCCC---CCEEEEEEEECCCCCCCCEECCCCCC--CEEEEECC-----------CCCCCCCEEEEEEECC
T ss_conf 72325786---63365654110386532012015888--38997267-----------6765852356874142
No 198
>KOG4134 consensus
Probab=76.94 E-value=1.6 Score=20.40 Aligned_cols=55 Identities=13% Similarity=0.289 Sum_probs=20.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC-CCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEEC
Q ss_conf 22330246788753147177744-8315788642024444433113326972589999874
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRIN 255 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~-g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d 255 (576)
++|+++.|+|..+....+-.-+. -+-+-+|..+++-++. ....+|+.+++|...|
T Consensus 106 k~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip~dw~-----fI~md~eee~~v~ntD 161 (253)
T KOG4134 106 KAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIPADWE-----FIAMDQEEEIRVKNTD 161 (253)
T ss_pred CCCCEEEEEEEECCHHHHCEEEHHHHHCCCCCCCCCCCEE-----EECCCCHHHHCEEECC
T ss_conf 8877444565532643520001102314578888863304-----4448855330135435
No 199
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=75.23 E-value=0.68 Score=22.69 Aligned_cols=68 Identities=21% Similarity=0.425 Sum_probs=52.0
Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCC------------CHHHCCCCCEEEEEEEEECCCCCEE
Q ss_conf 8987999999970890899961779849999974718212104------------2011068987999999970576869
Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQ------------DPGRFSKGQIVDACVVNVSKKDGKV 525 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~------------~~~~~~vG~~v~~~Vi~id~~~~ri 525 (576)
..+...+.|..+.-.|+=|.+.+ +|-..|||.+-|.+.+.+- -.-.|++|+.+++.+.++..+.+.|
T Consensus 561 ~~~~F~AEI~Di~R~G~RvrLle-NGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRsi 639 (645)
T COG4776 561 TNTRFAAEIQDISRGGMRVRLLE-NGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRSI 639 (645)
T ss_pred CCCHHHHHHHHHCCCCEEEEECC-CCCCEECCHHHHCCCHHHEEECCCCCEEEECCEEEEEECCEEEEEEHHHHHHHHHH
T ss_conf 57324432321226746898311-79622312465044546516567774699853799863467999858876766665
Q ss_pred E
Q ss_conf 9
Q gi|254780456|r 526 S 526 (576)
Q Consensus 526 ~ 526 (576)
+
T Consensus 640 i 640 (645)
T COG4776 640 I 640 (645)
T ss_pred H
T ss_conf 2
No 200
>PRK10409 hydrogenase isoenzymes formation protein; Provisional
Probab=74.54 E-value=4.7 Score=17.64 Aligned_cols=48 Identities=19% Similarity=0.101 Sum_probs=31.6
Q ss_pred EEEEEEEEEECCEEEEEECC-CEEEEEEHHHHCCCCCCCCCCCCCEEEEEE
Q ss_conf 79999999819989999479-603678997505664355637898799999
Q gi|254780456|r 29 VTKGIVVGLEKDTVVVDVGL-KFEGRIPRREFMGKGQYTPIKVGDEVEVYV 78 (576)
Q Consensus 29 iv~G~V~~i~~~~v~vdig~-k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V 78 (576)
-++|+|++|+++.+.||+++ +.+..+.. +.........++||.|-+.+
T Consensus 4 aIPg~Iv~I~~~~A~Vd~~Gv~r~V~l~l--v~~~~~~~~~~vGDyVLVHv 52 (90)
T PRK10409 4 GVPGQIRTIDGNQAKVDVCGIQRDVDLTL--VGSCDENGQPRVGQWVLVHV 52 (90)
T ss_pred CCCEEEEEECCCEEEEEECCCEEEEEEEE--EECCCCCCCCCCCCEEEEEC
T ss_conf 45438999859889999578079998765--40456777568898999970
No 201
>KOG3013 consensus
Probab=72.07 E-value=5.3 Score=17.32 Aligned_cols=32 Identities=31% Similarity=0.442 Sum_probs=14.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEECC-CEEEEEEE
Q ss_conf 223302467887531471777448-31578864
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLSG-VDGLLHVT 227 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~g-~~g~i~~~ 227 (576)
++||+|-|+|..+...---|+++. .++.+..+
T Consensus 84 EvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~Ls 116 (301)
T KOG3013 84 EVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLS 116 (301)
T ss_pred CCCCEEEEEEEEEECCEEEEECCCCCCEEEEEE
T ss_conf 557778887644402335775166543378753
No 202
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=70.20 E-value=5.9 Score=17.02 Aligned_cols=65 Identities=31% Similarity=0.367 Sum_probs=40.4
Q ss_pred CCEEEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEE
Q ss_conf 96658999981596699-98514200000011110111355742100378457999998621550478752
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGL 352 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~ 352 (576)
...+.|+|.+..+.+.| |.+.+|..-+.|+|- +-..+ .=-..+||.|.+.....|..+.+|.--+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~eng~~~~ahI~G----Kmr~~-~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISG----KMRKN-RIRILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred CCEEEEEEEEECCCCEEEEEECCCCEEEEECCC----CCCEE-EEEECCCCEEEEEECCCCCCCCCEEEEE
T ss_conf 428999999973897899994699699988258----74400-4885799999997456653335589983
No 203
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=66.85 E-value=6.9 Score=16.60 Aligned_cols=10 Identities=40% Similarity=0.461 Sum_probs=3.4
Q ss_pred CCCEEEEEEE
Q ss_conf 8987999999
Q gi|254780456|r 507 KGQIVDACVV 516 (576)
Q Consensus 507 vG~~v~~~Vi 516 (576)
.||.|++.|.
T Consensus 39 ~Gd~V~f~v~ 48 (64)
T smart00357 39 EGDEVEFKVV 48 (64)
T ss_pred CCCEEEEEEE
T ss_conf 5878999999
No 204
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=65.05 E-value=7.5 Score=16.39 Aligned_cols=16 Identities=13% Similarity=0.488 Sum_probs=6.1
Q ss_pred EEEEEECCCCEEEEEE
Q ss_conf 9998621550478752
Q gi|254780456|r 337 VILEVNPARKRISLGL 352 (576)
Q Consensus 337 ~Vl~id~~~~~i~lS~ 352 (576)
+|.++|.++.++.+++
T Consensus 114 ~V~~Vd~~k~~vtV~l 129 (153)
T PRK08559 114 RVVRVDESKEEVTVEL 129 (153)
T ss_pred EEEEECCCCCEEEEEE
T ss_conf 9999816688999999
No 205
>KOG3754 consensus
Probab=56.93 E-value=5 Score=17.47 Aligned_cols=32 Identities=25% Similarity=0.230 Sum_probs=24.7
Q ss_pred CCCCCCCCCCEEEEEEEEEECCCCEEEEEHHH
Q ss_conf 43556378987999999974799859996878
Q gi|254780456|r 63 GQYTPIKVGDEVEVYVERTENSFGEAVFSRDK 94 (576)
Q Consensus 63 ~~~~~~kvGd~i~v~V~~~~~~~g~i~lS~~k 94 (576)
...+.++=||+|+.+|.+.|+++....||.+.
T Consensus 40 r~~D~LkWGDEiEy~vV~fDd~~kk~rv~l~~ 71 (640)
T KOG3754 40 RHGDVLKWGDEIEYMVVKFDDKNKKARVSLRA 71 (640)
T ss_pred CCCCCCCCCCEEEEEEEECCCCCCEEEEEEEH
T ss_conf 13880004660589999505546302355209
No 206
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HUPF/HYPC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process . They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation , . .
Probab=55.38 E-value=11 Score=15.36 Aligned_cols=76 Identities=25% Similarity=0.310 Sum_probs=48.0
Q ss_pred EEEEEEEEECCE--EEEEE-CCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEHHHHH-HHHHHHHHH
Q ss_conf 999999981998--99994-79603678997505664355637898799999997479985999687875-557589999
Q gi|254780456|r 30 TKGIVVGLEKDT--VVVDV-GLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKAL-REGVWEKIE 105 (576)
Q Consensus 30 v~G~V~~i~~~~--v~vdi-g~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g~i~lS~~k~~-~~~~~~~i~ 105 (576)
++|.|+.+.++- +.+++ |-+.+-.+.+=+- .=..+.+.++||.|-+.+= .-.=+++...|. ...+|+++.
T Consensus 5 iP~qV~~i~~~~~~A~v~~~G~~~~v~l~Lv~k-sC~~N~~~~~GdyvLvH~G-----~A~~~~DeeeA~~~l~al~~l~ 78 (88)
T TIGR00074 5 IPGQVVEIDENIDLALVEFKGVKREVSLDLVGK-SCDENEEVKVGDYVLVHVG-----FAISVLDEEEAKETLEALEELF 78 (88)
T ss_pred CCCEEEEECCCCCEEEECCCCEEEEEEEEECCC-CCCCCCCCCCCCEEEEEEE-----HHHHHCCHHHHHHHHHHHHHHH
T ss_conf 771688854999878860152246676412355-4467859999877632000-----4663248888888999999998
Q ss_pred HHHHCC
Q ss_conf 985289
Q gi|254780456|r 106 AKFRAG 111 (576)
Q Consensus 106 ~a~~~g 111 (576)
++.+.+
T Consensus 79 ~a~~~~ 84 (88)
T TIGR00074 79 KAVEEG 84 (88)
T ss_pred HHHHHH
T ss_conf 850222
No 207
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=49.75 E-value=14 Score=14.81 Aligned_cols=68 Identities=25% Similarity=0.333 Sum_probs=41.3
Q ss_pred EEEEEEEEEECC--EEEEEEC-CCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEHHHHH-HHHHHHHH
Q ss_conf 799999998199--8999947-9603678997505664355637898799999997479985999687875-55758999
Q gi|254780456|r 29 VTKGIVVGLEKD--TVVVDVG-LKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKAL-REGVWEKI 104 (576)
Q Consensus 29 iv~G~V~~i~~~--~v~vdig-~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g~i~lS~~k~~-~~~~~~~i 104 (576)
.++|.|+.|+++ .+.||+| .+.+..++ +-. ...++||.|-+.+-.. .-.++...+. ....|+++
T Consensus 4 aiPgqI~~I~~~~~~A~Vd~gGvkreV~l~---Lv~----~~v~~GdyVLVHvGfA-----i~~idEeeAketle~l~e~ 71 (82)
T COG0298 4 AIPGQIVEIDDNNHLAIVDVGGVKREVNLD---LVG----EEVKVGDYVLVHVGFA-----MSKIDEEEAKETLEALQEM 71 (82)
T ss_pred CCCCEEEEEECCCCEEEEEECCEEEEEEEE---EEC----CCCCCCCEEEEEEEEE-----EEECCHHHHHHHHHHHHHH
T ss_conf 667278998078855899865676898753---304----7533477899995088-----7653899999999999999
Q ss_pred HHHH
Q ss_conf 9985
Q gi|254780456|r 105 EAKF 108 (576)
Q Consensus 105 ~~a~ 108 (576)
.++.
T Consensus 72 ~~~~ 75 (82)
T COG0298 72 FDAE 75 (82)
T ss_pred HHHH
T ss_conf 9863
No 208
>TIGR01067 rplN_bact ribosomal protein L14; InterPro: IPR005745 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 of 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 , . Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In bacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which have been grouped on the basis of sequence similarities . L14 is a protein of 119 to 137 amino-acid residues. This family distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=49.67 E-value=14 Score=14.80 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=5.6
Q ss_pred CCCCCEEEEEEEEE
Q ss_conf 04896658999981
Q gi|254780456|r 280 YVEGSKVSGVVTNL 293 (576)
Q Consensus 280 ~~~G~~v~g~V~~v 293 (576)
.+-|+++++.|++.
T Consensus 58 vKKGdV~kAViVRt 71 (128)
T TIGR01067 58 VKKGDVVKAVIVRT 71 (128)
T ss_pred CCCCCEEEEEEEEC
T ss_conf 31133679999847
No 209
>pfam09883 DUF2110 Uncharacterized protein conserved in archaea (DUF2110). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=46.87 E-value=15 Score=14.53 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=10.6
Q ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEECCC
Q ss_conf 96658999981596699985142000000111
Q gi|254780456|r 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQ 314 (576)
Q Consensus 283 G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~se 314 (576)
|+++.|+..+..+.|+.+.++ |+.+-+|..+
T Consensus 76 Ge~y~G~l~~~~e~G~~~~v~-G~~~~ip~de 106 (226)
T pfam09883 76 GEVYVGTLISWDEDGYGLDVD-GVTVPIPADE 106 (226)
T ss_pred CCEEEEEEEECCCCCEEEEEC-CEECCCCHHH
T ss_conf 877899987606641699865-7364671788
No 210
>KOG0125 consensus
Probab=44.20 E-value=17 Score=14.28 Aligned_cols=70 Identities=21% Similarity=0.323 Sum_probs=39.3
Q ss_pred EEEEEEEECCCCC-CCCCCEEE-CCCCEEEEEEEEECCCCCEE-EEEECCCCCCC--CCCCCCCCCCCCEEEEEEEEECC
Q ss_conf 1578864202444-44331133-26972589999874765279-98521555432--10000000489665899998159
Q gi|254780456|r 221 DGLLHVTDIAWHR-ILHPSKVL-SIGQQVKVKIIRINQETHRI-SLGMKQLEKNP--WDDVQDKYVEGSKVSGVVTNLTD 295 (576)
Q Consensus 221 ~g~i~~~~ls~~~-~~~~~~~~-~~G~~v~~~Vl~~d~~~~~i-~lslK~l~~dp--~~~~~~~~~~G~~v~g~V~~v~~ 295 (576)
.-.+|.++|.+.. -.++..+| +.|-.+.+.||--++..+-+ -+++ ++| .+....++. |.++.|+...|..
T Consensus 96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTm----en~~dadRARa~LH-gt~VEGRkIEVn~ 170 (376)
T KOG0125 96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTM----ENPADADRARAELH-GTVVEGRKIEVNN 170 (376)
T ss_pred CCEEEEECCCCCCCCCCHHHHHHHHCCEEEEEEEECCCCCCCCCEEEE----CCHHHHHHHHHHHH-CCEEECEEEEEEC
T ss_conf 853576458752468009999985175046899863677775234872----28246899999850-4643012788741
No 211
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.69 E-value=18 Score=14.05 Aligned_cols=47 Identities=19% Similarity=0.283 Sum_probs=22.6
Q ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEE
Q ss_conf 478987999999970890899961779849999974718212104201106898799999997
Q gi|254780456|r 456 LRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNV 518 (576)
Q Consensus 456 ~~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~i 518 (576)
+..|+.++..|..+...|-=|.= ..|..-|+|-. .+|+.|+++|.++
T Consensus 145 ~eeG~~y~v~I~~~g~~GdGia~--i~gf~vfVp~a--------------~~Ge~v~v~I~~v 191 (201)
T PRK12336 145 IEEGKTYEVEIESTGSKGDGVAK--IGKYTIFVPGA--------------KKGQVVKVKIKKI 191 (201)
T ss_pred CCCCCEEEEEEEECCCCCCCEEE--ECCEEEEECCC--------------CCCCEEEEEEEEE
T ss_conf 56796899999973667654799--88989995899--------------8798899999996
No 212
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=40.86 E-value=19 Score=13.97 Aligned_cols=97 Identities=12% Similarity=0.076 Sum_probs=49.0
Q ss_pred CCCCEE---EEEEEEEECCEEEEE-E----CCCEEEE---EEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEE-EEEH
Q ss_conf 898779---999999819989999-4----7960367---89975056643556378987999999974799859-9968
Q gi|254780456|r 25 AENCVT---KGIVVGLEKDTVVVD-V----GLKFEGR---IPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEA-VFSR 92 (576)
Q Consensus 25 ~~G~iv---~G~V~~i~~~~v~vd-i----g~k~~G~---i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~g~i-~lS~ 92 (576)
+.|.++ .|.|..+.|...-+. + -+...+. ++..++...-. .-+.-+.|+.+++...+-.|-- .-+.
T Consensus 41 ~~galLL~~~G~~~~~~d~~~r~~~l~~~l~G~~~~~lq~~~l~dvv~Ai~--~A~~D~~I~~~~~DL~~~~g~dG~~~l 118 (614)
T TIGR00705 41 SKGALLLDLAGVVVDVQDESPRLSDLLQELLGNQKERLQKISLFDVVNAIR--QAADDRRIEGLVLDLKNFEGVDGSPAL 118 (614)
T ss_pred HCCCEEEECCCEEEECCCCCHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHH--HHCCCCCEEEEEEECCCCCCCCCCCCH
T ss_conf 233134514733785477655799999975357530355402558999998--301278708999733323576677327
Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEE
Q ss_conf 787555758999998528976999999996795599
Q gi|254780456|r 93 DKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTV 128 (576)
Q Consensus 93 ~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V 128 (576)
. .--.-|.+--+.|.+|-++=.+--.++|-.
T Consensus 119 ~-----~~~~AL~~Fk~SgKpv~ay~~nYS~~~YYL 149 (614)
T TIGR00705 119 S-----EIGKALSEFKDSGKPVYAYGENYSQGQYYL 149 (614)
T ss_pred H-----HHHHHHHHHHHCCCEEEEEECCCCCHHHHH
T ss_conf 9-----889999999856990899852534023688
No 213
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=39.25 E-value=20 Score=13.81 Aligned_cols=98 Identities=13% Similarity=0.151 Sum_probs=45.8
Q ss_pred CCCCCCEEEEEEEEEEC--CCCEEEECC-CEEEEEEEECCC--CCC-CCCCEEECCCCEEEEEEEEECCCC-CEEEEEEC
Q ss_conf 12223302467887531--471777448-315788642024--444-433113326972589999874765-27998521
Q gi|254780456|r 194 KLEEGQVIEGTVKNITD--YGVFVDLSG-VDGLLHVTDIAW--HRI-LHPSKVLSIGQQVKVKIIRINQET-HRISLGMK 266 (576)
Q Consensus 194 ~l~~G~~v~g~V~~i~~--~g~~V~~~g-~~g~i~~~~ls~--~~~-~~~~~~~~~G~~v~~~Vl~~d~~~-~~i~lslK 266 (576)
...+=..|.|+|.++.- -|-+|.=|. +--.+|.++--- .++ ..-=...++||.+..|+-.++..+ +.+.-.++
T Consensus 278 ~~~irsPvdG~v~~l~~~T~GgVv~pG~~lm~IVP~~~~l~iEa~~~~~Dig~v~~Gq~a~ik~~AF~~~ryG~~~G~V~ 357 (434)
T TIGR01843 278 RLIIRSPVDGTVQSLKVHTVGGVVQPGETLMEIVPEDDPLEIEAKLSNKDIGFVHVGQPAEIKFSAFPYTRYGLLNGKVK 357 (434)
T ss_pred HHEEECCCCEEEEEEEEEEECCEECCCCCEEEEECCCCCEEEEEEECCCCCCEEECCCEEEEEEECCCCCCCCCEEEEEE
T ss_conf 21144254519999999840544327861789833999658999973546534555871699996368603351899999
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf 5554321000000048966589999
Q gi|254780456|r 267 QLEKNPWDDVQDKYVEGSKVSGVVT 291 (576)
Q Consensus 267 ~l~~dp~~~~~~~~~~G~~v~g~V~ 291 (576)
.+++|-+..-...-..+..|.++|.
T Consensus 358 ~iS~D~~~DE~~~~~~~~yY~~ri~ 382 (434)
T TIGR01843 358 SISPDTVEDERQGRQQGLYYRVRIS 382 (434)
T ss_pred EECCCCHHHHHCCCCCCCEEEEEEE
T ss_conf 8627511444247876766679999
No 214
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=39.06 E-value=20 Score=13.80 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=11.7
Q ss_pred EEEEEEEEECCCEEEEEEC
Q ss_conf 6589999815966999851
Q gi|254780456|r 285 KVSGVVTNLTDYGVFVELQ 303 (576)
Q Consensus 285 ~v~g~V~~v~~~G~~V~l~ 303 (576)
.+.|+|..+.+..++++.+
T Consensus 4 ~i~G~i~~~~~~~iil~v~ 22 (198)
T PRK00116 4 YLRGILTEKGPDYVVIEVN 22 (198)
T ss_pred EEEEEEEEEECCEEEEEEC
T ss_conf 7999999961998999979
No 215
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=37.19 E-value=21 Score=13.62 Aligned_cols=39 Identities=21% Similarity=0.408 Sum_probs=18.9
Q ss_pred CEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCC-CEEEEE
Q ss_conf 0000001111011135574210037845799999862155-047875
Q gi|254780456|r 306 IEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPAR-KRISLG 351 (576)
Q Consensus 306 v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~-~~i~lS 351 (576)
++|++|..+. -|.+.|++|+.+.+.+.++.... +.+.+|
T Consensus 2 ~~~~l~~~~~-------~~~e~~~~g~ri~~~~~~v~~~~~g~~~~s 41 (190)
T COG0195 2 VEAILPKREQ-------IPGENFKVGDRIRALLYEVQKEAKGQIELS 41 (190)
T ss_pred CEEECCHHHC-------CCCCCCCCCCEEEEEEEEEEECCCCCEEEE
T ss_conf 4167155453-------888644347679999825540576659998
No 216
>pfam04270 Strep_his_triad Streptococcal histidine triad protein. All members of this family are proteins from Streptococcal species. The proteins are characterized by having a HxxHxH motif that usually occurs multiple times throughout the protein.
Probab=35.46 E-value=11 Score=15.34 Aligned_cols=27 Identities=15% Similarity=0.395 Sum_probs=14.6
Q ss_pred EEEEECCCEEEEECCCHHHHHCCCCCC
Q ss_conf 999967955999744020000011234
Q gi|254780456|r 118 IFNQVKGGMTVDLNGEVAFLPRSQIDI 144 (576)
Q Consensus 118 V~~~~k~G~~V~i~gi~~FlP~s~~~~ 144 (576)
|++.+..||+|-.++..-|+|.++++.
T Consensus 14 Ii~~~~~gyvVpHGdH~HyIpk~dLS~ 40 (53)
T pfam04270 14 IISDEGDAYVVPHGGHYHYIPKDSLSA 40 (53)
T ss_pred HHHCCCCEEEECCCCEEEECCHHHCCH
T ss_conf 742048756860688244340422999
No 217
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=35.43 E-value=23 Score=13.45 Aligned_cols=19 Identities=11% Similarity=0.265 Sum_probs=13.7
Q ss_pred EEEEEEEEECCCEEEEEEC
Q ss_conf 6589999815966999851
Q gi|254780456|r 285 KVSGVVTNLTDYGVFVELQ 303 (576)
Q Consensus 285 ~v~g~V~~v~~~G~~V~l~ 303 (576)
.+.|+|..+.+..+.++++
T Consensus 4 ~l~G~i~~~~~~~vvl~v~ 22 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMAT 22 (196)
T ss_pred EEEEEEEEECCCEEEEEEC
T ss_conf 7999999962997999934
No 218
>TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270 The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . .
Probab=34.99 E-value=9.9 Score=15.64 Aligned_cols=35 Identities=29% Similarity=0.334 Sum_probs=24.5
Q ss_pred CCEE-EEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHH
Q ss_conf 9879-9999997089089996177984999997471821
Q gi|254780456|r 459 NDVV-SCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRD 496 (576)
Q Consensus 459 G~iv-~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~ 496 (576)
|-|. .+.|++-+.+|+.|==++++ =|||.+|||..
T Consensus 336 GLiF~P~Qi~~~~A~G~~VPHGdHY---H~IP~~Q~S~L 371 (376)
T TIGR01363 336 GLIFDPAQITSRTARGVAVPHGDHY---HFIPYSQLSEL 371 (376)
T ss_pred CCEECCHHHHCCCCEEEEECCCCCC---EECCHHHHHHH
T ss_conf 8543762330025204673178731---34583541068
No 219
>KOG3297 consensus
Probab=34.93 E-value=23 Score=13.40 Aligned_cols=23 Identities=30% Similarity=0.564 Sum_probs=11.4
Q ss_pred CCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 69725899998747652799852
Q gi|254780456|r 243 IGQQVKVKIIRINQETHRISLGM 265 (576)
Q Consensus 243 ~G~~v~~~Vl~~d~~~~~i~lsl 265 (576)
+|+.+.++|++-+++.-+++|+.
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~F 103 (202)
T KOG3297 81 VGEVITGKIKECSEEGLRVTLGF 103 (202)
T ss_pred CCEEEEEEEECCCCCCEEEEEEE
T ss_conf 65089988303772541899883
No 220
>pfam11813 DUF3334 Protein of unknown function (DUF3334). This family of proteins are functionally uncharacterized. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=33.09 E-value=25 Score=13.21 Aligned_cols=18 Identities=39% Similarity=0.744 Sum_probs=12.8
Q ss_pred ECCCCEEEE-CCCEEEEEE
Q ss_conf 314717774-483157886
Q gi|254780456|r 209 TDYGVFVDL-SGVDGLLHV 226 (576)
Q Consensus 209 ~~~g~~V~~-~g~~g~i~~ 226 (576)
.+.|+||-| ||+.|++-+
T Consensus 48 PDiGCFvlFDGGFsGLVvi 66 (227)
T pfam11813 48 PDIGCFVLFDGGFSGLVVI 66 (227)
T ss_pred CCCCEEEEECCCCCEEEEE
T ss_conf 8855599962885358999
No 221
>pfam06108 DUF952 Protein of unknown function (DUF952). This family consists of several hypothetical bacterial and plant proteins of unknown function.
Probab=32.50 E-value=20 Score=13.76 Aligned_cols=34 Identities=32% Similarity=0.495 Sum_probs=13.1
Q ss_pred EEEEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf 13540055300122001234211123422688521565
Q gi|254780456|r 394 DGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVG 431 (576)
Q Consensus 394 ~g~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~ 431 (576)
+||||.|... ........|-.|+. ...++.+|.+
T Consensus 25 dGFIH~St~~---Ql~~t~~~~f~~~~-~lvll~id~~ 58 (92)
T pfam06108 25 DGFIHLSTAE---QVAETAARFFAGQD-DLLLLAIDPA 58 (92)
T ss_pred CCEEECCCHH---HHHHHHHHHHCCCC-CEEEEEEEHH
T ss_conf 7878738889---99999999858998-4799998099
No 222
>TIGR02860 spore_IV_B stage IV sporulation protein B; InterPro: IPR014219 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. The members of this entry belong to MEROPS peptidase family S55 (SpoIVB peptidase, clan PA)..
Probab=30.75 E-value=27 Score=12.98 Aligned_cols=212 Identities=19% Similarity=0.287 Sum_probs=110.4
Q ss_pred CCHHHHHCCCCCCCC---CCCCCCC-CCCEEEECCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf 402000001123454---3334555-553023111335432331122121112222212111000112223302467887
Q gi|254780456|r 132 GEVAFLPRSQIDIRP---VRDVTPL-MHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKN 207 (576)
Q Consensus 132 gi~~FlP~s~~~~~~---~~d~~~~-vG~~i~~~Ii~~d~~~~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~ 207 (576)
.+-||+|....+.+. +.+..-+ =||.+=++. ...+-++|-+-.+..+.=.-.-..-...+++||.
T Consensus 86 ~l~G~~p~K~~~v~vPrn~p~i~V~PGGQSIGVkL----~T~GVLVVG~s~i~~~~G~i~sPg~~AGi~~GD~------- 154 (423)
T TIGR02860 86 KLFGLIPIKSISVKVPRNLPDIKVIPGGQSIGVKL----NTKGVLVVGFSDIETEKGKIESPGEEAGIQIGDI------- 154 (423)
T ss_pred CCCCCCCHHHCCCCCCCCCCEEEEECCCEEEEEEE----ECCCEEEEEEEEEECCCCCEECCHHHCCEEEEEE-------
T ss_conf 10045301203577863366589926970251698----3385799988654079883646365478456108-------
Q ss_pred EECCCCEEEECCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEE
Q ss_conf 53147177744831578864202444443311332697258999987476527998521555432100000004896658
Q gi|254780456|r 208 ITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVS 287 (576)
Q Consensus 208 i~~~g~~V~~~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~ 287 (576)
.+.++|. ++.++.+ -..-..+.=+-|+.++..|.. .+.+|.=.++....+ -+.+|++|=.+.
T Consensus 155 ------I~~iNg~----~i~~~~d-~~~~i~~~g~~g~~l~l~i~R---~~~~i~~~~~p~~~~----~e~~YrIGLyiR 216 (423)
T TIGR02860 155 ------ILKINGE----KIKNMED-IAKLINKAGKTGEKLKLTIKR---GGKIIETKIKPVKDK----EEGRYRIGLYIR 216 (423)
T ss_pred ------EEEECCC----HHCCHHH-HHHHHHHHHHCCCEEEEEEEE---CCCEEEEEEEEEEEC----CCCCEEEEEEEE
T ss_conf ------9998881----1035345-688887543059548999985---890899866133337----887538998994
Q ss_pred ------EEEEEECCCEEEEEECCCCEEEE--ECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCC
Q ss_conf ------99998159669998514200000--0111101113557421003784579999986215504787520345432
Q gi|254780456|r 288 ------GVVTNLTDYGVFVELQSGIEGLA--HISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINP 359 (576)
Q Consensus 288 ------g~V~~v~~~G~~V~l~~~v~G~i--~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p 359 (576)
|+-+=..| ..+..|=| ++||+. +++..+ +.-|+.+...|++|++-. ..+|
T Consensus 217 DsaAGiGTLTFY~p-------~~kkyGALGHvI~D~D-T~k~i~----v~~G~I~~S~i~SI~KG~----------~G~P 274 (423)
T TIGR02860 217 DSAAGIGTLTFYDP-------KTKKYGALGHVITDID-TGKPIS----VENGEIVNSSITSIEKGR----------RGNP 274 (423)
T ss_pred ECCCCCCEEEEEEC-------CCCCEECCCCEECCCC-CCCEEE----CCCCCEEEEEEEEECCCC----------CCCC
T ss_conf 16643321676708-------9885721275244177-896334----148817875899967899----------8988
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEEEEEEEEECC-CCEE
Q ss_conf 10000012222213699999850169997068-8413
Q gi|254780456|r 360 WEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDE-HLDG 395 (576)
Q Consensus 360 ~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~-~i~g 395 (576)
=|. ...|....-.=|.|.+=|++|+|-.+.. .+..
T Consensus 275 GEk-~g~F~~~~~~iG~i~~Nt~fGIFG~~~~a~~~n 310 (423)
T TIGR02860 275 GEK-LGIFSEEKKIIGNIKKNTPFGIFGKLNQAEIKN 310 (423)
T ss_pred CCE-EEEECCCCCEEEEEECCCCCEEEEEEECCCCCC
T ss_conf 513-567517884557874586631442110463547
No 223
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=30.38 E-value=28 Score=12.94 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=5.2
Q ss_pred CCCCCCCCCCCCE
Q ss_conf 1100011222330
Q gi|254780456|r 188 RSEIVQKLEEGQV 200 (576)
Q Consensus 188 ~~~~~~~l~~G~~ 200 (576)
+.+++++++.||.
T Consensus 37 ~~~ml~sL~kGD~ 49 (97)
T COG1862 37 HQELLNSLKKGDE 49 (97)
T ss_pred HHHHHHHCCCCCE
T ss_conf 9999974568998
No 224
>pfam01938 TRAM TRAM domain. This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).
Probab=30.11 E-value=28 Score=12.91 Aligned_cols=16 Identities=13% Similarity=0.127 Sum_probs=5.7
Q ss_pred CCCEEEEEEEEEECCE
Q ss_conf 8987999999970890
Q gi|254780456|r 458 KNDVVSCEVISVSEGG 473 (576)
Q Consensus 458 ~G~iv~g~V~~v~~~G 473 (576)
+|+.++..|......|
T Consensus 4 vG~~~~V~Ie~~~~~G 19 (59)
T pfam01938 4 VGQTQEVLVEGLGSNG 19 (59)
T ss_pred CCCEEEEEEEECCCCC
T ss_conf 5879999998557799
No 225
>pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1.
Probab=29.62 E-value=29 Score=12.86 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=10.1
Q ss_pred EEEEEECC--CEEEEEECCCCEEEEECC
Q ss_conf 99998159--669998514200000011
Q gi|254780456|r 288 GVVTNLTD--YGVFVELQSGIEGLAHIS 313 (576)
Q Consensus 288 g~V~~v~~--~G~~V~l~~~v~G~i~~s 313 (576)
|+|+.+.+ |.+-++-.+|++-|+|+-
T Consensus 49 G~V~~v~~T~HAigi~~~~G~eiLiHiG 76 (133)
T pfam00358 49 GTIVQIFPTKHAIGIESDGGVEILIHVG 76 (133)
T ss_pred EEEEEECCCCCEEEEEECCCCEEEEEEC
T ss_conf 7999986899799999689989999986
No 226
>PRK10949 protease 4; Provisional
Probab=28.33 E-value=30 Score=12.72 Aligned_cols=57 Identities=14% Similarity=0.049 Sum_probs=32.9
Q ss_pred CCCCCEEEEEEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEE
Q ss_conf 37898799999997479985999687875557589999985289769999999967955999
Q gi|254780456|r 68 IKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVD 129 (576)
Q Consensus 68 ~kvGd~i~v~V~~~~~~~g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~k~G~~V~ 129 (576)
-+.-+.|+.+++..++-.| .+.-++ ..--+.|.+--+.|.+|-+.-......+|.+-
T Consensus 107 Aa~D~rI~givLdl~~~~g---~~~a~l--~eI~~AL~~FK~SGK~ViAy~d~ysq~~YyLA 163 (618)
T PRK10949 107 AKDDRNITGIVLDLKNFAG---ADQPSM--QYIGKALREFRDSGKPVYAVGDNYSQGQYYLA 163 (618)
T ss_pred HCCCCCEEEEEEECCCCCC---CCHHHH--HHHHHHHHHHHHHCCEEEEEECCCCCCCEEEE
T ss_conf 5149982599997777888---788999--99999999999819939999667785301021
No 227
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=27.32 E-value=31 Score=12.61 Aligned_cols=26 Identities=31% Similarity=0.470 Sum_probs=10.7
Q ss_pred EEEEEECC--CEEEEEECCCCEEEEECC
Q ss_conf 99998159--669998514200000011
Q gi|254780456|r 288 GVVTNLTD--YGVFVELQSGIEGLAHIS 313 (576)
Q Consensus 288 g~V~~v~~--~G~~V~l~~~v~G~i~~s 313 (576)
|+|+.+.+ |.+-+.-.+|++-|||+-
T Consensus 44 G~V~~v~~T~HAigi~t~~G~evLiHiG 71 (124)
T cd00210 44 GTIVQIFPTKHAIGIESDSGVEILIHIG 71 (124)
T ss_pred EEEEEECCCCCEEEEEECCCCEEEEEEE
T ss_conf 7999986789699999689989999973
No 228
>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=26.16 E-value=33 Score=12.48 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=8.0
Q ss_pred EEEEEEEECCCE--EEEEEC
Q ss_conf 589999815966--999851
Q gi|254780456|r 286 VSGVVTNLTDYG--VFVELQ 303 (576)
Q Consensus 286 v~g~V~~v~~~G--~~V~l~ 303 (576)
+.|+|.++.++| +|++|-
T Consensus 4 v~GrV~~~R~~G~l~FidLr 23 (108)
T cd04322 4 VAGRIMSKRGSGKLSFADLQ 23 (108)
T ss_pred EEEEEEEEECCCCCEEEEEE
T ss_conf 99999847067982999999
No 229
>pfam07703 A2M_N_2 Alpha-2-macroglobulin family N-terminal region. This family includes a region of the alpha-2-macroglobulin family.
Probab=25.93 E-value=33 Score=12.46 Aligned_cols=15 Identities=27% Similarity=0.399 Sum_probs=6.6
Q ss_pred EECCCCEEEEEEEEE
Q ss_conf 332697258999987
Q gi|254780456|r 240 VLSIGQQVKVKIIRI 254 (576)
Q Consensus 240 ~~~~G~~v~~~Vl~~ 254 (576)
.|++|++.++.|.+.
T Consensus 9 ~y~~Ge~~~v~i~s~ 23 (136)
T pfam07703 9 SYKVGETAKVTITSP 23 (136)
T ss_pred HCCCCCEEEEEEECC
T ss_conf 349999999999799
No 230
>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This family consists serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=25.45 E-value=34 Score=12.40 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=10.2
Q ss_pred CCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 69725899998747652799852
Q gi|254780456|r 243 IGQQVKVKIIRINQETHRISLGM 265 (576)
Q Consensus 243 ~G~~v~~~Vl~~d~~~~~i~lsl 265 (576)
=|.+.+||++..|+.+--=.|.+
T Consensus 123 DgrefkAklvG~D~~~D~AvlKi 145 (484)
T TIGR02037 123 DGREFKAKLVGKDPRTDIAVLKI 145 (484)
T ss_pred CCCEEEEEEECCCCCEEEEEEEE
T ss_conf 99485568866677213899998
No 231
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=25.36 E-value=34 Score=12.39 Aligned_cols=23 Identities=35% Similarity=0.475 Sum_probs=10.3
Q ss_pred CCCCEEEEEEEEEECCCCEEEEC
Q ss_conf 22330246788753147177744
Q gi|254780456|r 196 EEGQVIEGTVKNITDYGVFVDLS 218 (576)
Q Consensus 196 ~~G~~v~g~V~~i~~~g~~V~~~ 218 (576)
.+|.+-+|.|.+....|.+|++|
T Consensus 104 ~~Ge~ReG~v~~~~~~~~~v~iG 126 (272)
T COG2106 104 KEGEYREGLVIRRGKKGNLVDIG 126 (272)
T ss_pred CCEEECCEEEEEECCCCEEEECC
T ss_conf 62561050798736882389805
No 232
>TIGR02222 chap_CsaA export-related chaperone CsaA; InterPro: IPR008231 The CsaA protein is required for SecA-mediated translocation of a subset of proteins , . CsaA and its relatives are typified by the presence of little more than a tRNA-binding motif that adopts an OB-fold. The Aquifex aeolicus member, Trbp111, has been demonstrated to bind tRNA, likely in a structure-specific manner .; GO: 0000049 tRNA binding, 0008565 protein transporter activity, 0015031 protein transport.
Probab=25.00 E-value=35 Score=12.35 Aligned_cols=21 Identities=29% Similarity=0.259 Sum_probs=8.4
Q ss_pred CCCEE-EEEEEEEECCCCEEEE
Q ss_conf 89879-9999997479985999
Q gi|254780456|r 70 VGDEV-EVYVERTENSFGEAVF 90 (576)
Q Consensus 70 vGd~i-~v~V~~~~~~~g~i~l 90 (576)
+++.. ||+|++..++.|.+.|
T Consensus 72 iA~f~SEVLVlG~~~~~g~VvL 93 (107)
T TIGR02222 72 IAGFKSEVLVLGVIDEEGEVVL 93 (107)
T ss_pred ECCCEEEEEECCCCCCCCCEEE
T ss_conf 5692404886183378787798
No 233
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.68 E-value=37 Score=12.20 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=13.1
Q ss_pred CCCCCHHHHHCCCCCCHHHHCCCCCCCEE-EEEE
Q ss_conf 53201132210111000011004789879-9999
Q gi|254780456|r 434 RISLGVKQLSGSAPDVVDSVSSLRKNDVV-SCEV 466 (576)
Q Consensus 434 ~i~LS~K~l~~~~~~~~~~~~~~~~G~iv-~g~V 466 (576)
.+..|+.++.... ..+-.+++||++ +|+.
T Consensus 207 ~Mi~~i~~lI~~l----S~~~tL~pGDvI~TGTP 236 (266)
T COG0179 207 DMIFSIPELIAYL----SRFMTLEPGDVILTGTP 236 (266)
T ss_pred HCCCCHHHHHHHH----HCCCCCCCCCEEEECCC
T ss_conf 7061899999998----66765079899886898
No 234
>TIGR01648 hnRNP-R-Q hnRNP-R, Q splicing factor family; InterPro: IPR006535 Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein) . These proteins contain three RNA recognition domains and a somewhat variable C-terminal domain. .
Probab=23.34 E-value=37 Score=12.16 Aligned_cols=32 Identities=31% Similarity=0.520 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEE
Q ss_conf 22121110001122233024678875314717774
Q gi|254780456|r 183 SRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDL 217 (576)
Q Consensus 183 ~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g~~V~~ 217 (576)
..++-..+.|+++++|.+ =+||+|.|| +||.|
T Consensus 250 ttEE~ieKsF~~f~PG~v--ERVKKirDY-AFVHF 281 (611)
T TIGR01648 250 TTEEIIEKSFSEFKPGAV--ERVKKIRDY-AFVHF 281 (611)
T ss_pred HHHHHHHHHCCCCCCCCE--EEEEEECCE-EEEEE
T ss_conf 214333201256799724--543110121-36401
No 235
>pfam01330 RuvA_N RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.
Probab=23.07 E-value=38 Score=12.13 Aligned_cols=30 Identities=27% Similarity=0.476 Sum_probs=17.3
Q ss_pred EEEEEEEEECCEEEEEEC-CCEEEEEEHHHH
Q ss_conf 999999981998999947-960367899750
Q gi|254780456|r 30 TKGIVVGLEKDTVVVDVG-LKFEGRIPRREF 59 (576)
Q Consensus 30 v~G~V~~i~~~~v~vdig-~k~~G~i~~~e~ 59 (576)
+.|+|..++++.+.+|.+ -..+-++|.+.+
T Consensus 5 l~G~i~~~~~~~ivi~~~GvGY~v~is~~~~ 35 (61)
T pfam01330 5 LRGKVTEVGPDYIVVEVNGVGYEINVSARTL 35 (61)
T ss_pred EEEEEEEECCCEEEEEECCEEEEEEECHHHH
T ss_conf 9999999729999999678799999888999
No 236
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=22.72 E-value=38 Score=12.08 Aligned_cols=13 Identities=15% Similarity=0.445 Sum_probs=6.1
Q ss_pred CCCCCCCCCCCCE
Q ss_conf 1100011222330
Q gi|254780456|r 188 RSEIVQKLEEGQV 200 (576)
Q Consensus 188 ~~~~~~~l~~G~~ 200 (576)
..++.+.|+.||.
T Consensus 47 ~~~m~~~L~~Gd~ 59 (107)
T PRK05585 47 HKKMLSSLAKGDE 59 (107)
T ss_pred HHHHHHHCCCCCE
T ss_conf 9999984589999
No 237
>PRK03598 hypothetical protein; Provisional
Probab=21.61 E-value=41 Score=11.95 Aligned_cols=40 Identities=18% Similarity=0.251 Sum_probs=20.4
Q ss_pred CCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEE
Q ss_conf 877999999981998999947960367899750566435563789879
Q gi|254780456|r 27 NCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEV 74 (576)
Q Consensus 27 G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i 74 (576)
.....|.|- +-.|++..+..|+|..-.+. ..+.++.||.+
T Consensus 32 ~~~~~g~ve-----~~~V~vs~~v~G~V~~v~V~---eGd~Vk~Gq~L 71 (331)
T PRK03598 32 GLTLYGNVD-----IRTVNLSFRVGGRLASLAVD---EGDAVKAGQVL 71 (331)
T ss_pred CEEEEEEEE-----EEEEEECCCCCEEEEEEECC---CCCEECCCCEE
T ss_conf 603579999-----99999913277599999868---97987799889
No 238
>smart00815 AMA-1 Apical membrane antigen 1. Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites.
Probab=21.19 E-value=39 Score=12.05 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=5.8
Q ss_pred EECCCEEEEEECC
Q ss_conf 8159669998514
Q gi|254780456|r 292 NLTDYGVFVELQS 304 (576)
Q Consensus 292 ~v~~~G~~V~l~~ 304 (576)
+++..|++|+|+.
T Consensus 13 ~~HgSGI~VDLGe 25 (240)
T smart00815 13 KVHGSGIYVDLGE 25 (240)
T ss_pred HHCCCCEEEECCC
T ss_conf 1117722886688
No 239
>TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849 This entry describes proteins of unknown function..
Probab=21.03 E-value=42 Score=11.87 Aligned_cols=31 Identities=23% Similarity=0.583 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCCEEE------EEEEEEECCC--CEEEEC
Q ss_conf 110001122233024------6788753147--177744
Q gi|254780456|r 188 RSEIVQKLEEGQVIE------GTVKNITDYG--VFVDLS 218 (576)
Q Consensus 188 ~~~~~~~l~~G~~v~------g~V~~i~~~g--~~V~~~ 218 (576)
..++.++|+.||.|- |+|.++.+.. +.+.++
T Consensus 31 ~~kl~~~L~KGd~V~T~gGi~G~V~~i~e~~~~i~i~~~ 69 (86)
T TIGR00739 31 HKKLIESLKKGDKVLTIGGIIGTVTKIAENTNNIVIELN 69 (86)
T ss_pred HHHHHHCCCCCCEEEECCCEEEEEEEEECCCCEEEEEEC
T ss_conf 888885279977899838838999885238867899987
No 240
>pfam07405 DUF1506 Protein of unknown function (DUF1506). This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.
Probab=20.95 E-value=42 Score=11.86 Aligned_cols=27 Identities=22% Similarity=0.321 Sum_probs=11.4
Q ss_pred EECCCCEEEEEEEEECCCCCEEEEEEC
Q ss_conf 332697258999987476527998521
Q gi|254780456|r 240 VLSIGQQVKVKIIRINQETHRISLGMK 266 (576)
Q Consensus 240 ~~~~G~~v~~~Vl~~d~~~~~i~lslK 266 (576)
...+++.+-+.|.++|..-+-+.|.+|
T Consensus 101 RISi~d~~yfEIfSIdsSigYfTLvLK 127 (133)
T pfam07405 101 RISIADLIYFEIFSIDSSIGYFTLVLK 127 (133)
T ss_pred CCCCCCEEEEEEEEEECCCEEEEEEHH
T ss_conf 231332389999997064205440212
No 241
>pfam01176 eIF-1a Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Probab=20.67 E-value=42 Score=11.83 Aligned_cols=57 Identities=35% Similarity=0.433 Sum_probs=25.2
Q ss_pred EEEEEEEECCCEEE-EEECCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCCEE
Q ss_conf 58999981596699-9851420000001111011135574210037845799999862155047
Q gi|254780456|r 286 VSGVVTNLTDYGVF-VELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRI 348 (576)
Q Consensus 286 v~g~V~~v~~~G~~-V~l~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i 348 (576)
+.|+|.+....+.| |.+.+|.+-+.+++- + ..+ .=-+..||.|.+..-.++..+..|
T Consensus 5 ~~g~V~~~lg~~~~~V~~~dg~~~l~~i~G----K-~rk-riwi~~GD~VlV~~~~~~~~kg~I 62 (65)
T pfam01176 5 MIGQVTEMLGNGRFEVELEDGHERLAHIPG----K-RRK-RIWILRGDFVLVELSPYDKVKGRI 62 (65)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEECC----C-EEE-EEEECCCCEEEEEECCCCCCEEEE
T ss_conf 999999982998899997999999999822----0-545-799749999999967877863999
No 242
>COG5009 MrcA Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]
Probab=20.33 E-value=43 Score=11.78 Aligned_cols=54 Identities=26% Similarity=0.500 Sum_probs=23.7
Q ss_pred CCCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCC-----CCCEEECCCCEEEEE
Q ss_conf 233024678875314717774-483157886420244444-----331133269725899
Q gi|254780456|r 197 EGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRIL-----HPSKVLSIGQQVKVK 250 (576)
Q Consensus 197 ~G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~-----~~~~~~~~G~~v~~~ 250 (576)
.++...+.|..+.+.|+.+-+ .+-..-+...+|-|.+-. .|.+.++.|+.+-++
T Consensus 345 ~~~~~~AvV~~~~~~~a~i~~~~~~~~~~~~~~m~wa~~~~~~~~~~~~~l~~G~~i~V~ 404 (797)
T COG5009 345 VGELLPAVVLSVAKSGAKIGLADGSKVTLSMEAMRWARRLLSDNKSPEDVLKPGDVIYVR 404 (797)
T ss_pred CCCCEEEEEEEECCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEE
T ss_conf 666138899985367766982056401343877544543033556733346888889999
No 243
>PRK13289 nitric oxide dioxygenase; Provisional
Probab=20.25 E-value=43 Score=11.77 Aligned_cols=13 Identities=23% Similarity=0.284 Sum_probs=9.7
Q ss_pred EECCCCEEEEEEE
Q ss_conf 3326972589999
Q gi|254780456|r 240 VLSIGQQVKVKII 252 (576)
Q Consensus 240 ~~~~G~~v~~~Vl 252 (576)
.|+.||-+.+++-
T Consensus 184 ~f~pGQYisv~~~ 196 (399)
T PRK13289 184 EFKPGQYLGVRLD 196 (399)
T ss_pred CCCCCCEEEEEEE
T ss_conf 9899997899996
Done!