Query 019315
Match_columns 343
No_of_seqs 180 out of 1126
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:27:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019315hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07400 30S ribosomal protein 99.9 2.4E-24 5.2E-29 209.4 16.5 137 157-331 16-153 (318)
2 COG0539 RpsA Ribosomal protein 99.9 4.3E-24 9.2E-29 219.4 16.5 145 157-342 3-152 (541)
3 PRK07899 rpsA 30S ribosomal pr 99.9 7.4E-23 1.6E-27 209.0 15.9 146 157-341 20-167 (486)
4 PRK06299 rpsA 30S ribosomal pr 99.9 1.4E-21 3E-26 201.1 18.2 144 157-341 13-160 (565)
5 TIGR00717 rpsA ribosomal prote 99.9 2.3E-21 5E-26 196.8 17.7 142 157-341 1-146 (516)
6 COG0539 RpsA Ribosomal protein 99.9 7.5E-22 1.6E-26 202.9 13.6 163 167-331 187-399 (541)
7 PRK13806 rpsA 30S ribosomal pr 99.8 3.8E-20 8.2E-25 188.9 17.7 142 157-341 15-161 (491)
8 PRK12269 bifunctional cytidyla 99.8 3.1E-20 6.8E-25 200.3 16.5 176 111-341 265-447 (863)
9 PRK06676 rpsA 30S ribosomal pr 99.8 1.1E-19 2.4E-24 179.0 17.2 146 157-341 3-151 (390)
10 PRK12269 bifunctional cytidyla 99.8 4.4E-19 9.5E-24 191.5 12.9 169 161-331 482-701 (863)
11 PRK13806 rpsA 30S ribosomal pr 99.8 4.3E-19 9.4E-24 181.2 10.5 164 167-331 197-415 (491)
12 PRK00087 4-hydroxy-3-methylbut 99.8 3.4E-18 7.4E-23 179.7 16.1 140 164-341 294-435 (647)
13 PRK07899 rpsA 30S ribosomal pr 99.7 5.8E-17 1.3E-21 165.9 9.6 158 170-331 120-329 (486)
14 PRK06299 rpsA 30S ribosomal pr 99.7 1.6E-16 3.5E-21 163.7 12.3 163 167-331 196-409 (565)
15 TIGR00717 rpsA ribosomal prote 99.7 3E-16 6.5E-21 159.6 11.9 163 166-330 181-394 (516)
16 PRK06676 rpsA 30S ribosomal pr 99.6 3.8E-16 8.2E-21 154.1 9.2 161 168-331 101-313 (390)
17 PRK00087 4-hydroxy-3-methylbut 99.6 4.9E-15 1.1E-19 156.0 10.7 165 169-336 386-604 (647)
18 PTZ00248 eukaryotic translatio 99.5 2.3E-14 4.9E-19 140.1 5.7 129 169-336 13-154 (319)
19 PRK07400 30S ribosomal protein 99.5 7.8E-13 1.7E-17 129.0 14.8 121 170-337 116-238 (318)
20 COG1098 VacB Predicted RNA bin 99.1 3.4E-10 7.4E-15 97.5 7.0 77 169-283 2-78 (129)
21 PF00575 S1: S1 RNA binding do 98.9 6.6E-09 1.4E-13 79.2 9.2 73 169-279 1-74 (74)
22 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.9 6.6E-09 1.4E-13 81.9 7.6 81 168-282 2-82 (86)
23 cd05705 S1_Rrp5_repeat_hs14 S1 98.9 9.8E-09 2.1E-13 80.2 7.8 73 170-277 1-74 (74)
24 cd04454 S1_Rrp4_like S1_Rrp4_l 98.8 1.5E-08 3.3E-13 79.4 8.5 75 168-280 2-76 (82)
25 PRK08582 hypothetical protein; 98.8 1.9E-08 4.1E-13 87.9 7.9 82 169-289 2-83 (139)
26 cd05687 S1_RPS1_repeat_ec1_hs1 98.8 2.9E-08 6.3E-13 75.1 7.9 69 173-279 1-70 (70)
27 cd04455 S1_NusA S1_NusA: N-uti 98.7 6.8E-08 1.5E-12 73.6 7.9 36 171-207 2-37 (67)
28 cd05694 S1_Rrp5_repeat_hs2_sc2 98.6 1.2E-07 2.6E-12 74.3 7.8 69 170-282 2-72 (74)
29 cd04461 S1_Rrp5_repeat_hs8_sc7 98.6 1.3E-07 2.9E-12 74.3 7.8 77 164-278 6-83 (83)
30 cd05703 S1_Rrp5_repeat_hs12_sc 98.6 2.2E-07 4.8E-12 72.2 7.5 71 173-279 1-72 (73)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 98.6 2.8E-07 6E-12 69.6 7.6 69 173-279 1-70 (70)
32 cd05704 S1_Rrp5_repeat_hs13 S1 98.6 2.7E-07 6E-12 71.3 7.6 71 170-279 1-72 (72)
33 cd05686 S1_pNO40 S1_pNO40: pNO 98.5 6.6E-07 1.4E-11 69.0 9.3 71 170-278 1-72 (73)
34 PRK07252 hypothetical protein; 98.5 3.2E-07 7E-12 78.4 7.0 80 171-288 2-82 (120)
35 PLN00207 polyribonucleotide nu 98.5 3E-07 6.4E-12 100.5 8.1 94 163-295 744-838 (891)
36 cd04465 S1_RPS1_repeat_ec2_hs2 98.5 2.9E-07 6.3E-12 69.4 5.5 45 297-341 1-46 (67)
37 cd05706 S1_Rrp5_repeat_sc10 S1 98.5 9.4E-07 2E-11 67.4 8.4 72 170-279 1-73 (73)
38 cd05691 S1_RPS1_repeat_ec6 S1_ 98.5 5.3E-07 1.1E-11 68.1 6.7 71 173-281 1-72 (73)
39 cd04452 S1_IF2_alpha S1_IF2_al 98.4 1.1E-06 2.4E-11 67.1 8.0 73 170-280 1-76 (76)
40 PRK05807 hypothetical protein; 98.4 1.1E-06 2.4E-11 76.6 8.6 75 169-282 2-76 (136)
41 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.4 1.4E-06 3E-11 66.0 8.0 68 173-278 1-69 (69)
42 cd04465 S1_RPS1_repeat_ec2_hs2 98.4 1.8E-06 3.9E-11 65.1 8.0 66 173-279 1-67 (67)
43 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 1.8E-06 3.9E-11 65.2 7.4 67 173-277 1-68 (68)
44 PRK03987 translation initiatio 98.3 1.5E-06 3.2E-11 83.4 8.4 87 169-293 5-94 (262)
45 cd05692 S1_RPS1_repeat_hs4 S1_ 98.3 3.4E-06 7.3E-11 62.1 7.9 69 173-279 1-69 (69)
46 PRK08059 general stress protei 98.3 2E-06 4.3E-11 73.4 7.5 78 168-283 3-81 (123)
47 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.3 4.4E-06 9.5E-11 64.4 8.2 68 173-278 1-71 (71)
48 cd05708 S1_Rrp5_repeat_sc12 S1 98.3 4E-06 8.6E-11 63.7 7.7 72 171-280 1-74 (77)
49 smart00316 S1 Ribosomal protei 98.3 6.2E-06 1.4E-10 60.2 8.1 71 171-279 1-72 (72)
50 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.2 7.7E-06 1.7E-10 62.3 8.2 65 173-277 1-66 (66)
51 cd04453 S1_RNase_E S1_RNase_E: 98.2 9.8E-06 2.1E-10 65.5 8.4 40 168-207 3-44 (88)
52 TIGR02696 pppGpp_PNP guanosine 98.1 8.7E-06 1.9E-10 87.6 9.3 75 169-277 644-718 (719)
53 cd05690 S1_RPS1_repeat_ec5 S1_ 98.1 1.4E-05 3E-10 59.9 7.6 68 173-277 1-69 (69)
54 cd05688 S1_RPS1_repeat_ec3 S1_ 98.1 1.7E-05 3.7E-10 58.6 8.0 67 172-277 1-68 (68)
55 cd05684 S1_DHX8_helicase S1_DH 98.1 1.1E-05 2.3E-10 62.8 6.9 72 173-282 1-75 (79)
56 cd04472 S1_PNPase S1_PNPase: P 98.1 2.1E-05 4.5E-10 58.3 7.9 68 173-278 1-68 (68)
57 cd05685 S1_Tex S1_Tex: The C-t 98.1 1.8E-05 3.9E-10 58.2 7.4 35 173-207 1-35 (68)
58 cd05693 S1_Rrp5_repeat_hs1_sc1 98.0 1E-05 2.2E-10 67.0 6.2 92 170-280 1-96 (100)
59 COG1093 SUI2 Translation initi 98.0 1E-05 2.2E-10 77.7 6.7 87 169-293 8-103 (269)
60 cd05689 S1_RPS1_repeat_ec4 S1_ 98.0 4.6E-05 9.9E-10 57.9 8.8 38 170-207 1-38 (72)
61 PRK11824 polynucleotide phosph 97.9 2.9E-05 6.3E-10 83.4 9.0 76 168-281 617-692 (693)
62 PRK04163 exosome complex RNA-b 97.9 3.5E-05 7.6E-10 72.6 8.2 79 168-280 59-137 (235)
63 cd04473 S1_RecJ_like S1_RecJ_l 97.9 0.00011 2.4E-09 57.4 9.2 39 168-206 12-50 (77)
64 PRK09521 exosome complex RNA-b 97.9 3.2E-05 7E-10 70.3 7.1 74 167-280 59-142 (189)
65 PRK09202 nusA transcription el 97.9 2.7E-05 5.8E-10 80.4 7.2 74 256-330 88-168 (470)
66 PF00575 S1: S1 RNA binding do 97.9 2.4E-05 5.3E-10 59.5 5.2 38 294-331 2-40 (74)
67 cd05702 S1_Rrp5_repeat_hs11_sc 97.8 0.00011 2.3E-09 56.0 7.5 35 173-207 1-35 (70)
68 PHA02945 interferon resistance 97.8 7.9E-05 1.7E-09 61.1 6.8 74 168-282 7-85 (88)
69 cd05705 S1_Rrp5_repeat_hs14 S1 97.7 5E-05 1.1E-09 59.3 4.6 43 294-336 1-45 (74)
70 TIGR01953 NusA transcription t 97.7 0.00014 3.1E-09 72.3 8.7 36 171-207 130-166 (341)
71 PRK09202 nusA transcription el 97.7 0.00011 2.3E-09 76.0 7.9 39 168-207 128-168 (470)
72 cd04471 S1_RNase_R S1_RNase_R: 97.5 0.00078 1.7E-08 51.9 8.8 36 172-207 1-37 (83)
73 cd05697 S1_Rrp5_repeat_hs5 S1_ 97.5 0.00017 3.8E-09 54.4 4.7 35 297-331 1-36 (69)
74 TIGR03591 polynuc_phos polyrib 97.5 0.00036 7.8E-09 75.1 8.6 71 168-276 614-684 (684)
75 cd05698 S1_Rrp5_repeat_hs6_sc5 97.5 0.00018 3.8E-09 54.2 4.5 41 297-337 1-43 (70)
76 cd00164 S1_like S1_like: Ribos 97.5 0.00052 1.1E-08 49.1 6.7 32 176-207 1-32 (65)
77 cd04461 S1_Rrp5_repeat_hs8_sc7 97.5 0.00018 4E-09 56.4 4.6 49 287-336 6-56 (83)
78 cd05694 S1_Rrp5_repeat_hs2_sc2 97.4 0.00018 3.9E-09 56.3 4.4 37 294-330 2-40 (74)
79 COG2183 Tex Transcriptional ac 97.4 0.00018 3.8E-09 77.9 5.4 78 167-282 653-731 (780)
80 PRK12327 nusA transcription el 97.4 0.00035 7.6E-09 70.2 7.2 36 171-207 133-168 (362)
81 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.4 0.00075 1.6E-08 55.1 7.3 77 168-280 2-86 (92)
82 TIGR01953 NusA transcription t 97.3 0.00056 1.2E-08 68.1 7.3 74 256-330 85-166 (341)
83 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.3 0.0003 6.6E-09 53.5 4.1 34 297-330 1-35 (66)
84 cd05703 S1_Rrp5_repeat_hs12_sc 97.3 0.00034 7.4E-09 54.3 4.4 34 297-330 1-35 (73)
85 COG1185 Pnp Polyribonucleotide 97.3 0.00047 1E-08 73.7 6.7 79 166-282 613-691 (692)
86 COG1097 RRP4 RNA-binding prote 97.3 0.0014 2.9E-08 62.6 9.0 78 167-278 59-136 (239)
87 cd04455 S1_NusA S1_NusA: N-uti 97.3 0.00032 6.9E-09 53.4 3.8 35 296-330 3-37 (67)
88 cd05686 S1_pNO40 S1_pNO40: pNO 97.2 0.00072 1.6E-08 52.1 5.7 43 295-337 2-47 (73)
89 cd05687 S1_RPS1_repeat_ec1_hs1 97.2 0.00067 1.5E-08 51.2 5.0 41 297-337 1-43 (70)
90 cd05707 S1_Rrp5_repeat_sc11 S1 97.2 0.00059 1.3E-08 51.4 4.7 35 297-331 1-36 (68)
91 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.2 0.0026 5.6E-08 51.9 8.7 39 168-206 2-40 (86)
92 cd05691 S1_RPS1_repeat_ec6 S1_ 97.1 0.00088 1.9E-08 50.4 5.1 40 297-336 1-42 (73)
93 PTZ00248 eukaryotic translatio 97.1 0.00066 1.4E-08 67.2 5.2 48 292-339 12-64 (319)
94 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.1 0.00067 1.5E-08 52.2 4.1 34 297-330 1-37 (71)
95 cd05706 S1_Rrp5_repeat_sc10 S1 97.1 0.0013 2.8E-08 50.0 5.6 37 295-331 2-39 (73)
96 cd04453 S1_RNase_E S1_RNase_E: 97.0 0.001 2.2E-08 53.8 4.9 38 293-330 4-44 (88)
97 cd05692 S1_RPS1_repeat_hs4 S1_ 97.0 0.0017 3.8E-08 47.5 5.4 35 297-331 1-36 (69)
98 KOG1070 rRNA processing protei 97.0 0.0028 6.1E-08 72.2 9.3 134 167-338 1157-1297(1710)
99 smart00316 S1 Ribosomal protei 97.0 0.0012 2.7E-08 48.0 4.4 36 296-331 2-38 (72)
100 cd04452 S1_IF2_alpha S1_IF2_al 97.0 0.0019 4.2E-08 49.1 5.7 43 295-337 2-48 (76)
101 COG2996 Predicted RNA-bindinin 96.9 0.0045 9.9E-08 60.2 9.2 120 168-332 69-192 (287)
102 cd05689 S1_RPS1_repeat_ec4 S1_ 96.9 0.0014 3E-08 49.7 4.5 37 294-330 1-38 (72)
103 cd05704 S1_Rrp5_repeat_hs13 S1 96.9 0.0014 3.1E-08 50.5 4.6 43 295-337 2-47 (72)
104 cd04460 S1_RpoE S1_RpoE: RpoE, 96.8 0.0035 7.6E-08 51.0 6.4 90 174-292 1-96 (99)
105 cd05688 S1_RPS1_repeat_ec3 S1_ 96.8 0.0027 5.9E-08 46.7 5.1 36 296-331 1-36 (68)
106 COG1098 VacB Predicted RNA bin 96.7 0.0012 2.6E-08 57.5 3.2 46 294-339 3-50 (129)
107 PRK08582 hypothetical protein; 96.7 0.0031 6.7E-08 55.3 5.5 38 294-331 3-41 (139)
108 PRK05807 hypothetical protein; 96.7 0.0037 8E-08 54.5 5.9 43 294-336 3-46 (136)
109 cd04454 S1_Rrp4_like S1_Rrp4_l 96.7 0.0034 7.4E-08 49.1 5.0 37 295-331 5-42 (82)
110 cd05702 S1_Rrp5_repeat_hs11_sc 96.6 0.0046 9.9E-08 47.0 5.4 35 297-331 1-36 (70)
111 KOG1070 rRNA processing protei 96.6 0.012 2.6E-07 67.3 10.5 163 168-330 983-1197(1710)
112 cd05708 S1_Rrp5_repeat_sc12 S1 96.6 0.0053 1.1E-07 46.5 5.3 36 296-331 2-39 (77)
113 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 96.6 0.0035 7.6E-08 49.3 4.5 36 295-330 5-41 (86)
114 TIGR02696 pppGpp_PNP guanosine 96.5 0.0084 1.8E-07 65.1 8.1 72 267-338 612-695 (719)
115 TIGR00448 rpoE DNA-directed RN 96.4 0.023 4.9E-07 51.4 9.1 40 168-208 77-116 (179)
116 PRK12327 nusA transcription el 96.3 0.0084 1.8E-07 60.4 6.8 43 287-329 123-167 (362)
117 cd05690 S1_RPS1_repeat_ec5 S1_ 96.3 0.0053 1.1E-07 45.8 3.9 34 297-330 1-35 (69)
118 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.3 0.0091 2E-07 47.4 5.1 35 297-331 1-37 (72)
119 PRK08059 general stress protei 96.2 0.0093 2E-07 50.9 5.2 38 294-331 5-43 (123)
120 cd05685 S1_Tex S1_Tex: The C-t 96.1 0.0097 2.1E-07 43.5 4.4 35 297-331 1-36 (68)
121 PF10246 MRP-S35: Mitochondria 96.1 0.019 4.1E-07 48.6 6.4 50 157-206 5-57 (104)
122 TIGR02063 RNase_R ribonuclease 96.0 0.045 9.7E-07 59.1 10.7 85 167-278 622-708 (709)
123 cd05684 S1_DHX8_helicase S1_DH 96.0 0.012 2.6E-07 45.6 4.6 35 297-331 1-39 (79)
124 PRK07252 hypothetical protein; 96.0 0.013 2.8E-07 50.2 5.1 37 295-331 2-39 (120)
125 PRK12328 nusA transcription el 95.9 0.018 3.9E-07 58.4 6.8 39 168-207 134-173 (374)
126 PHA02945 interferon resistance 95.9 0.012 2.5E-07 48.5 4.3 42 295-338 10-57 (88)
127 KOG2916 Translation initiation 95.8 0.0046 1E-07 60.0 1.9 90 169-297 13-105 (304)
128 cd04471 S1_RNase_R S1_RNase_R: 95.8 0.017 3.6E-07 44.4 4.7 34 297-330 2-37 (83)
129 cd04472 S1_PNPase S1_PNPase: P 95.8 0.018 3.8E-07 42.4 4.5 35 297-331 1-36 (68)
130 PRK09521 exosome complex RNA-b 95.7 0.0065 1.4E-07 55.3 2.4 47 285-331 53-110 (189)
131 PRK11642 exoribonuclease R; Pr 95.7 0.048 1E-06 60.2 9.2 86 167-279 638-725 (813)
132 cd05699 S1_Rrp5_repeat_hs7 S1_ 95.6 0.043 9.3E-07 43.6 6.5 35 173-207 1-36 (72)
133 PHA02858 EIF2a-like PKR inhibi 95.6 0.027 5.8E-07 46.2 5.3 39 168-207 12-52 (86)
134 TIGR03591 polynuc_phos polyrib 95.6 0.038 8.3E-07 59.8 8.0 70 268-337 586-661 (684)
135 PRK08563 DNA-directed RNA poly 95.5 0.13 2.8E-06 46.5 9.9 39 168-207 77-115 (187)
136 cd04473 S1_RecJ_like S1_RecJ_l 95.5 0.028 6E-07 43.8 4.9 38 293-330 13-51 (77)
137 cd00164 S1_like S1_like: Ribos 95.4 0.017 3.7E-07 41.1 3.4 32 300-331 1-33 (65)
138 PRK11824 polynucleotide phosph 95.4 0.051 1.1E-06 58.9 8.3 70 268-337 589-664 (693)
139 PRK12329 nusA transcription el 95.4 0.05 1.1E-06 56.3 7.7 40 168-207 148-192 (449)
140 PF13509 S1_2: S1 domain; PDB: 95.4 0.095 2.1E-06 39.6 7.3 35 172-206 1-35 (61)
141 cd05693 S1_Rrp5_repeat_hs1_sc1 95.3 0.016 3.5E-07 47.9 3.3 36 295-330 2-38 (100)
142 cd04462 S1_RNAPII_Rpb7 S1_RNAP 95.3 0.033 7.2E-07 45.2 4.9 35 296-330 1-35 (88)
143 PLN00207 polyribonucleotide nu 95.2 0.043 9.2E-07 61.0 7.1 71 268-338 721-798 (891)
144 TIGR00358 3_prime_RNase VacB a 94.7 0.22 4.8E-06 53.6 10.5 39 169-207 569-608 (654)
145 COG1095 RPB7 DNA-directed RNA 94.6 0.032 6.9E-07 51.5 3.4 39 168-207 77-115 (183)
146 cd04460 S1_RpoE S1_RpoE: RpoE, 94.6 0.059 1.3E-06 43.8 4.7 33 298-330 1-33 (99)
147 TIGR00757 RNaseEG ribonuclease 94.5 0.05 1.1E-06 55.7 5.0 40 168-207 21-62 (414)
148 KOG1067 Predicted RNA-binding 93.9 0.086 1.9E-06 56.1 5.3 78 168-283 664-741 (760)
149 COG1095 RPB7 DNA-directed RNA 93.7 0.057 1.2E-06 49.9 3.3 35 296-330 81-115 (183)
150 PTZ00162 DNA-directed RNA poly 93.4 0.1 2.2E-06 47.6 4.3 35 296-330 81-115 (176)
151 cd04462 S1_RNAPII_Rpb7 S1_RNAP 93.1 0.2 4.3E-06 40.6 5.1 34 172-206 1-34 (88)
152 PRK04163 exosome complex RNA-b 91.6 0.28 6.1E-06 46.4 4.9 37 295-331 62-99 (235)
153 PTZ00162 DNA-directed RNA poly 91.5 0.28 6.1E-06 44.7 4.6 38 168-206 77-114 (176)
154 PRK08563 DNA-directed RNA poly 91.1 0.37 8E-06 43.6 4.9 36 296-331 81-116 (187)
155 PF09883 DUF2110: Uncharacteri 91.0 0.43 9.2E-06 45.4 5.3 87 168-289 68-157 (225)
156 TIGR00448 rpoE DNA-directed RN 91.0 0.34 7.4E-06 43.7 4.6 35 296-330 81-115 (179)
157 COG1185 Pnp Polyribonucleotide 90.6 0.58 1.3E-05 50.8 6.5 71 267-337 586-662 (692)
158 COG2996 Predicted RNA-bindinin 90.5 1.2 2.5E-05 43.9 8.0 66 172-283 155-220 (287)
159 KOG4078 Putative mitochondrial 89.6 0.86 1.9E-05 41.0 5.8 51 156-206 63-116 (173)
160 PRK11642 exoribonuclease R; Pr 87.6 1.2 2.7E-05 49.4 6.6 44 287-330 633-679 (813)
161 PRK12328 nusA transcription el 87.6 1.3 2.9E-05 45.1 6.4 35 295-329 137-172 (374)
162 TIGR02063 RNase_R ribonuclease 87.2 1.3 2.8E-05 48.1 6.5 35 295-329 626-662 (709)
163 PRK11712 ribonuclease G; Provi 86.5 0.85 1.8E-05 47.9 4.4 39 168-206 34-74 (489)
164 COG1096 Predicted RNA-binding 86.4 2.9 6.2E-05 39.0 7.3 103 168-329 60-174 (188)
165 TIGR00358 3_prime_RNase VacB a 85.7 2 4.3E-05 46.4 6.8 36 295-330 571-608 (654)
166 KOG3013 Exosomal 3'-5' exoribo 84.3 1.5 3.4E-05 42.8 4.7 41 166-206 79-119 (301)
167 PRK10811 rne ribonuclease E; R 83.3 1.4 3E-05 49.9 4.5 37 170-206 36-74 (1068)
168 PF13509 S1_2: S1 domain; PDB: 83.3 1.9 4.1E-05 32.5 4.0 34 297-330 2-36 (61)
169 PF10447 EXOSC1: Exosome compo 81.9 2.1 4.5E-05 34.8 3.9 23 170-192 2-24 (82)
170 COG1093 SUI2 Translation initi 79.8 2.5 5.5E-05 41.3 4.4 64 227-316 13-80 (269)
171 PF08292 RNA_pol_Rbc25: RNA po 79.7 4.5 9.7E-05 35.0 5.5 35 172-206 3-37 (122)
172 TIGR00757 RNaseEG ribonuclease 79.1 2.2 4.7E-05 43.9 3.9 35 295-329 24-61 (414)
173 COG2183 Tex Transcriptional ac 77.9 1.9 4.2E-05 47.6 3.3 55 284-339 647-703 (780)
174 PRK05054 exoribonuclease II; P 77.8 5.4 0.00012 43.2 6.6 33 297-329 562-596 (644)
175 PRK12329 nusA transcription el 77.5 5.7 0.00012 41.5 6.4 35 295-329 151-191 (449)
176 COG1107 Archaea-specific RecJ- 76.7 3.7 8E-05 44.4 4.8 41 166-206 116-156 (715)
177 PHA02858 EIF2a-like PKR inhibi 75.1 2.6 5.7E-05 34.7 2.6 44 295-339 15-62 (86)
178 PF08292 RNA_pol_Rbc25: RNA po 73.6 9.3 0.0002 33.1 5.7 34 296-329 3-37 (122)
179 COG1530 CafA Ribonucleases G a 72.3 2.6 5.5E-05 44.3 2.4 40 168-207 33-74 (487)
180 KOG3298 DNA-directed RNA polym 71.1 4.9 0.00011 36.8 3.6 32 169-201 78-109 (170)
181 PRK03987 translation initiatio 69.8 2.5 5.3E-05 41.0 1.5 60 226-310 9-71 (262)
182 TIGR02062 RNase_B exoribonucle 68.5 15 0.00034 39.7 7.3 33 297-329 558-592 (639)
183 KOG3298 DNA-directed RNA polym 62.9 13 0.00029 34.1 4.7 34 296-329 81-114 (170)
184 PRK05054 exoribonuclease II; P 62.2 14 0.0003 40.1 5.5 36 171-206 558-596 (644)
185 KOG3409 Exosomal 3'-5' exoribo 61.5 38 0.00083 31.6 7.4 44 157-206 59-110 (193)
186 KOG1004 Exosomal 3'-5' exoribo 61.1 45 0.00097 32.0 8.0 40 167-206 60-99 (230)
187 cd05791 S1_CSL4 S1_CSL4: CSL4, 59.8 11 0.00023 30.7 3.3 32 168-199 59-91 (92)
188 KOG1856 Transcription elongati 59.5 28 0.00061 40.5 7.4 43 165-207 978-1023(1299)
189 KOG1856 Transcription elongati 50.7 25 0.00053 40.9 5.2 45 295-339 984-1033(1299)
190 TIGR02062 RNase_B exoribonucle 49.8 27 0.00058 38.0 5.2 34 173-206 558-592 (639)
191 KOG1067 Predicted RNA-binding 48.6 16 0.00035 39.6 3.3 43 296-338 668-712 (760)
192 PRK05585 yajC preprotein trans 48.0 71 0.0015 27.0 6.5 35 168-202 51-91 (106)
193 PF09883 DUF2110: Uncharacteri 47.3 48 0.001 31.8 5.8 53 285-337 61-116 (225)
194 COG4044 Uncharacterized protei 47.2 39 0.00084 32.5 5.2 41 166-206 69-115 (247)
195 TIGR00739 yajC preprotein tran 46.4 92 0.002 25.2 6.6 36 158-197 30-71 (84)
196 PRK05886 yajC preprotein trans 46.0 83 0.0018 27.0 6.6 46 157-206 30-81 (109)
197 PF07653 SH3_2: Variant SH3 do 44.7 38 0.00083 24.3 3.8 34 295-328 19-52 (55)
198 PF09953 DUF2187: Uncharacteri 42.9 25 0.00055 27.0 2.7 19 176-194 16-34 (57)
199 PF01330 RuvA_N: RuvA N termin 42.2 42 0.00091 25.1 3.8 31 175-205 4-35 (61)
200 COG1862 YajC Preprotein transl 40.6 1E+02 0.0022 25.9 6.2 37 168-204 42-84 (97)
201 COG0557 VacB Exoribonuclease R 37.4 38 0.00082 37.1 4.0 48 159-206 609-657 (706)
202 COG4776 Rnb Exoribonuclease II 37.4 13 0.00028 39.5 0.5 35 295-329 560-596 (645)
203 COG1096 Predicted RNA-binding 37.2 51 0.0011 30.9 4.3 35 167-202 116-150 (188)
204 PF01330 RuvA_N: RuvA N termin 36.8 81 0.0017 23.5 4.6 31 299-329 4-36 (61)
205 PF10447 EXOSC1: Exosome compo 36.2 34 0.00074 27.7 2.6 17 167-183 66-82 (82)
206 cd05790 S1_Rrp40 S1_Rrp40: Rrp 33.4 63 0.0014 26.4 3.8 35 295-329 5-40 (86)
207 PRK10811 rne ribonuclease E; R 30.3 50 0.0011 38.0 3.6 34 296-329 38-74 (1068)
208 COG0557 VacB Exoribonuclease R 29.2 1.1E+02 0.0024 33.6 5.9 37 294-330 620-658 (706)
209 PRK11712 ribonuclease G; Provi 27.3 64 0.0014 34.2 3.6 33 296-328 38-73 (489)
210 PF02237 BPL_C: Biotin protein 27.3 97 0.0021 22.1 3.5 19 172-190 11-29 (48)
211 PF14604 SH3_9: Variant SH3 do 24.7 1.1E+02 0.0023 21.8 3.4 33 295-328 16-48 (49)
212 PF05339 DUF739: Protein of un 23.6 20 0.00044 32.0 -0.7 16 117-132 75-90 (138)
213 PF04270 Strep_his_triad: Stre 23.1 1.3E+02 0.0028 22.8 3.6 27 304-330 14-40 (53)
214 COG4873 Uncharacterized protei 22.3 1.1E+02 0.0023 24.6 3.1 26 169-194 23-54 (81)
215 PF02699 YajC: Preprotein tran 22.1 42 0.00092 26.9 0.9 29 168-196 35-69 (82)
No 1
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.92 E-value=2.4e-24 Score=209.38 Aligned_cols=137 Identities=28% Similarity=0.356 Sum_probs=120.0
Q ss_pred hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (343)
Q Consensus 157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i 236 (343)
++|+++|+++.+++++|++|+|+|++++++|+|||||+|++|+||++|+++.+...
T Consensus 16 ~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~------------------------ 71 (318)
T PRK07400 16 EDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEG------------------------ 71 (318)
T ss_pred HHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccC------------------------
Confidence 68999998766779999999999999999999999999999999999998532100
Q ss_pred cCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEE
Q 019315 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (343)
Q Consensus 237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVe 315 (343)
+ .....+|+.+.+.|+.. +++++++||+|++....+|+++++++++|.+|+|+|++++++|++|+
T Consensus 72 -------~-------~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~ 137 (318)
T PRK07400 72 -------P-------EEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVR 137 (318)
T ss_pred -------H-------HHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence 0 11235677888888875 46789999999998889999999999999999999999999999999
Q ss_pred ECCeEEEEeCCccccC
Q 019315 316 IEGLRAFLPKAELLSR 331 (343)
Q Consensus 316 IeGlrgFIP~SQl~~r 331 (343)
++|++||||.||++.+
T Consensus 138 l~Gv~gfip~s~ls~~ 153 (318)
T PRK07400 138 IEGLRGFIPGSHISTR 153 (318)
T ss_pred ECCEEEEEEHHHcCcc
Confidence 9999999999999986
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=4.3e-24 Score=219.41 Aligned_cols=145 Identities=30% Similarity=0.340 Sum_probs=125.4
Q ss_pred hhHHHHhh---cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhccee
Q 019315 157 KVGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKM 233 (343)
Q Consensus 157 ~dFa~lLe---~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV 233 (343)
.+|+++|. .+.+.+++|++|+|+|++|.+++|+||||+|++|+||++||+....
T Consensus 3 ~~f~~~~~~~~~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~----------------------- 59 (541)
T COG0539 3 EEFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPV----------------------- 59 (541)
T ss_pred hhHHHHHHhhhcchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccc-----------------------
Confidence 34555554 3457899999999999999999999999999999999999983210
Q ss_pred eeecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCee
Q 019315 234 GIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (343)
Q Consensus 234 ~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGl 312 (343)
..++.+|+.+.+.|+.. +++|.++||++++.+..+|+++++++++|++|+|+|++.+|||+
T Consensus 60 ------------------~~~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~ 121 (541)
T COG0539 60 ------------------EDVVQVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGL 121 (541)
T ss_pred ------------------cceecCCCEEEEEEEEEecCCceEEeeHHHHHHHHhHHHHHHHHhcCCeEEEEEEEEecCcE
Confidence 01346677788888753 56689999999999999999999999999999999999999999
Q ss_pred EEEECCeEEEEeCCccccC-CCChhhhcccC
Q 019315 313 LTRIEGLRAFLPKAELLSR-VNNFTELKEKV 342 (343)
Q Consensus 313 iVeIeGlrgFIP~SQl~~r-v~nleel~g~v 342 (343)
+|+++|+|||||+||++.| ++|+++|+|+.
T Consensus 122 ~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~ 152 (541)
T COG0539 122 TVDIEGVRAFLPGSLVDVRPVRDLDPLIGKE 152 (541)
T ss_pred EEEECCEEEeccHHHhcccccccccccCCce
Confidence 9999999999999999998 79999999874
No 3
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.89 E-value=7.4e-23 Score=209.01 Aligned_cols=146 Identities=27% Similarity=0.358 Sum_probs=126.9
Q ss_pred hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (343)
Q Consensus 157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i 236 (343)
++|+++++.....+++|++|+|+|++|++++++||||+|++|+||++|+++.... +
T Consensus 20 e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~-------~----------------- 75 (486)
T PRK07899 20 EDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDV-------D----------------- 75 (486)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccC-------C-----------------
Confidence 6899999877788999999999999999999999999999999999999843100 0
Q ss_pred cCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEE
Q 019315 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR 315 (343)
Q Consensus 237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVe 315 (343)
. ...+++|+++.+.|+.. +.+|+++||+|++....+|++++++++.|.+|+|+|++++++|++|+
T Consensus 76 -------~-------~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vd 141 (486)
T PRK07899 76 -------P-------NEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILD 141 (486)
T ss_pred -------h-------hhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEE
Confidence 0 12246788899999875 46789999999999889999999999999999999999999999999
Q ss_pred ECCeEEEEeCCccccC-CCChhhhccc
Q 019315 316 IEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 316 IeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
+ |++||||.||++.+ ++++++++|+
T Consensus 142 l-Gi~gflP~Sel~~~~~~~~~~~vGq 167 (486)
T PRK07899 142 I-GLRGFLPASLVEMRRVRDLQPYIGQ 167 (486)
T ss_pred E-CCEEEEEhhHhcccccCChhhcCCC
Confidence 9 89999999999987 6778888775
No 4
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.88 E-value=1.4e-21 Score=201.08 Aligned_cols=144 Identities=23% Similarity=0.265 Sum_probs=125.4
Q ss_pred hhHHHHhhccc--CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceee
Q 019315 157 KVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG 234 (343)
Q Consensus 157 ~dFa~lLe~~~--~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~ 234 (343)
++|++||+++. +.+++|++|+|+|+++++++++||||+|++|+||.+|++...
T Consensus 13 ~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~------------------------- 67 (565)
T PRK06299 13 ESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ------------------------- 67 (565)
T ss_pred HHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc-------------------------
Confidence 78999998765 668999999999999999999999999999999999997310
Q ss_pred eecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeE
Q 019315 235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313 (343)
Q Consensus 235 ~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGli 313 (343)
. .....+|+++.+.|+.. +.+|+++||+|++.....|+++.++++.|++|+|+|++++++|++
T Consensus 68 ---~-------------~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~ 131 (565)
T PRK06299 68 ---G-------------ELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFT 131 (565)
T ss_pred ---c-------------cccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEE
Confidence 0 01235677888888875 466899999999999999999999999999999999999999999
Q ss_pred EEECCeEEEEeCCccccC-CCChhhhccc
Q 019315 314 TRIEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 314 VeIeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
|+++|++||||+||++.+ .++++.++|+
T Consensus 132 V~~~g~~gfip~s~~~~~~~~~~~~~vG~ 160 (565)
T PRK06299 132 VDLNGVEAFLPGSQVDVRPVRDTDPLEGK 160 (565)
T ss_pred EEECCEEEEEEHHHccCcCCCChHHhCCC
Confidence 999999999999999987 5677766664
No 5
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.87 E-value=2.3e-21 Score=196.82 Aligned_cols=142 Identities=22% Similarity=0.320 Sum_probs=122.4
Q ss_pred hhHHHHhhcc--cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceee
Q 019315 157 KVGEDKVSVE--YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG 234 (343)
Q Consensus 157 ~dFa~lLe~~--~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~ 234 (343)
++|++||+++ ...+++|++|+|+|+++++++++||+|+|++|+||++|++..
T Consensus 1 ~~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~-------------------------- 54 (516)
T TIGR00717 1 ESFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA-------------------------- 54 (516)
T ss_pred ChHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCC--------------------------
Confidence 4799999765 346899999999999999999999999999999999999721
Q ss_pred eecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeE
Q 019315 235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313 (343)
Q Consensus 235 ~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGli 313 (343)
....++|+++.+.|+.. ++.|++.||++++.+...|+++++++++|.+|+|+|++++++|++
T Consensus 55 -----------------~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~ 117 (516)
T TIGR00717 55 -----------------PLEIQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFI 117 (516)
T ss_pred -----------------ccCCCCCCEEEEEEEEEeCCCCcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEE
Confidence 01235677888888864 467999999999998899999999999999999999999999999
Q ss_pred EEECCeEEEEeCCccccC-CCChhhhccc
Q 019315 314 TRIEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 314 VeIeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
|+++|++||||.||++.+ .++.+.++|+
T Consensus 118 V~i~g~~~flP~s~~~~~~~~~~~~~vG~ 146 (516)
T TIGR00717 118 VDLNGVEAFLPGSQVDVKPIKDLDSLIGK 146 (516)
T ss_pred EEECCEEEEEeHHHhcCcccCchhhhCCC
Confidence 999999999999999876 4566666654
No 6
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=7.5e-22 Score=202.93 Aligned_cols=163 Identities=20% Similarity=0.188 Sum_probs=140.0
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhh------------------hhh
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDF------------------LLC 218 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~------------------l~~ 218 (343)
...+++|++|+|+|.+|+++|+|||||+ .+|++|++|++|.+. +++.. +.-
T Consensus 187 ~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~ 265 (541)
T COG0539 187 LNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEE 265 (541)
T ss_pred HhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhccc
Confidence 4679999999999999999999999987 999999999997641 12211 122
Q ss_pred hhhhhh-----hHhhhcceeeeecCCcc-eeccCCCCCCCCceecc--------------ceEEEEEEeec-CCCceEEe
Q 019315 219 DLKKDA-----EEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVETG--------------TVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 219 d~~k~~-----ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~eiG--------------d~v~~eVl~~d-e~G~I~LS 277 (343)
|+|... .+..+.|+|++++++|+ |++..+++||+|+++++ +++.++|+..+ +++||+||
T Consensus 266 dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~ 345 (541)
T COG0539 266 DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLG 345 (541)
T ss_pred CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEee
Confidence 233222 24789999999999999 99999999999999655 77889999876 67999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 278 TRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 278 ~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
+|++. .+||+.+.+.|+.|..|+|+|+++.+.|++|.++ |++||++.|++++.
T Consensus 346 iKq~~-~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~ 399 (541)
T COG0539 346 LKQLK-ENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWD 399 (541)
T ss_pred ehhhh-cChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCcc
Confidence 99999 5999999999999999999999999999999995 59999999999975
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.84 E-value=3.8e-20 Score=188.90 Aligned_cols=142 Identities=20% Similarity=0.189 Sum_probs=119.2
Q ss_pred hhHHHHhhcccC----CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcce
Q 019315 157 KVGEDKVSVEYY----EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK 232 (343)
Q Consensus 157 ~dFa~lLe~~~~----~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGk 232 (343)
++|+++|+++.+ .+++|++|+|+|++|++++++||||+|++|+||++|+....
T Consensus 15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~----------------------- 71 (491)
T PRK13806 15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD----------------------- 71 (491)
T ss_pred HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc-----------------------
Confidence 689999987643 38999999999999999999999999999999999986210
Q ss_pred eeeecCCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCee
Q 019315 233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312 (343)
Q Consensus 233 V~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGl 312 (343)
.+ ....+|+++.+.|+..+ ++.+.||++.+ ....|+++.+++++|++|+|+|++++++|+
T Consensus 72 -----~~-------------~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~ 131 (491)
T PRK13806 72 -----GE-------------LTVAVGDEVELYVVSVN-GQEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGF 131 (491)
T ss_pred -----cc-------------ccccCCCEEEEEEEEEc-CCEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCE
Confidence 00 01256777888887654 35799998755 468999999999999999999999999999
Q ss_pred EEEECCeEEEEeCCccccC-CCChhhhccc
Q 019315 313 LTRIEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 313 iVeIeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
+|++.|++||||+||++.+ .++++.++|+
T Consensus 132 ~V~i~g~~~flP~s~~~~~~~~~~~~~vG~ 161 (491)
T PRK13806 132 NVEVLGRRAFCPVSQIDLRYVEDPESYVGQ 161 (491)
T ss_pred EEEECCEEEEEEHHHhccccCCChHHcCCC
Confidence 9999999999999999987 5777777664
No 8
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.84 E-value=3.1e-20 Score=200.32 Aligned_cols=176 Identities=22% Similarity=0.215 Sum_probs=134.3
Q ss_pred ccCCCCChhhhhhhhhhccCCCCChhHHhhhcccccccccccC-cCc-hhHHHHhhcc-cCCCCCCCEEEEEEEEEeCCe
Q 019315 111 KKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESID-VDD-KVGEDKVSVE-YYEPKPGDFVIGVVVSGNENK 187 (343)
Q Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~dFa~lLe~~-~~~~k~GdiVeG~VVsI~~~g 187 (343)
-.+..++.+|.+.=.++..+.+--- |++. +.++.+ .+. ---..|++++ +..+++|++|+|+|++|++++
T Consensus 265 iDts~l~ieevv~~i~~~~~~~~~~------~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~iV~G~Vv~i~~~~ 336 (863)
T PRK12269 265 VDTSCLTIEEVCERIAREAHRRALW------GGER--SVENQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTVVQVNAGT 336 (863)
T ss_pred EECCCCCHHHHHHHHHHHHHhcccc------cccc--ccccccccCCCchhHHHHHhhccccCCCCCEEEEEEEEEECCE
Confidence 3456688888888888888753211 0000 000100 111 1123455544 577999999999999999999
Q ss_pred EEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCCCceeccceEEEEEEe
Q 019315 188 LDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLG 267 (343)
Q Consensus 188 v~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~ 267 (343)
+|||||+|+||+||++|+... .++|+++.+.|+.
T Consensus 337 v~VdiG~K~eGiI~~~E~~~~----------------------------------------------~kvGd~i~~~V~~ 370 (863)
T PRK12269 337 VFVDIGGKSEGRVPVEEFEAP----------------------------------------------PKAGDGVRVYVER 370 (863)
T ss_pred EEEEeCCCceEEeEHHHhccC----------------------------------------------CCCCCEEEEEEEE
Confidence 999999999999999998511 1456777888877
Q ss_pred ecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEE--ecCeeEEEEC-CeEEEEeCCccccC-CCChhhhccc
Q 019315 268 RTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEW--NTGGLLTRIE-GLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 268 ~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~--nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
.+++| +.||++++.....|++++++|++|++|+|+|+++ +|||++|+++ |++||||+||++.+ .++++.++|+
T Consensus 371 ~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~~vG~ 447 (863)
T PRK12269 371 VTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGL 447 (863)
T ss_pred EcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHHhCCC
Confidence 65556 8999999999999999999999999999999996 6799999995 89999999999977 5678777764
No 9
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.83 E-value=1.1e-19 Score=179.04 Aligned_cols=146 Identities=32% Similarity=0.459 Sum_probs=123.9
Q ss_pred hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeee
Q 019315 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI 235 (343)
Q Consensus 157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~ 235 (343)
..|++++. ....+++|++|+|+|+++++++++||| |++.+|+||.+|+++...+
T Consensus 3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~------------------------ 57 (390)
T PRK06676 3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIE------------------------ 57 (390)
T ss_pred HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhcccccc------------------------
Confidence 46888886 567899999999999999999999999 8899999999999742100
Q ss_pred ecCCcceeccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEE
Q 019315 236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT 314 (343)
Q Consensus 236 i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliV 314 (343)
+ . .....+|+.+.+.|+..+ +++++.||+|++....+|+++.++++.|++++|+|+++.++|++|
T Consensus 58 --~-----~-------~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V 123 (390)
T PRK06676 58 --D-----I-------NDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV 123 (390)
T ss_pred --C-----c-------ccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 0 0 112467888888888764 557899999999988999999999999999999999999999999
Q ss_pred EECCeEEEEeCCccccC-CCChhhhccc
Q 019315 315 RIEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 315 eIeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
+++|++||||.|+++.+ ..++++++|+
T Consensus 124 ~~~G~~gflp~~el~~~~~~~~~~~vG~ 151 (390)
T PRK06676 124 DVEGVRGFIPASLISTRFVEDFSDFKGK 151 (390)
T ss_pred EECCEEEEEEHHHcCCccCCChHHcCCC
Confidence 99999999999999876 5677777664
No 10
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.79 E-value=4.4e-19 Score=191.49 Aligned_cols=169 Identities=17% Similarity=0.214 Sum_probs=138.3
Q ss_pred HHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc----------ccchhhhhhhh----------
Q 019315 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY----------DKEMDFLLCDL---------- 220 (343)
Q Consensus 161 ~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~----------~ke~e~l~~d~---------- 220 (343)
+++++.+.++++|++|+|+|.++.++|+||+++ +.+||||++++++.+ ++++.+.+++.
T Consensus 482 ~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LS 560 (863)
T PRK12269 482 QAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLS 560 (863)
T ss_pred HHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEE
Confidence 334444567889999999999999999999996 689999999998543 12222222111
Q ss_pred --------hhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCceec---------------cceEEEEEEeec-C
Q 019315 221 --------KKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVET---------------GTVLFAEVLGRT-L 270 (343)
Q Consensus 221 --------~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~ei---------------Gd~v~~eVl~~d-e 270 (343)
|.. ..+.+++|+|+.++++|+ |.++.+++|++|++++ |+++.+.|+..+ +
T Consensus 561 lK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e 640 (863)
T PRK12269 561 LKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQ 640 (863)
T ss_pred EeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecc
Confidence 111 134789999999999999 9999899999997654 467888898876 6
Q ss_pred CCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 271 SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 271 ~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
++++.||+|++.. +||+.+.+.|+.|++|+|+|+++.++|++|++ +|++||||.|++++.
T Consensus 641 ~~rIsLS~K~l~~-~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~ 701 (863)
T PRK12269 641 AGRVSLGLKQVTA-NPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWV 701 (863)
T ss_pred cCceEEEehhccc-CchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhcc
Confidence 7899999999984 89999999999999999999999999999999 699999999999863
No 11
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.78 E-value=4.3e-19 Score=181.20 Aligned_cols=164 Identities=17% Similarity=0.110 Sum_probs=135.4
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhhhh--hh---------------
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDFLL--CD--------------- 219 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~l~--~d--------------- 219 (343)
+..+++|++|+|+|+++.++|+||+++.+.+|+||++|+++.+. +.+.+.+ +|
T Consensus 197 ~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K 276 (491)
T PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIK 276 (491)
T ss_pred HhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEeh
Confidence 34688999999999999999999999888999999999986431 1111111 11
Q ss_pred -----hhhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCcee---------------ccceEEEEEEeec-CCC
Q 019315 220 -----LKKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE---------------TGTVLFAEVLGRT-LSG 272 (343)
Q Consensus 220 -----~~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e---------------iGd~v~~eVl~~d-e~G 272 (343)
.|.. ..+..++|+|+.++++|+ |.++.+++||+|+++ +|+.+.+.|+..+ +++
T Consensus 277 ~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ 356 (491)
T PRK13806 277 QAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKR 356 (491)
T ss_pred hhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCC
Confidence 1211 124789999999999999 999888999999655 4467788888776 678
Q ss_pred ceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 273 RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 273 ~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
+|.||+|++. ..||+.+.+.|+.|++|+|+|+++.+.|++|++ +|+.||||.|+++..
T Consensus 357 ri~Ls~K~~~-~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~ 415 (491)
T PRK13806 357 RISLSLRDAE-GDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRA 415 (491)
T ss_pred EEEEEEeecc-cChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcc
Confidence 9999999987 489999999999999999999999999999999 699999999999864
No 12
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.78 E-value=3.4e-18 Score=179.70 Aligned_cols=140 Identities=30% Similarity=0.392 Sum_probs=119.7
Q ss_pred hcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315 164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA 243 (343)
Q Consensus 164 e~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~ 243 (343)
+.....+++|++|+|+|++++++++|||+|++.+|+||++|+++...+ +
T Consensus 294 ~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~--------------------------~----- 342 (647)
T PRK00087 294 NELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEIS--------------------------S----- 342 (647)
T ss_pred HHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccC--------------------------C-----
Confidence 455678999999999999999999999999999999999999842100 0
Q ss_pred ccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEECCeEEE
Q 019315 244 MSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAF 322 (343)
Q Consensus 244 Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIeGlrgF 322 (343)
. .....+|+.+.+.|+.. +++|++.||+|++....+|++++++++.|++++|+|++++++|++|+++|++||
T Consensus 343 ~-------~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gf 415 (647)
T PRK00087 343 L-------KESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAF 415 (647)
T ss_pred h-------hhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEE
Confidence 0 12246788888888875 467899999999998899999999999999999999999999999999999999
Q ss_pred EeCCccccC-CCChhhhccc
Q 019315 323 LPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 323 IP~SQl~~r-v~nleel~g~ 341 (343)
||.|+++.+ .+++..++|+
T Consensus 416 iP~sel~~~~~~d~~~~vG~ 435 (647)
T PRK00087 416 LPASHVELGYVEDLSEYKGQ 435 (647)
T ss_pred EEHHHhCccccCCHHHhCCC
Confidence 999999877 6777777664
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.69 E-value=5.8e-17 Score=165.93 Aligned_cols=158 Identities=20% Similarity=0.253 Sum_probs=128.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc--------ccchhhhhh--hhh------------------
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY--------DKEMDFLLC--DLK------------------ 221 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~--------~ke~e~l~~--d~~------------------ 221 (343)
++.|++|+|+|+++.++|++|++| ..||||.+++...+ ++.+.+.++ |..
T Consensus 120 ~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~ 197 (486)
T PRK07899 120 KEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSE 197 (486)
T ss_pred hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHH
Confidence 467999999999999999999995 68999999987432 222222111 110
Q ss_pred -------hhhhHhhhcceeeeecCCcc-eeccCCCCCCCCcee--------------ccceEEEEEEeec-CCCceEEeH
Q 019315 222 -------KDAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE--------------TGTVLFAEVLGRT-LSGRPLLST 278 (343)
Q Consensus 222 -------k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e--------------iGd~v~~eVl~~d-e~G~I~LS~ 278 (343)
+...+.+++|+|+.++++|+ |.++ +++||+|+++ +|+.+.+.|+..+ ++++|.||+
T Consensus 198 ~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSl 276 (486)
T PRK07899 198 VRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276 (486)
T ss_pred HHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEE
Confidence 00124688999999999999 8896 5999998665 4567888888876 569999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 279 RRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 279 Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|++. ..||+++.+.++.|++++|+|+++.+.|++|++ +|+.||+|.|++..+
T Consensus 277 K~~~-~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~ 329 (486)
T PRK07899 277 KATQ-EDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAER 329 (486)
T ss_pred eecc-ccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcc
Confidence 9988 489999999999999999999999999999999 599999999999754
No 14
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.68 E-value=1.6e-16 Score=163.73 Aligned_cols=163 Identities=17% Similarity=0.178 Sum_probs=133.7
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc----------ccchhhhh--hh---------------
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY----------DKEMDFLL--CD--------------- 219 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~----------~ke~e~l~--~d--------------- 219 (343)
...+++|++++|+|+++.++|+||++| +.+|+||++|+++.. ++.+.+.+ .|
T Consensus 196 ~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~ 274 (565)
T PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE 274 (565)
T ss_pred HhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc
Confidence 356899999999999999999999998 899999999998542 11122111 11
Q ss_pred -hhhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCce---------------eccceEEEEEEeec-CCCceEE
Q 019315 220 -LKKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVV---------------ETGTVLFAEVLGRT-LSGRPLL 276 (343)
Q Consensus 220 -~~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~---------------eiGd~v~~eVl~~d-e~G~I~L 276 (343)
+|.. ..+..+.|+|+.++++|+ +.++.+++|++|++ .+|+.+.+.|+..+ +++++.|
T Consensus 275 ~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~l 354 (565)
T PRK06299 275 DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISL 354 (565)
T ss_pred ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence 1211 124788999999999999 89988899998854 35677888888876 5689999
Q ss_pred eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
|+|++. ..+|.++.+.++.|++|+|+|+++.+.|++|+++ |+.||||.|++++.
T Consensus 355 s~k~~~-~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~ 409 (565)
T PRK06299 355 GLKQCK-ENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD 409 (565)
T ss_pred ehHHhc-cchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc
Confidence 999987 4899999988999999999999999999999995 89999999999853
No 15
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.67 E-value=3e-16 Score=159.60 Aligned_cols=163 Identities=15% Similarity=0.152 Sum_probs=132.4
Q ss_pred ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhhh--hhhh-------------
Q 019315 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDFL--LCDL------------- 220 (343)
Q Consensus 166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~l--~~d~------------- 220 (343)
....+++|++|+|+|+++.++|+||++| +.+|+||.+|+++... +.+.+. ..|.
T Consensus 181 ~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~ 259 (516)
T TIGR00717 181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLG 259 (516)
T ss_pred HHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecc
Confidence 3457899999999999999999999997 5899999999984321 111111 1111
Q ss_pred ---hh-----hhhHhhhcceeeeecCCcc-eeccCCCCCCCCce---------------eccceEEEEEEeec-CCCceE
Q 019315 221 ---KK-----DAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVV---------------ETGTVLFAEVLGRT-LSGRPL 275 (343)
Q Consensus 221 ---~k-----~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~---------------eiGd~v~~eVl~~d-e~G~I~ 275 (343)
|. ...+..++|+|+.+.+.|+ |.++++++|++|++ .+|+.+.+.|+..+ +++++.
T Consensus 260 ~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~ 339 (516)
T TIGR00717 260 EDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLS 339 (516)
T ss_pred hhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEE
Confidence 11 1124678999999999999 99998999999854 46678888888766 568999
Q ss_pred EeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315 276 LSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS 330 (343)
Q Consensus 276 LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~ 330 (343)
||+|++. ..+|.++.+.++.|++++|+|+++.+.|++|+++ |++||+|.|++++
T Consensus 340 lS~k~~~-~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~ 394 (516)
T TIGR00717 340 LGLKQCK-ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISW 394 (516)
T ss_pred EEehhcc-cCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcC
Confidence 9999987 4899999998999999999999999999999996 8999999999975
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.64 E-value=3.8e-16 Score=154.06 Aligned_cols=161 Identities=17% Similarity=0.192 Sum_probs=129.5
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc--------ccchhhhhh--hhh----------------
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY--------DKEMDFLLC--DLK---------------- 221 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~--------~ke~e~l~~--d~~---------------- 221 (343)
..+++|++|+|+|+++.++|++|+++ +.+|+||++|+++.. ++.+.+.++ |..
T Consensus 101 ~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~ 179 (390)
T PRK06676 101 EKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEER 179 (390)
T ss_pred HhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCccCCChHHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhh
Confidence 34678999999999999999999995 459999999998432 122222221 110
Q ss_pred ---------hhhhHhhhcceeeeecCCcc-eeccCCCCCCCCceec--------------cceEEEEEEeec-CCCceEE
Q 019315 222 ---------KDAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVET--------------GTVLFAEVLGRT-LSGRPLL 276 (343)
Q Consensus 222 ---------k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~ei--------------Gd~v~~eVl~~d-e~G~I~L 276 (343)
+...+..++|+|..+++.|+ |.++ +++|++|.+++ |+.+.+.|+..+ ++++|.|
T Consensus 180 ~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~l 258 (390)
T PRK06676 180 AAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL 258 (390)
T ss_pred hhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence 00124788999999999999 8885 58999987664 678888888875 5689999
Q ss_pred eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
|+|++. ..+|+.+.+.++.|++++|+|+++.+.|++|+++ |+.||+|.|++...
T Consensus 259 S~k~~~-~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~ 313 (390)
T PRK06676 259 SLKDTL-PGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK 313 (390)
T ss_pred EEeecc-cCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc
Confidence 999887 4799999889999999999999999999999994 89999999999754
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.58 E-value=4.9e-15 Score=155.96 Aligned_cols=165 Identities=19% Similarity=0.214 Sum_probs=132.7
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc--------cchhhhh--hhhh--h--------------
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD--------KEMDFLL--CDLK--K-------------- 222 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~--------ke~e~l~--~d~~--k-------------- 222 (343)
.+++|++++|+|+++.++|++|++|. .+||||.+|+++... +.+.+.+ .|.. .
T Consensus 386 ~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~ 464 (647)
T PRK00087 386 AFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEK 464 (647)
T ss_pred HhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhh
Confidence 46789999999999999999999986 999999999885421 1121111 1110 0
Q ss_pred ----------hhhHhhhcceeeeecCCcc-eeccCCCCCCCCcee--------------ccceEEEEEEeec-CCCceEE
Q 019315 223 ----------DAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE--------------TGTVLFAEVLGRT-LSGRPLL 276 (343)
Q Consensus 223 ----------~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e--------------iGd~v~~eVl~~d-e~G~I~L 276 (343)
...+..+.|+|..++++|+ |.+ ++++|++|+++ +|+.+.+.|+..+ +++++.|
T Consensus 465 ~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~l 543 (647)
T PRK00087 465 EKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL 543 (647)
T ss_pred hhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 0124688999999999999 888 67899998765 6678888888875 6789999
Q ss_pred eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315 277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle 336 (343)
|+|++. .++|+.+.+.++.|++++|+|+++.+.|++|++ +|+.||+|.|++... ..++.
T Consensus 544 S~K~~~-~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~ 604 (647)
T PRK00087 544 SLKKLL-PDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPE 604 (647)
T ss_pred Eeeccc-cChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHh
Confidence 999987 589999988899999999999999999999999 589999999999754 44443
No 18
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.49 E-value=2.3e-14 Score=140.11 Aligned_cols=129 Identities=16% Similarity=0.112 Sum_probs=105.2
Q ss_pred CCC-CCCEEEEEEEEEeCCeEEEEeC-C-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315 169 EPK-PGDFVIGVVVSGNENKLDVNVG-A-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS 245 (343)
Q Consensus 169 ~~k-~GdiVeG~VVsI~~~gv~VDIG-~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig 245 (343)
.|. +|++|.|+|++|.++|+||+|+ | +.+|+||++|+++.. +.. +
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~r-----------------------i~~--------i- 60 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRR-----------------------IRS--------I- 60 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccc-----------------------cCC--------H-
Confidence 344 7999999999999999999994 4 799999999999642 111 1
Q ss_pred CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec-CeeEEE------E-
Q 019315 246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT-GGLLTR------I- 316 (343)
Q Consensus 246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK-GGliVe------I- 316 (343)
..++++|+++.+.|+..+ ++|+|.||+|++.. .+|..+.+.|+.|.+|+++|..+.+ .|+.++ .
T Consensus 61 ------~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~-~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~ 133 (319)
T PTZ00248 61 ------NKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP-EDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIW 133 (319)
T ss_pred ------HHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc-chHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHH
Confidence 234578888999999865 67999999999995 6999999999999999999999954 899887 3
Q ss_pred CCeEEEEeCCccccC-CCChh
Q 019315 317 EGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 317 eGlrgFIP~SQl~~r-v~nle 336 (343)
.++++|.+.+++... +.+.+
T Consensus 134 pl~~~~gh~y~af~~~v~~~~ 154 (319)
T PTZ00248 134 PLYKKYGHALDALKEALTNPD 154 (319)
T ss_pred HHHHhcCCHHHHHHHHhcCch
Confidence 578999998887543 44444
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.47 E-value=7.8e-13 Score=129.05 Aligned_cols=121 Identities=19% Similarity=0.149 Sum_probs=97.5
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
++.|++|+|+|++++++|++|+++ +.+||||.+++++...+
T Consensus 116 ~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~~-------------------------------------- 156 (318)
T PRK07400 116 QKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKPK-------------------------------------- 156 (318)
T ss_pred ccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCCc--------------------------------------
Confidence 456999999999999999999996 79999999999853100
Q ss_pred CCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315 250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl 328 (343)
. .-+|..+.+.|+..+ +++++.||+|++... ...+.++.|++|+|+|+++...|++|++.|+.||||.|++
T Consensus 157 ---~-~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~----~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisel 228 (318)
T PRK07400 157 ---E-ELVGEELPLKFLEVDEERNRLVLSHRRALVE----RKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEI 228 (318)
T ss_pred ---c-ccCCCEEEEEEEEEEcccCEEEEEhhHhhhh----hhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHc
Confidence 0 024566778888776 568999999876642 3345678999999999999999999999999999999999
Q ss_pred ccC-CCChhh
Q 019315 329 LSR-VNNFTE 337 (343)
Q Consensus 329 ~~r-v~nlee 337 (343)
+.. +.++.+
T Consensus 229 s~~~~~~~~~ 238 (318)
T PRK07400 229 SHEHIETPHS 238 (318)
T ss_pred ccccccChhh
Confidence 875 444443
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=3.4e-10 Score=97.53 Aligned_cols=77 Identities=19% Similarity=0.193 Sum_probs=64.0
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
+++.|++++|+|+.|+++||||++..+..|+||++|++..+ +.|+
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~f-------VkdI---------------------------- 46 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGF-------VKDI---------------------------- 46 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhh-------HHhH----------------------------
Confidence 57899999999999999999999988788999999998432 1111
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR 283 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~ 283 (343)
-+...+|+++.++|+.++++|+|.||+|.+..
T Consensus 47 ---~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e 78 (129)
T COG1098 47 ---HDHLKVGQEVKVKVLDIDENGKISLSIRKLEE 78 (129)
T ss_pred ---HHHhcCCCEEEEEEEeeccCCCcceehHHhhh
Confidence 12346788999999999999999999999885
No 21
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.94 E-value=6.6e-09 Score=79.20 Aligned_cols=73 Identities=26% Similarity=0.258 Sum_probs=57.7
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
+++.|++++|+|.+++++|+||+++.+.+|+||++|+.+.... .
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~--------------------------~---------- 44 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRID--------------------------D---------- 44 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEES--------------------------S----------
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCcccc--------------------------c----------
Confidence 3689999999999999999999999999999999999842100 0
Q ss_pred CCCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
......+|+.+.+.|+..+ +.+++.||+|
T Consensus 45 --~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 45 --PSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp --SHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred --cccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 0123467788888998865 6688999975
No 22
>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=98.88 E-value=6.6e-09 Score=81.95 Aligned_cols=81 Identities=28% Similarity=0.315 Sum_probs=61.9
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
|.+++|++|+|+|+++.+++++|+++++.+|++|++|+++.. + +. .+. .+
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~-----~~-----------~~~--------~~--- 51 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---T-----DE-----------DEL--------NM--- 51 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---C-----cc-----------chH--------HH---
Confidence 457899999999999999999999999999999999997310 0 00 000 01
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~ 282 (343)
.....+|+.+.+.|+..++++++.||+++..
T Consensus 52 ----~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~~ 82 (86)
T cd05789 52 ----RSYLDEGDLIVAEVQSVDSDGSVSLHTRSLK 82 (86)
T ss_pred ----HhhCCCCCEEEEEEEEECCCCCEEEEeCccc
Confidence 1234778889999998876699999987753
No 23
>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=98.86 E-value=9.8e-09 Score=80.20 Aligned_cols=73 Identities=21% Similarity=0.233 Sum_probs=56.4
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
+++|++|+|+|.+++++|+||+++.+.+|++|++|+++...+.. .
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~-----------------------------------~ 45 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDP-----------------------------------S 45 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccCh-----------------------------------h
Confidence 57899999999999999999999999999999999985420000 0
Q ss_pred CCCCceeccceEEEEEEeec-CCCceEEe
Q 019315 250 PGRPVVETGTVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS 277 (343)
.+...+.+|+.+.+.|+..+ ++++|.||
T Consensus 46 ~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 46 LYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred hHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 00134577888889999875 56888886
No 24
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.84 E-value=1.5e-08 Score=79.43 Aligned_cols=75 Identities=25% Similarity=0.332 Sum_probs=59.9
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
|.+++||+|.|+|+++++++++|||+++.+|++|.++++....++ +
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~-------------------------------~--- 47 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKE-------------------------------I--- 47 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHH-------------------------------H---
Confidence 457899999999999999999999999999999999997321000 0
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr 280 (343)
.+.+++||.+.+.|+..+.++++.||.+.
T Consensus 48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 48 ----RKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred ----HhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 12347788899999987655899999865
No 25
>PRK08582 hypothetical protein; Provisional
Probab=98.78 E-value=1.9e-08 Score=87.92 Aligned_cols=82 Identities=18% Similarity=0.133 Sum_probs=66.9
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
.+++|++|+|+|+.|++.|+||+|+.+.+|+||++|+++.+ +. + +
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~-----------------------v~---~-----~---- 46 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNY-----------------------VK---D-----I---- 46 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCccc-----------------------cc---c-----c----
Confidence 47799999999999999999999999999999999998431 00 0 0
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR 289 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~ 289 (343)
..+..+|+.+.+.|+.++.+|+|.||++++.. .+|..
T Consensus 47 ---~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~-~~~~~ 83 (139)
T PRK08582 47 ---NDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKD-RPKRQ 83 (139)
T ss_pred ---ccccCCCCEEEEEEEEECCCCcEEEEEEeccc-Cchhh
Confidence 12357788899999988767999999999974 78864
No 26
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.78 E-value=2.9e-08 Score=75.12 Aligned_cols=69 Identities=28% Similarity=0.277 Sum_probs=54.8
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|+|+|+++.+++++|+++.+.+|++|.+|+++...+. + .
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~-------------------------------~-------~ 42 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIEN-------------------------------G-------E 42 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCC-------------------------------H-------h
Confidence 8999999999999999999999999999999998431000 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEeHH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
....+|+.+.+.|+..+ +++++.||+|
T Consensus 43 ~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 43 DEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred HcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 22467788888888765 6689999974
No 27
>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=98.71 E-value=6.8e-08 Score=73.61 Aligned_cols=36 Identities=25% Similarity=0.499 Sum_probs=33.4
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
+.|++|+|+|++++++++|||+|+ ++|+||.+|+++
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~ 37 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP 37 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC
Confidence 469999999999999999999986 999999999973
No 28
>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=98.64 E-value=1.2e-07 Score=74.25 Aligned_cols=69 Identities=17% Similarity=0.138 Sum_probs=55.5
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
++.|++|.|+|.+|+++|++||+| .+.+||||.+|+++.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~---------------------------------------- 41 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF---------------------------------------- 41 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----------------------------------------
Confidence 678999999999999999999998 478999999999731
Q ss_pred CCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF 282 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~ 282 (343)
....+|+.+.+.|+..+ +++++.||.|++.
T Consensus 42 ----~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 42 ----SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred ----cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 01245667778888765 6678999988754
No 29
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.63 E-value=1.3e-07 Score=74.26 Aligned_cols=77 Identities=22% Similarity=0.141 Sum_probs=59.7
Q ss_pred hcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315 164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA 243 (343)
Q Consensus 164 e~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~ 243 (343)
...+..++.|+++.|+|+++.++|+||+++.+.+|++|++|+++.+. . +
T Consensus 6 ~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~-----------------------~---~----- 54 (83)
T cd04461 6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-----------------------T---D----- 54 (83)
T ss_pred hhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccc-----------------------c---C-----
Confidence 34456789999999999999999999999888999999999974310 0 0
Q ss_pred ccCCCCCCCCceeccceEEEEEEeec-CCCceEEeH
Q 019315 244 MSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLST 278 (343)
Q Consensus 244 Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~ 278 (343)
+ .....+|+.+.+.|+..+ +.+++.||.
T Consensus 55 ~-------~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 55 P-------SFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred H-------HHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 0 123467788888888765 568999883
No 30
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.57 E-value=2.2e-07 Score=72.23 Aligned_cols=71 Identities=20% Similarity=0.188 Sum_probs=55.2
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|+|+|+++.++|+||.++.+.+|+||++++++.. ...+ + ..
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~-~~~~----~-------------------------------~~ 44 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV-SVLE----H-------------------------------PE 44 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc-cccc----C-------------------------------HH
Confidence 8999999999999999999999999999999997421 0000 0 01
Q ss_pred CceeccceEEEEEEeec-CCCceEEeHH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
....+|+.+.+.|+..+ ++.+|.||+|
T Consensus 45 ~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 45 KKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred HhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 23467888999999876 6689999974
No 31
>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=98.56 E-value=2.8e-07 Score=69.63 Aligned_cols=69 Identities=23% Similarity=0.191 Sum_probs=53.8
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++++|+|+++.++|+||+++.+.+|++|++++++.+. .+ . .
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~-------~~------------------------~-------~ 42 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFI-------KD------------------------P-------E 42 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhc-------CC------------------------H-------H
Confidence 89999999999999999999888999999999973210 00 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEeHH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
....+|+.+.+.|+..+ +++++.||+|
T Consensus 43 ~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 43 EHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred HcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 12466788888888865 5689999964
No 32
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.56 E-value=2.7e-07 Score=71.31 Aligned_cols=71 Identities=18% Similarity=0.202 Sum_probs=55.8
Q ss_pred CCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 170 PKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~-~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
+++|++|.|+|+++.+ .|++|+++.+.+|++|++++++.+.+. +
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~-------------------------------~---- 45 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTEN-------------------------------P---- 45 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCC-------------------------------H----
Confidence 4689999999999986 799999999999999999998532100 0
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEeHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTR 279 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~K 279 (343)
.+++.+|+.+.++|++.+. +++.||+|
T Consensus 46 ---~~~~~~Gd~v~~kV~~~~~-~~i~LSl~ 72 (72)
T cd05704 46 ---LEGFKPGKIVRCCILSKKD-GKYQLSLR 72 (72)
T ss_pred ---HHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence 1234677888899988755 89999974
No 33
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.54 E-value=6.6e-07 Score=69.04 Aligned_cols=71 Identities=25% Similarity=0.324 Sum_probs=54.3
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
++.|++++|+|+++.++|+||++ |.+.+|++|++|+++.. +. . .
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~---~~-----------------------~-----~---- 45 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCR---VD-----------------------D-----P---- 45 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCc---cc-----------------------C-----H----
Confidence 35799999999999999999999 43479999999998431 00 0 0
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLST 278 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~ 278 (343)
..+..+|+.+.+.|+..+.++++.||+
T Consensus 46 ---~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 46 ---SEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred ---hhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 123467888889998877666899985
No 34
>PRK07252 hypothetical protein; Provisional
Probab=98.49 E-value=3.2e-07 Score=78.42 Aligned_cols=80 Identities=18% Similarity=0.254 Sum_probs=64.2
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP 250 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg 250 (343)
++|+++.|+|++|.++|+||+++.+.+|++|++++++.. +. . +
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~-----------------------~~---~-----~------ 44 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF-----------------------ID---N-----I------ 44 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc-----------------------cc---C-----h------
Confidence 579999999999999999999988899999999997421 00 0 0
Q ss_pred CCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHH
Q 019315 251 GRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWH 288 (343)
Q Consensus 251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe 288 (343)
.....+|+.+.+.|+..+ +.+++.||.+++....+|.
T Consensus 45 -~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~~~ 82 (120)
T PRK07252 45 -HQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQHF 82 (120)
T ss_pred -hhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence 123467888888998876 5799999999998877775
No 35
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.48 E-value=3e-07 Score=100.47 Aligned_cols=94 Identities=18% Similarity=0.082 Sum_probs=74.0
Q ss_pred hhcccCCCCCCCEEE-EEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcc
Q 019315 163 VSVEYYEPKPGDFVI-GVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA 241 (343)
Q Consensus 163 Le~~~~~~k~GdiVe-G~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dga 241 (343)
++..+..++.|++++ |+|++|.++|+||+|..+.+|+||++|+++.+. .+
T Consensus 744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv-----------------------~~------ 794 (891)
T PLN00207 744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWL-----------------------AK------ 794 (891)
T ss_pred HHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccc-----------------------cC------
Confidence 344445688999995 699999999999999888999999999985320 00
Q ss_pred eeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhh
Q 019315 242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ 295 (343)
Q Consensus 242 V~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e 295 (343)
+ ..++++|+.+.++|++.+..|+|.||+|++. .+||++.....+
T Consensus 795 --~-------~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~-~~Pw~~~~~~~~ 838 (891)
T PLN00207 795 --P-------EDAFKVGDRIDVKLIEVNDKGQLRLSRRALL-PEANSEKSSQKQ 838 (891)
T ss_pred --H-------HHhcCCCCEEEEEEEEECCCCcEEEEEeccc-cCchhhhhhhhh
Confidence 0 1235778889999998887899999999986 589998876543
No 36
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.47 E-value=2.9e-07 Score=69.44 Aligned_cols=45 Identities=44% Similarity=0.635 Sum_probs=39.0
Q ss_pred CCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC-CCChhhhccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFTELKEK 341 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r-v~nleel~g~ 341 (343)
|++|+|+|++++++|++|+++|++||||.||++.+ .+++.+++|+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~~~~~~~~~vG~ 46 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGK 46 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHHhCCC
Confidence 68999999999999999999999999999999865 5566666554
No 37
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.47 E-value=9.4e-07 Score=67.35 Aligned_cols=72 Identities=24% Similarity=0.284 Sum_probs=56.3
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
+++|++|.|+|.++.+++++|+++.+.+|++|.+++++.+.. . .
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~--------------------------~-----~----- 44 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE--------------------------A-----L----- 44 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccc--------------------------c-----c-----
Confidence 368999999999999999999999899999999999743100 0 0
Q ss_pred CCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315 250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
.....+|+.+.+.|+..+ .++++.||+|
T Consensus 45 --~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 45 --PYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred --ccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 123467888889998765 4688999863
No 38
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.46 E-value=5.3e-07 Score=68.07 Aligned_cols=71 Identities=18% Similarity=0.184 Sum_probs=55.4
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|.|+|+++.+++++|+++.+.+|++|.+++++.+.. + + .
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~--------------------------~-----~-------~ 42 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--------------------------D-----A-------T 42 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcccc--------------------------C-----H-------H
Confidence 799999999999999999999899999999999843100 0 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEeHHHH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLSTRRL 281 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl 281 (343)
....+|+.+.+.|+..+ .++++.||+|++
T Consensus 43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 43 ERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred HccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 22467788888888766 458899998764
No 39
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.43 E-value=1.1e-06 Score=67.09 Aligned_cols=73 Identities=23% Similarity=0.271 Sum_probs=55.3
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
++.|+++.|+|+++.++|+||++.. +.+|++|.+|+++.+.. . +
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~--------------------------~-----~--- 46 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR--------------------------S-----I--- 46 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC--------------------------C-----H---
Confidence 4689999999999999999999963 48999999999743100 0 0
Q ss_pred CCCCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR 280 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr 280 (343)
.....+|+.+.+.|+..+ ..+++.||+|+
T Consensus 47 ----~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 47 ----RKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred ----HHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 122366778888888765 56889999764
No 40
>PRK05807 hypothetical protein; Provisional
Probab=98.42 E-value=1.1e-06 Score=76.56 Aligned_cols=75 Identities=21% Similarity=0.213 Sum_probs=59.7
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
++++|++|+|+|+.|+++|+||++ .+.+|+||++|+++.+ +.. +
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~-----------------------v~~--------~---- 45 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTY-----------------------VKD--------I---- 45 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhccccc-----------------------ccC--------c----
Confidence 367899999999999999999999 4679999999997431 110 0
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~ 282 (343)
.....+|+.+.+.|+..+.+|+|.||+|++.
T Consensus 46 ---~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 46 ---REHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred ---cccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 1224678888899988777899999998876
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=98.41 E-value=1.4e-06 Score=66.00 Aligned_cols=68 Identities=16% Similarity=0.152 Sum_probs=53.2
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++++|+|+++.++|++|+++.+.+|++|++++++.+... . .
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~-------------------------------~-------~ 42 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKH-------------------------------P-------E 42 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccC-------------------------------H-------H
Confidence 7999999999999999999988899999999997431000 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEeH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLST 278 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~ 278 (343)
....+|+.+.+.|+..+ +++++.||+
T Consensus 43 ~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 43 KKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred HcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 12467788888998876 568898883
No 42
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.39 E-value=1.8e-06 Score=65.14 Aligned_cols=66 Identities=20% Similarity=0.160 Sum_probs=50.9
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|+|+|+++.++|++|++ .+.+||||.+++++.... + .
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~-------~------------------------~-------- 40 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVE-------D------------------------L-------- 40 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccC-------C------------------------h--------
Confidence 79999999999999999999 579999999999743100 0 0
Q ss_pred CceeccceEEEEEEeec-CCCceEEeHH
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
...+|+.+.+.|+..+ +++++.||+|
T Consensus 41 -~~~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 41 -DEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred -HHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 0125677788888766 5789999974
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.35 E-value=1.8e-06 Score=65.16 Aligned_cols=67 Identities=22% Similarity=0.292 Sum_probs=52.0
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|.|+|+++.++|+||+++.+.+|++|++++++.+.+ . . .
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~--------------------------~-----~-------~ 42 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK--------------------------D-----W-------K 42 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc--------------------------C-----H-------h
Confidence 799999999999999999999889999999999743100 0 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEe
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS 277 (343)
....+|+.+.+.|+..+ +.+++.||
T Consensus 43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 43 KRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred hccCCCCEEEEEEEEEeCCCCEEecC
Confidence 22366788888888765 46888886
No 44
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.35 E-value=1.5e-06 Score=83.42 Aligned_cols=87 Identities=20% Similarity=0.252 Sum_probs=66.5
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
-+++|++|.|+|++|.++|+||++.. +.+|+||++|+++.. +.. +
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~-----------------------i~~--------i-- 51 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGW-----------------------VKN--------I-- 51 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCccc-----------------------ccC--------H--
Confidence 36789999999999999999999964 699999999997431 000 1
Q ss_pred CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHH
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQI 293 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa 293 (343)
.....+|+.+.+.|+..+ ..++|.||+|++.....|+.+.+.
T Consensus 52 -----~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~e~~~~~~~~ 94 (262)
T PRK03987 52 -----RDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEHQRREKIQEW 94 (262)
T ss_pred -----HHhCCCCCEEEEEEEEEecccCeEEEEEEecccchHHHHHHHH
Confidence 123467888889998876 568999999987766666655543
No 45
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.31 E-value=3.4e-06 Score=62.12 Aligned_cols=69 Identities=25% Similarity=0.288 Sum_probs=52.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|+++.|+|+++.++|+||+++.+.+|++|.+|+++.+.. + . .
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~-------~------------------------~-------~ 42 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK-------D------------------------V-------K 42 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccC-------C------------------------H-------H
Confidence 799999999999999999999889999999999742100 0 0 0
Q ss_pred CceeccceEEEEEEeecCCCceEEeHH
Q 019315 253 PVVETGTVLFAEVLGRTLSGRPLLSTR 279 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~de~G~I~LS~K 279 (343)
....+|+.+.+.++..+.++++.||.|
T Consensus 43 ~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 43 DVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred HccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 123567777788877655788999864
No 46
>PRK08059 general stress protein 13; Validated
Probab=98.31 E-value=2e-06 Score=73.36 Aligned_cols=78 Identities=19% Similarity=0.187 Sum_probs=61.1
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
.++++|++|.|+|+++.+.|++|+++.+.+|++|.+++++.. +. + +
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~-----------------------~~---~-----~--- 48 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGF-----------------------VK---D-----I--- 48 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccc-----------------------cc---C-----H---
Confidence 358899999999999999999999999999999999997421 00 0 0
Q ss_pred CCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR 283 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~ 283 (343)
.....+|+.+.+.|+..+ +++++.||++++..
T Consensus 49 ----~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 49 ----HDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred ----HHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 112466788888888764 67899999888763
No 47
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.28 E-value=4.4e-06 Score=64.42 Aligned_cols=68 Identities=19% Similarity=0.105 Sum_probs=52.9
Q ss_pred CCEEE-EEEEEE-eCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315 173 GDFVI-GVVVSG-NENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP 250 (343)
Q Consensus 173 GdiVe-G~VVsI-~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg 250 (343)
|++++ |+|+++ .++|+||++..+.+|+||.+++++.+. ..
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~-----------------------~~--------------- 42 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKV-----------------------PS--------------- 42 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchh-----------------------cC---------------
Confidence 78999 999999 699999999878999999999974210 00
Q ss_pred CCCceeccceEEEEEEeec-CCCceEEeH
Q 019315 251 GRPVVETGTVLFAEVLGRT-LSGRPLLST 278 (343)
Q Consensus 251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~ 278 (343)
......+|+.+.+.|+..+ .++++.||.
T Consensus 43 ~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 43 DTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred cccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 0123477888999999875 678999983
No 48
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.27 E-value=4e-06 Score=63.74 Aligned_cols=72 Identities=18% Similarity=0.165 Sum_probs=55.3
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 171 KPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
++|++++|+|++++++|+||++.. +.+|++|.+++++.+.. + .
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~-------~------------------------~----- 44 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA-------D------------------------A----- 44 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC-------C------------------------H-----
Confidence 469999999999999999999974 79999999999743100 0 0
Q ss_pred CCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315 250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR 280 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr 280 (343)
.....+|+.+.+.|+..+ +.+++.||+|+
T Consensus 45 --~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 45 --SKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred --hHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence 123467788888888765 57899999765
No 49
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.25 E-value=6.2e-06 Score=60.24 Aligned_cols=71 Identities=25% Similarity=0.271 Sum_probs=54.0
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP 250 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg 250 (343)
++|++++|+|+++++++++|+++.+..|++|.+++.+....+ .
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~-------------------------------~------ 43 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKD-------------------------------P------ 43 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCC-------------------------------H------
Confidence 369999999999999999999998899999999997431000 0
Q ss_pred CCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315 251 GRPVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
.....+|+.+.+.|+..+ .++++.||.+
T Consensus 44 -~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 44 -EEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred -HHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 112466777888888765 4488998863
No 50
>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=98.22 E-value=7.7e-06 Score=62.29 Aligned_cols=65 Identities=20% Similarity=0.086 Sum_probs=51.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|++|+|+|+++.++|++|++....+|++|.++++.... . .
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~---------------------------~-------------~ 40 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS---------------------------S-------------K 40 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC---------------------------c-------------c
Confidence 89999999999999999999667999999999863200 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEe
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS 277 (343)
....+|+++.+.|+..+ ++++|.||
T Consensus 41 ~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 41 STYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred cCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 23467788889998765 56788887
No 51
>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=98.17 E-value=9.8e-06 Score=65.51 Aligned_cols=40 Identities=25% Similarity=0.344 Sum_probs=36.8
Q ss_pred CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~ 207 (343)
.+++.|+++.|+|++|.+. |+||+++.+.+||||++|+++
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~ 44 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILP 44 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCc
Confidence 4578999999999999996 999999988999999999975
No 52
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.13 E-value=8.7e-06 Score=87.56 Aligned_cols=75 Identities=17% Similarity=0.135 Sum_probs=58.5
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS 248 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i 248 (343)
.++.|++++|+|++|.++|+||+|+.+.+|++|++|+++.. | ..+|..
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls-----~--------------~~rv~~------------- 691 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLA-----G--------------GKRVEN------------- 691 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccc-----c--------------ccCcCC-------------
Confidence 47899999999999999999999988899999999996210 0 001111
Q ss_pred CCCCCceeccceEEEEEEeecCCCceEEe
Q 019315 249 GPGRPVVETGTVLFAEVLGRTLSGRPLLS 277 (343)
Q Consensus 249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS 277 (343)
...++++|+++.++|++++++|++.||
T Consensus 692 --~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 692 --VEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred --HHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 123457889999999998888999986
No 53
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.11 E-value=1.4e-05 Score=59.90 Aligned_cols=68 Identities=18% Similarity=0.146 Sum_probs=51.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|+++.|+|+++.++|+||++..+.+|++|.+++++.. .. .. . .
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~--~~-----------------------~~-----~-------~ 43 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQ--RV-----------------------RH-----P-------S 43 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCcc--cc-----------------------CC-----h-------h
Confidence 7899999999999999999988999999999997320 00 00 0 1
Q ss_pred CceeccceEEEEEEeec-CCCceEEe
Q 019315 253 PVVETGTVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~d-e~G~I~LS 277 (343)
....+|+.+.+.|+..+ +.+++.||
T Consensus 44 ~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 44 EIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred hEECCCCEEEEEEEEEECCcCEEeCC
Confidence 23467788888888765 55778775
No 54
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.11 E-value=1.7e-05 Score=58.61 Aligned_cols=67 Identities=25% Similarity=0.166 Sum_probs=50.6
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCC
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG 251 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~ 251 (343)
+|++++|+|+++++++++|+++ ..+|++|.+|+++.+.. . .
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~--------------------------~-----~------- 41 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVK--------------------------H-----P------- 41 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCcccc--------------------------C-----H-------
Confidence 4899999999999999999998 69999999999732100 0 0
Q ss_pred CCceeccceEEEEEEeec-CCCceEEe
Q 019315 252 RPVVETGTVLFAEVLGRT-LSGRPLLS 277 (343)
Q Consensus 252 i~v~eiGd~v~~eVl~~d-e~G~I~LS 277 (343)
....++|+.+.+.++..+ .++++.||
T Consensus 42 ~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 42 SEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred hHEECCCCEEEEEEEEEECCCCEEecC
Confidence 122467778888888765 56788876
No 55
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.10 E-value=1.1e-05 Score=62.78 Aligned_cols=72 Identities=19% Similarity=0.116 Sum_probs=55.7
Q ss_pred CCEEEEEEEEEeCCeEEEEeC---CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVG---ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG---~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
|++++|+|+++.++|+||+++ .+.+|++|.+++.+.. . +.. .
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~-----------------------~--~~~-----~----- 45 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEG-----------------------R--VAN-----P----- 45 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCC-----------------------C--cCC-----h-----
Confidence 789999999999999999997 3689999999997431 0 000 0
Q ss_pred CCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315 250 PGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~ 282 (343)
.....+|+.+.+.++..+ .+++.||+|+++
T Consensus 46 --~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~ 75 (79)
T cd05684 46 --SDVVKRGQKVKVKVISIQ-NGKISLSMKDVD 75 (79)
T ss_pred --hheeCCCCEEEEEEEEEe-CCEEEEEEEecc
Confidence 123467788888888877 899999988765
No 56
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.08 E-value=2.1e-05 Score=58.29 Aligned_cols=68 Identities=21% Similarity=0.138 Sum_probs=52.3
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR 252 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i 252 (343)
|+++.|+|+++.++|+||+++.+.+|++|.+++.+.. +.. . .
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~-----------------------~~~--------~-------~ 42 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDER-----------------------VEK--------V-------E 42 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcc-----------------------ccC--------H-------H
Confidence 7899999999999999999998899999999997421 000 0 0
Q ss_pred CceeccceEEEEEEeecCCCceEEeH
Q 019315 253 PVVETGTVLFAEVLGRTLSGRPLLST 278 (343)
Q Consensus 253 ~v~eiGd~v~~eVl~~de~G~I~LS~ 278 (343)
....+|+.+.+.|+..+.++++.||+
T Consensus 43 ~~~~~Gd~v~v~v~~~d~~~~i~ls~ 68 (68)
T cd04472 43 DVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred HccCCCCEEEEEEEEECCCCcEEeeC
Confidence 12366777888888766678898884
No 57
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.07 E-value=1.8e-05 Score=58.21 Aligned_cols=35 Identities=20% Similarity=0.228 Sum_probs=33.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
|+++.|+|+++.++|+||+++.+.+|++|.+++.+
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~ 35 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMAD 35 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCC
Confidence 78999999999999999999999999999999973
No 58
>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=98.05 E-value=1e-05 Score=66.98 Aligned_cols=92 Identities=15% Similarity=0.121 Sum_probs=59.8
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG 249 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie 249 (343)
+++|++|.|+|.+|.+.+++|++..+.+|++|++|+++.+..... ..+.+. ++ ++. + . ...
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~---~~~~~~--~~---~~~-----~-~-----~~~ 61 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLE---ELDEES--EE---EDD-----E-E-----ELP 61 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHH---Hhhhhc--cc---ccc-----c-c-----ccC
Confidence 468999999999999999999998899999999999843100000 000000 00 000 0 0 000
Q ss_pred CCCCceeccceEEEEEEeecC----CCceEEeHHH
Q 019315 250 PGRPVVETGTVLFAEVLGRTL----SGRPLLSTRR 280 (343)
Q Consensus 250 g~i~v~eiGd~v~~eVl~~de----~G~I~LS~Kr 280 (343)
.....+.+|+.+.+.|+..+. +++|.||+|-
T Consensus 62 ~~~~~f~vGd~V~~kVi~~d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 62 DLEDLFSVGQLVRCKVVSLDKSKSGKKRIELSLEP 96 (100)
T ss_pred CHHHhccCCCEEEEEEEEccCCcCCCcEEEEEecH
Confidence 112345788899999997654 5799999864
No 59
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.03 E-value=1e-05 Score=77.74 Aligned_cols=87 Identities=23% Similarity=0.315 Sum_probs=64.3
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
-++.|++|-|+|.+|.+.|+||.+ .| +.+||||++|++. |.|.+|+
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas-----------------------~wVknIr--------- 55 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVAS-----------------------GWVKNIR--------- 55 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHH-----------------------HHHHHHH---------
Confidence 367899999999999999999999 33 4899999999972 3333332
Q ss_pred CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHH------HHHHHHHHHH
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR------KMAWHRVRQI 293 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~------~~aWe~l~qa 293 (343)
..++.|..+.++||..| +.|.|-||+||... ...|.+-..+
T Consensus 56 ------d~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~q~~~k~~~wk~~qka 103 (269)
T COG1093 56 ------DYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEHQRRKKIQEWKKEQKA 103 (269)
T ss_pred ------HHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHHHHHHHHHHHHHHHHH
Confidence 23456677888999865 66999999988542 2346555444
No 60
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.01 E-value=4.6e-05 Score=57.87 Aligned_cols=38 Identities=16% Similarity=0.065 Sum_probs=35.1
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
+.+|++++|+|++|.+.|+||.+....+|++|.+++.+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~ 38 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW 38 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC
Confidence 46899999999999999999999888999999999963
No 61
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.94 E-value=2.9e-05 Score=83.44 Aligned_cols=76 Identities=22% Similarity=0.193 Sum_probs=61.7
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
..+++|++++|+|++|.++|+||+|+.+.+|++|++++++.+ +.. +
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~-----------------------v~~--------~--- 662 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADER-----------------------VEK--------V--- 662 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcc-----------------------ccC--------c---
Confidence 467899999999999999999999988899999999997431 100 0
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEEeHHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL 281 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl 281 (343)
..++++|+.+.++|+..+.+|++.||+|.+
T Consensus 663 ----~~v~kvGD~V~VkV~~iD~~grI~LS~k~~ 692 (693)
T PRK11824 663 ----EDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692 (693)
T ss_pred ----cceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 134578888999999887569999998764
No 62
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.92 E-value=3.5e-05 Score=72.63 Aligned_cols=79 Identities=23% Similarity=0.271 Sum_probs=59.8
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
|.+++||+|.|+|+++.+++++|||+...+|+||++++++.+. + .|.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~---~---~d~--------------------------- 105 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPV---N---VEG--------------------------- 105 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcc---c---cch---------------------------
Confidence 6678999999999999999999999989999999999985310 0 000
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr 280 (343)
.-..+.+++||.+.++|+..+.++.+.||.+.
T Consensus 106 -~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~ 137 (235)
T PRK04163 106 -TDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG 137 (235)
T ss_pred -hhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence 00123457788888888877666678888753
No 63
>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=97.89 E-value=0.00011 Score=57.37 Aligned_cols=39 Identities=15% Similarity=0.189 Sum_probs=36.1
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
..++.|++++|+|.++++.|+||++..+.+|++|.+|+.
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~ 50 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL 50 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc
Confidence 458899999999999999999999988899999999974
No 64
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.89 E-value=3.2e-05 Score=70.27 Aligned_cols=74 Identities=26% Similarity=0.218 Sum_probs=57.4
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGA----------DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV 236 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~----------KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i 236 (343)
.+.+++||+|.|+|++|.+++++|+|+. ..+|++|.+++++.... +
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~-------~----------------- 114 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE-------S----------------- 114 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh-------h-----------------
Confidence 3567899999999999999999999963 57899999999742100 0
Q ss_pred cCCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315 237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (343)
Q Consensus 237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr 280 (343)
..+.+.+||.+.+.|+..+ +++.||.|+
T Consensus 115 --------------~~~~~~~GD~V~akV~~i~--~~i~LS~k~ 142 (189)
T PRK09521 115 --------------LTDAFKIGDIVRAKVISYT--DPLQLSTKG 142 (189)
T ss_pred --------------HHhccCCCCEEEEEEEecC--CcEEEEEec
Confidence 0233577888999998776 789999864
No 65
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.88 E-value=2.7e-05 Score=80.44 Aligned_cols=74 Identities=20% Similarity=0.231 Sum_probs=56.6
Q ss_pred eccceEEEEEEeecCCCceEEeHHHHHHHHHHH-----HHHHHhh--CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315 256 ETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH-----RVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (343)
Q Consensus 256 eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe-----~l~qa~e--~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl 328 (343)
++|+.+.+.+...+ -|++.++..|......|. .+.+.|+ .|++|+|+|+++.++|++|+++|++||||+|++
T Consensus 88 ~vGD~ie~~I~~~~-fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ 166 (470)
T PRK09202 88 EVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQ 166 (470)
T ss_pred cCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEECCeEEEecHHHc
Confidence 55666666554333 566666665544344555 7777887 999999999999999999999999999999998
Q ss_pred cc
Q 019315 329 LS 330 (343)
Q Consensus 329 ~~ 330 (343)
..
T Consensus 167 ip 168 (470)
T PRK09202 167 IP 168 (470)
T ss_pred CC
Confidence 63
No 66
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=97.88 E-value=2.4e-05 Score=59.46 Aligned_cols=38 Identities=24% Similarity=0.388 Sum_probs=35.5
Q ss_pred hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
++.|++++|+|++++++|++|+++ |++||||.++++..
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~ 40 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD 40 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc
Confidence 578999999999999999999997 99999999999864
No 67
>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=97.79 E-value=0.00011 Score=56.05 Aligned_cols=35 Identities=29% Similarity=0.440 Sum_probs=33.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
|++|.|+|+++.+++++|+++.+.+|++|++|+++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~ 35 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD 35 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc
Confidence 89999999999999999999999999999999974
No 68
>PHA02945 interferon resistance protein; Provisional
Probab=97.77 E-value=7.9e-05 Score=61.08 Aligned_cols=74 Identities=15% Similarity=0.178 Sum_probs=55.8
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEecccc--CcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEV--LPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA 243 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEl--s~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~ 243 (343)
.-+.+|++|.|+|.. .++|+||++ .| +.+|+||++|+ +. |-+.+ +
T Consensus 7 ~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~-----------------------~wvK~-r------ 55 (88)
T PHA02945 7 SLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMN-----------------------RYFKY-R------ 55 (88)
T ss_pred cCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhcc-----------------------ceEee-e------
Confidence 346899999999999 999999999 55 69999999966 52 22222 1
Q ss_pred ccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315 244 MSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF 282 (343)
Q Consensus 244 Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~ 282 (343)
+.. .|.++.++|+..| ..|.|=||+|+..
T Consensus 56 ---------d~l-~GqkvV~KVirVd~~kg~IDlSlK~V~ 85 (88)
T PHA02945 56 ---------DKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC 85 (88)
T ss_pred ---------eEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence 223 4566778888765 6699999998764
No 69
>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=97.71 E-value=5e-05 Score=59.31 Aligned_cols=43 Identities=7% Similarity=0.059 Sum_probs=37.8
Q ss_pred hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle 336 (343)
++.|++|+|+|+++..+|++|++ .|++||+|.|+++.+ +.+++
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~ 45 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPS 45 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChh
Confidence 36799999999999999999999 589999999999876 45554
No 70
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.69 E-value=0.00014 Score=72.31 Aligned_cols=36 Identities=33% Similarity=0.511 Sum_probs=32.9
Q ss_pred CCCCEEEEEEEEEeCCe-EEEEeCCCeeEEEeccccCc
Q 019315 171 KPGDFVIGVVVSGNENK-LDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~g-v~VDIG~KsEG~IPisEls~ 207 (343)
+.|++|+|+|.++++++ ++||+| +.+|+||.+|..+
T Consensus 130 k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~ip 166 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQIP 166 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcCC
Confidence 58999999999999977 799997 8999999999874
No 71
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.68 E-value=0.00011 Score=76.00 Aligned_cols=39 Identities=28% Similarity=0.405 Sum_probs=34.9
Q ss_pred CCCC--CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPK--PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k--~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
..|+ .|++|+|+|.++++++++||+| +.+|+||.+|+.+
T Consensus 128 ~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~ip 168 (470)
T PRK09202 128 EEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQIP 168 (470)
T ss_pred HHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcCC
Confidence 3454 8999999999999999999996 7999999999974
No 72
>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=97.52 E-value=0.00078 Score=51.88 Aligned_cols=36 Identities=17% Similarity=0.111 Sum_probs=33.1
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCc
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLP 207 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~ 207 (343)
.|++++|+|+++.+.|+||+++. +.+|++|.+++.+
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~ 37 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGD 37 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCC
Confidence 38999999999999999999986 7999999999873
No 73
>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=97.48 E-value=0.00017 Score=54.45 Aligned_cols=35 Identities=9% Similarity=0.377 Sum_probs=32.3
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|++++|+|+++.+.|++|++ +|++||+|.|+++..
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~ 36 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV 36 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc
Confidence 68899999999999999999 589999999999754
No 74
>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=97.47 E-value=0.00036 Score=75.07 Aligned_cols=71 Identities=23% Similarity=0.170 Sum_probs=55.7
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
..+++|++++|+|++|.++|+||++..+.+|++|++|+++.+ +.. +
T Consensus 614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~-----------------------v~~--------~--- 659 (684)
T TIGR03591 614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANER-----------------------VEK--------V--- 659 (684)
T ss_pred cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCc-----------------------ccC--------h---
Confidence 457899999999999999999999988899999999997431 000 1
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEE
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLL 276 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~L 276 (343)
..++++|+.+.++|++.+..|++.|
T Consensus 660 ----~~~~kvGD~V~VkVi~id~~gki~L 684 (684)
T TIGR03591 660 ----EDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred ----hhccCCCCEEEEEEEEECCCCCccC
Confidence 1234778888999988776677654
No 75
>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=97.46 E-value=0.00018 Score=54.25 Aligned_cols=41 Identities=20% Similarity=0.353 Sum_probs=34.6
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee 337 (343)
|++++|+|+++.++|++|++ ++++||+|.|+++.. ..++.+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~ 43 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEE 43 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHH
Confidence 67899999999999999999 479999999999754 444443
No 76
>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=97.46 E-value=0.00052 Score=49.10 Aligned_cols=32 Identities=25% Similarity=0.192 Sum_probs=29.6
Q ss_pred EEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 176 VIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 176 VeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
+.|+|+++.+++++|+++.+.+|++|.+++.+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~ 32 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD 32 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCC
Confidence 57999999999999999988999999999874
No 77
>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=97.45 E-value=0.00018 Score=56.44 Aligned_cols=49 Identities=12% Similarity=0.142 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315 287 WHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 287 We~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle 336 (343)
|..+.+ ++.|+++.|+|+++.+.|++|++ +|++||+|.++++.+ ..++.
T Consensus 6 ~~~~~~-~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~ 56 (83)
T cd04461 6 PTNFSD-LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPS 56 (83)
T ss_pred hhhHHh-CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHH
Confidence 344433 67999999999999999999999 589999999999765 34443
No 78
>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=97.44 E-value=0.00018 Score=56.30 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=33.9
Q ss_pred hhCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS 330 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~ 330 (343)
++.|.+|.|+|+++...|++|+++ |++||||+++++.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~ 40 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN 40 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc
Confidence 357999999999999999999995 8999999999975
No 79
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.42 E-value=0.00018 Score=77.86 Aligned_cols=78 Identities=22% Similarity=0.204 Sum_probs=61.8
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
...+++|.+++|+|.++.++|+|||||-+.+|+||+++++... + .++
T Consensus 653 i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~f---v----~~P-------------------------- 699 (780)
T COG2183 653 ITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKF---V----KDP-------------------------- 699 (780)
T ss_pred HhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhh---c----CCh--------------------------
Confidence 3579999999999999999999999999999999999998320 0 000
Q ss_pred CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF 282 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~ 282 (343)
..++++|+.+.+.|++.+ ..++|.||.+.-+
T Consensus 700 -----~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 700 -----NEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred -----HHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 234577788888888765 6689999986644
No 80
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.41 E-value=0.00035 Score=70.16 Aligned_cols=36 Identities=31% Similarity=0.515 Sum_probs=33.5
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
+.|++|+|+|.++++++++||+|. .+|+||.+|..+
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip 168 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP 168 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC
Confidence 899999999999999999999975 999999999864
No 81
>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=97.36 E-value=0.00075 Score=55.05 Aligned_cols=77 Identities=21% Similarity=0.251 Sum_probs=56.6
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEe--------CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD 239 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDI--------G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~d 239 (343)
+-+++||+|.|+|+++....+.||| .....|++|.+++......+.
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~-------------------------- 55 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKV-------------------------- 55 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchH--------------------------
Confidence 3468999999999999999999999 878899999999874311000
Q ss_pred cceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315 240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR 280 (343)
Q Consensus 240 gaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr 280 (343)
.+ ...+.+||.+.++|+..++...+.||.+.
T Consensus 56 ---~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~ 86 (92)
T cd05791 56 ---EM-------YKCFRPGDIVRAKVISLGDASSYYLSTAE 86 (92)
T ss_pred ---HH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence 01 12346778888888876555668888643
No 82
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.32 E-value=0.00056 Score=68.14 Aligned_cols=74 Identities=23% Similarity=0.223 Sum_probs=56.7
Q ss_pred eccceEEEEEEeecCCCceEEeHHHH-----HHHHHHHHHHHHhh--CCCcEEEEEEEEecCe-eEEEECCeEEEEeCCc
Q 019315 256 ETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGG-LLTRIEGLRAFLPKAE 327 (343)
Q Consensus 256 eiGd~v~~eVl~~de~G~I~LS~Krl-----~~~~aWe~l~qa~e--~g~~VeGkVve~nKGG-liVeIeGlrgFIP~SQ 327 (343)
++|+.+...+.. .+-|++.++..+. .+...|+.+.+.|. .|++|+|+|.++.++| ++|+++|++||||.++
T Consensus 85 ~vGD~I~~~I~~-~~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E 163 (341)
T TIGR01953 85 QIGDEVKKEIPP-ENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKE 163 (341)
T ss_pred ccCCEEEEEecc-cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHH
Confidence 556666555432 3446666665554 34677899999885 9999999999999988 5999999999999999
Q ss_pred ccc
Q 019315 328 LLS 330 (343)
Q Consensus 328 l~~ 330 (343)
...
T Consensus 164 ~ip 166 (341)
T TIGR01953 164 QIP 166 (341)
T ss_pred cCC
Confidence 864
No 83
>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=97.30 E-value=0.0003 Score=53.51 Aligned_cols=34 Identities=9% Similarity=0.115 Sum_probs=31.4
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
|++|+|+|+++...|++|++ +|++||+|.||+..
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~ 35 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDP 35 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCC
Confidence 68899999999999999999 68999999999963
No 84
>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=97.30 E-value=0.00034 Score=54.31 Aligned_cols=34 Identities=9% Similarity=0.091 Sum_probs=31.8
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
|++|+|+|+++...|++|++ +|++||||.|+++.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~ 35 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSD 35 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCC
Confidence 68899999999999999999 58999999999974
No 85
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.00047 Score=73.71 Aligned_cols=79 Identities=18% Similarity=0.117 Sum_probs=64.7
Q ss_pred ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS 245 (343)
Q Consensus 166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig 245 (343)
....+++|++.+|+|++|.++|+||.+-.+.+|++|++++.... |.+ +
T Consensus 613 i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~r-----------------------v~k--------v- 660 (692)
T COG1185 613 ITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKER-----------------------VEK--------V- 660 (692)
T ss_pred HHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhh-----------------------hhc--------c-
Confidence 34679999999999999999999999988889999999997321 111 1
Q ss_pred CCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315 246 GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282 (343)
Q Consensus 246 ~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~ 282 (343)
-+++++|+.+.++++..++.|++.||++.+.
T Consensus 661 ------~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 661 ------EDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL 691 (692)
T ss_pred ------cceeecCceEEEEEeeecccCCccceehhcc
Confidence 2456788899999999999999999987653
No 86
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.27 E-value=0.0014 Score=62.61 Aligned_cols=78 Identities=22% Similarity=0.393 Sum_probs=62.6
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
.|.++.||+|-|+|+.+...+..||||++..+++|++++..+. ++ .
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~---~~-------------------------------~ 104 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRK---FE-------------------------------N 104 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccc---cc-------------------------------c
Confidence 5788999999999999999999999999999999999995321 00 0
Q ss_pred CCCCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLST 278 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~ 278 (343)
.-..+.+..++||-+.++|...+.++.+.|+.
T Consensus 105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~ 136 (239)
T COG1097 105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTL 136 (239)
T ss_pred cccccccccccCCEEEEEEEEccCCCceEEEe
Confidence 00122566788999999998888888888886
No 87
>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=97.26 E-value=0.00032 Score=53.36 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=32.8
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
.|++|+|+|++++++|++|++++++||||.+++..
T Consensus 3 ~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~ 37 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP 37 (67)
T ss_pred CCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC
Confidence 68999999999999999999988999999999963
No 88
>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=97.24 E-value=0.00072 Score=52.09 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=36.7
Q ss_pred hCCCcEEEEEEEEecCeeEEEECC--eEEEEeCCccccC-CCChhh
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIeG--lrgFIP~SQl~~r-v~nlee 337 (343)
+.|++++|+|+++.+.|++|+++| ++||+|.|++..+ +.++.+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~ 47 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSE 47 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhh
Confidence 469999999999999999999977 5999999999765 555444
No 89
>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=97.20 E-value=0.00067 Score=51.17 Aligned_cols=41 Identities=12% Similarity=0.217 Sum_probs=35.1
Q ss_pred CCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhh
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nlee 337 (343)
|++|+|+|+++...|++|++. +.+||||.+++... ..++.+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~ 43 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGED 43 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhH
Confidence 688999999999999999994 79999999999754 455544
No 90
>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=97.20 E-value=0.00059 Score=51.39 Aligned_cols=35 Identities=14% Similarity=0.239 Sum_probs=32.1
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|+++.|+|+++.+.|++|++ +++.||+|.|+++.+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~ 36 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDS 36 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCch
Confidence 67899999999999999999 589999999999754
No 91
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.20 E-value=0.0026 Score=51.90 Aligned_cols=39 Identities=28% Similarity=0.472 Sum_probs=36.0
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
|.+++||+|-|+|+.+..+...|||+....|++|..+|.
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ 40 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFE 40 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcc
Confidence 568899999999999999999999999999999997774
No 92
>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=97.14 E-value=0.00088 Score=50.38 Aligned_cols=40 Identities=30% Similarity=0.431 Sum_probs=34.3
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle 336 (343)
|++|.|+|+++...|++|++ ++++||+|.|+++.+ ..++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~ 42 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDAT 42 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHH
Confidence 67899999999999999999 689999999999764 44433
No 93
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=97.10 E-value=0.00066 Score=67.20 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=42.8
Q ss_pred HHhh-CCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCccccC-CCChhhhc
Q 019315 292 QIKQ-LNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELLSR-VNNFTELK 339 (343)
Q Consensus 292 qa~e-~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl~~r-v~nleel~ 339 (343)
+.|+ .|++|.|+|+++...|++|++ +|++||||.|+++++ ++++.+++
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v 64 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI 64 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc
Confidence 4676 699999999999999999999 489999999999986 78888764
No 94
>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=97.09 E-value=0.00067 Score=52.23 Aligned_cols=34 Identities=24% Similarity=0.356 Sum_probs=30.5
Q ss_pred CCcEE-EEEEEE-ecCeeEEEE-CCeEEEEeCCcccc
Q 019315 297 NEPIE-VKFTEW-NTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 297 g~~Ve-GkVve~-nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
|++++ |+|+++ .+.|++|++ +|++||||.||++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~ 37 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSD 37 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCc
Confidence 67888 999998 599999999 68999999999974
No 95
>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=97.08 E-value=0.0013 Score=50.02 Aligned_cols=37 Identities=11% Similarity=0.095 Sum_probs=33.9
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
+.|++++|+|+++...|++|+++ +++||+|.|++..+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~ 39 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD 39 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc
Confidence 47999999999999999999994 89999999999754
No 96
>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=97.04 E-value=0.001 Score=53.80 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=34.5
Q ss_pred HhhCCCcEEEEEEEEecC--eeEEEEC-CeEEEEeCCcccc
Q 019315 293 IKQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS 330 (343)
Q Consensus 293 a~e~g~~VeGkVve~nKG--GliVeIe-GlrgFIP~SQl~~ 330 (343)
.++.|+++.|+|+++.++ |++|+++ |.+||||.|++++
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~ 44 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILP 44 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCc
Confidence 356899999999999997 9999995 8999999999975
No 97
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=96.99 E-value=0.0017 Score=47.54 Aligned_cols=35 Identities=11% Similarity=0.262 Sum_probs=32.0
Q ss_pred CCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
|++++|+|+++.+.|++|+++ +++||||.+++..+
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~ 36 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK 36 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc
Confidence 678999999999999999995 89999999999754
No 98
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.98 E-value=0.0028 Score=72.21 Aligned_cols=134 Identities=16% Similarity=0.112 Sum_probs=88.5
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
...++.|++|.|.|..+.+.|+||-++++.+|++|++++.+...+ .|+. +
T Consensus 1157 ~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k--------~w~k---~------------------- 1206 (1710)
T KOG1070|consen 1157 IEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEK--------EWEK---H------------------- 1206 (1710)
T ss_pred hhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhh--------hhhc---c-------------------
Confidence 356889999999999999999999999999999999998743110 1110 0
Q ss_pred CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHH--HHHHHhhCCCcEEEEEEEEecCeeEEEEC-C--eE
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWH--RVRQIKQLNEPIEVKFTEWNTGGLLTRIE-G--LR 320 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe--~l~qa~e~g~~VeGkVve~nKGGliVeIe-G--lr 320 (343)
..+|..+...|+..+ ..+++.||.|.-+...+-. ........|+...|.|...-++|++++++ + +-
T Consensus 1207 --------~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~ 1278 (1710)
T KOG1070|consen 1207 --------LPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMV 1278 (1710)
T ss_pred --------CCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceec
Confidence 011111222333322 3356666665533211111 11123468999999999999999999995 3 58
Q ss_pred EEEeCCccccC-CCChhhh
Q 019315 321 AFLPKAELLSR-VNNFTEL 338 (343)
Q Consensus 321 gFIP~SQl~~r-v~nleel 338 (343)
|.+|.++.... ..+...+
T Consensus 1279 g~~~~~e~~d~~~e~it~~ 1297 (1710)
T KOG1070|consen 1279 GLCHISEEADDRGENITAL 1297 (1710)
T ss_pred ccccceeecchhhhhcccc
Confidence 99999998753 5555544
No 99
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.97 E-value=0.0012 Score=47.97 Aligned_cols=36 Identities=22% Similarity=0.417 Sum_probs=33.3
Q ss_pred CCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
.|++++|+|+++++.|++|+++ ++.||+|.+++..+
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~ 38 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK 38 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc
Confidence 5899999999999999999996 89999999999754
No 100
>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=96.97 E-value=0.0019 Score=49.08 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=36.1
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCCccccC-CCChhh
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~SQl~~r-v~nlee 337 (343)
+.|+.+.|+|+++.+.|++|++. |+.||||.|+++.+ ..++.+
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~ 48 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRK 48 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHH
Confidence 36899999999999999999994 59999999999865 444443
No 101
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.95 E-value=0.0045 Score=60.19 Aligned_cols=120 Identities=16% Similarity=0.092 Sum_probs=81.7
Q ss_pred CCCCCCCEEEEEEEEEe-CCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~-~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
....+|+---++|+.++ +-|||||.|-..+-++|.+|+... .+.|
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~---------~~~w------------------------- 114 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL---------KSLW------------------------- 114 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc---------cccC-------------------------
Confidence 34567999999999999 679999999999999999998632 0111
Q ss_pred CCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhh--CCCcEEEEEEEEecCeeEEEE-CCeEEEE
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRI-EGLRAFL 323 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e--~g~~VeGkVve~nKGGliVeI-eGlrgFI 323 (343)
.++|+...+.+ ..+..+||.-..+ ..+.-|.-...++. .++.|.|+|.+...-|.+|-+ ++..|||
T Consensus 115 --------pq~Gd~l~v~l-~~Dkk~Ri~g~~a--~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI 183 (287)
T COG2996 115 --------PQKGDKLLVYL-YVDKKGRIWGTLA--IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI 183 (287)
T ss_pred --------CCCCCEEEEEE-EEccCCcEEEEec--chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence 12334443333 3355566554321 11112222222333 489999999999999999988 5899999
Q ss_pred eCCccccCC
Q 019315 324 PKAELLSRV 332 (343)
Q Consensus 324 P~SQl~~rv 332 (343)
|.|+.-..+
T Consensus 184 h~sEr~~~p 192 (287)
T COG2996 184 HKSERFAEP 192 (287)
T ss_pred cchhhcccc
Confidence 999975443
No 102
>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=96.92 E-value=0.0014 Score=49.68 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=34.0
Q ss_pred hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
|+.|++++|+|+++.+.|++|++ +|+.||+|.+++.+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~ 38 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW 38 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC
Confidence 56899999999999999999999 58999999999974
No 103
>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=96.92 E-value=0.0014 Score=50.54 Aligned_cols=43 Identities=16% Similarity=0.067 Sum_probs=37.0
Q ss_pred hCCCcEEEEEEEEec-CeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315 295 QLNEPIEVKFTEWNT-GGLLTRI-EGLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 295 e~g~~VeGkVve~nK-GGliVeI-eGlrgFIP~SQl~~r-v~nlee 337 (343)
+.|+++.|+|+++.+ .|++|++ .|.+||+|.|+++.+ ..++.+
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~ 47 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLE 47 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHH
Confidence 479999999999986 8999999 599999999999875 566544
No 104
>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=96.83 E-value=0.0035 Score=50.97 Aligned_cols=90 Identities=18% Similarity=0.237 Sum_probs=57.5
Q ss_pred CEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCCC
Q 019315 174 DFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRP 253 (343)
Q Consensus 174 diVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i~ 253 (343)
+++.|+|+++.+.|+||+++ ..+|++|++++.+.+ +.+ +. ... .+ ++.. -..
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~---~~~---~~----------~~~-~~-------~~~~---~~~ 52 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDY---ISY---DP----------KNK-RL-------IGEE---TKR 52 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCc---eEe---ch----------hhe-ee-------cccC---cCC
Confidence 47999999999999999997 499999999997431 100 00 000 00 0000 012
Q ss_pred ceeccceEEEEEEeecC------CCceEEeHHHHHHHHHHHHHHH
Q 019315 254 VVETGTVLFAEVLGRTL------SGRPLLSTRRLFRKMAWHRVRQ 292 (343)
Q Consensus 254 v~eiGd~v~~eVl~~de------~G~I~LS~Krl~~~~aWe~l~q 292 (343)
+..+|+.+.+.|...+. .+++.||++.-.. -+|+-+++
T Consensus 53 ~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~~~-g~~~~~~~ 96 (99)
T cd04460 53 VLKVGDVVRARIVAVSLKERRPRESKIGLTMRQPGL-GKLEWIEE 96 (99)
T ss_pred EECCCCEEEEEEEEEeHHHCcCCCceEEEEEecCCC-CcHHHhhh
Confidence 34778888888876542 2689999988553 55554443
No 105
>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=96.80 E-value=0.0027 Score=46.71 Aligned_cols=36 Identities=11% Similarity=0.156 Sum_probs=32.8
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r 331 (343)
.|++++|+|+++.+.|++|+++++.||||.+++..+
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~ 36 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWG 36 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCc
Confidence 378999999999999999999889999999998743
No 106
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=96.75 E-value=0.0012 Score=57.51 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=40.6
Q ss_pred hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhhhc
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTELK 339 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel~ 339 (343)
++.|..++|+|+++.+.|++|+++ |-+|+++.|++... ++|+.++.
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L 50 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL 50 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh
Confidence 568999999999999999999995 79999999999876 77777663
No 107
>PRK08582 hypothetical protein; Provisional
Probab=96.70 E-value=0.0031 Score=55.27 Aligned_cols=38 Identities=16% Similarity=0.241 Sum_probs=34.8
Q ss_pred hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
++.|++|+|+|+++.+.|++|++ +++.||||.|++...
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~ 41 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN 41 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc
Confidence 56899999999999999999999 589999999999754
No 108
>PRK05807 hypothetical protein; Provisional
Probab=96.68 E-value=0.0037 Score=54.54 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=37.3
Q ss_pred hhCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC-CCChh
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFT 336 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r-v~nle 336 (343)
++.|++|+|+|+++.+.|++|+++|..||||.|++... +.+..
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~ 46 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIR 46 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCcc
Confidence 56799999999999999999999999999999999754 44433
No 109
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.65 E-value=0.0034 Score=49.09 Aligned_cols=37 Identities=16% Similarity=0.014 Sum_probs=33.9
Q ss_pred hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
+.|++|.|+|+++...|++|++ .+..||||.|++...
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~ 42 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK 42 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc
Confidence 5799999999999999999999 579999999999754
No 110
>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=96.62 E-value=0.0046 Score=47.04 Aligned_cols=35 Identities=9% Similarity=0.216 Sum_probs=32.1
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|++|.|+|+++...|++|++ .|++|++|.+++..+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~ 36 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDE 36 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccc
Confidence 68899999999999999999 599999999999754
No 111
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.59 E-value=0.012 Score=67.32 Aligned_cols=163 Identities=17% Similarity=0.116 Sum_probs=107.7
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc-cc-----------ccchhhhhhhhh--------------
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP-LY-----------DKEMDFLLCDLK-------------- 221 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~-~~-----------~ke~e~l~~d~~-------------- 221 (343)
.+|+.||.|+|-|..++.+.++|-|-.-..|.||+-.++. .+ ++-+..+.....
T Consensus 983 ~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~~~tv~~iG~~~~~ 1062 (1710)
T KOG1070|consen 983 KQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDKSKTVRAIGFSKSD 1062 (1710)
T ss_pred hhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCchhhcccccceeeEEecccceeEEEecccccCC
Confidence 5789999999999999999999999999999999998871 11 000000000000
Q ss_pred -hhhhHhhhcceeeeecCCcc-eeccCCCCC-CCCceecc--------------ceEEEEEEeec-CCCceEEeHH----
Q 019315 222 -KDAEEFMVRGKMGIVKDDDA-IAMSGGSGP-GRPVVETG--------------TVLFAEVLGRT-LSGRPLLSTR---- 279 (343)
Q Consensus 222 -k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg-~i~v~eiG--------------d~v~~eVl~~d-e~G~I~LS~K---- 279 (343)
...++...-|+|..+....+ +..+...-| ..-+.++. ..+...++..+ .++.+-||.|
T Consensus 1063 k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~ 1142 (1710)
T KOG1070|consen 1063 KNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRT 1142 (1710)
T ss_pred CCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEecccccceeecccccc
Confidence 00134566688888766553 444333322 11111111 12333445443 4445999998
Q ss_pred ---HHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 280 ---RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 280 ---rl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
.++....=-+..+.++.|+++.|.|..+.+.|+++.+ -++.||+|.|++..
T Consensus 1143 ~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~d 1197 (1710)
T KOG1070|consen 1143 KITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSD 1197 (1710)
T ss_pred cCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEcccccc
Confidence 5554444444567788999999999999999999998 58999999998864
No 112
>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=96.56 E-value=0.0053 Score=46.47 Aligned_cols=36 Identities=14% Similarity=0.269 Sum_probs=32.8
Q ss_pred CCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccccC
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSR 331 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~r 331 (343)
.|++++|+|+++.+.|++|++. ++.||+|.+++...
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~ 39 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN 39 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCC
Confidence 5899999999999999999996 69999999999754
No 113
>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=96.56 E-value=0.0035 Score=49.27 Aligned_cols=36 Identities=19% Similarity=0.165 Sum_probs=33.4
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS 330 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~ 330 (343)
+.|++|+|+|+++...|++|++. ++.||||.|++..
T Consensus 5 ~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~ 41 (86)
T cd05789 5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNL 41 (86)
T ss_pred CCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccC
Confidence 58999999999999999999994 8999999999974
No 114
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=96.48 E-value=0.0084 Score=65.10 Aligned_cols=72 Identities=14% Similarity=0.148 Sum_probs=52.6
Q ss_pred eecCCCceEEeHHHHH-HHHHHHHHHHH-----hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccc-----cCCCC
Q 019315 267 GRTLSGRPLLSTRRLF-RKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL-----SRVNN 334 (343)
Q Consensus 267 ~~de~G~I~LS~Krl~-~~~aWe~l~qa-----~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~-----~rv~n 334 (343)
.++++|.+.++-.... ..++-+.+... .+.|++++|+|+++..+|++|++ .|++||||.||++ .++.+
T Consensus 612 di~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~ 691 (719)
T TIGR02696 612 SIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN 691 (719)
T ss_pred EEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCC
Confidence 3457898887653222 22344444432 46999999999999999999999 5999999999995 24677
Q ss_pred hhhh
Q 019315 335 FTEL 338 (343)
Q Consensus 335 leel 338 (343)
+.++
T Consensus 692 ~~dv 695 (719)
T TIGR02696 692 VEDV 695 (719)
T ss_pred HHHc
Confidence 7764
No 115
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=96.36 E-value=0.023 Score=51.36 Aligned_cols=40 Identities=25% Similarity=0.313 Sum_probs=35.9
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcc
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPL 208 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~ 208 (343)
.++.+|++++|+|+++++.|+||++|. .+|+++.+++.+.
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~lg~-~~gi~~~~~l~~~ 116 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSLGP-FDGLFHVSQVTDD 116 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEeCC-ceEEEEcHHhCCC
Confidence 567789999999999999999999975 9999999999743
No 116
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.35 E-value=0.0084 Score=60.39 Aligned_cols=43 Identities=12% Similarity=0.095 Sum_probs=36.1
Q ss_pred HHHHHHHh--hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccc
Q 019315 287 WHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL 329 (343)
Q Consensus 287 We~l~qa~--e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~ 329 (343)
.+.+.+.| +.|++|+|+|+++.++|++|+++|++||||.+++.
T Consensus 123 re~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~i 167 (362)
T PRK12327 123 REIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQI 167 (362)
T ss_pred HHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcC
Confidence 44455555 79999999999999999999999999999966553
No 117
>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=96.30 E-value=0.0053 Score=45.81 Aligned_cols=34 Identities=9% Similarity=0.201 Sum_probs=31.4
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
|+++.|+|+++.+.|++|++ .|++||+|.|++.+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~ 35 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISW 35 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCC
Confidence 67899999999999999999 58999999999974
No 118
>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=96.25 E-value=0.0091 Score=47.44 Aligned_cols=35 Identities=26% Similarity=0.410 Sum_probs=32.1
Q ss_pred CCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~r 331 (343)
|..|+|+|.++.+.+++|+++ |++||||.-|++..
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~ 37 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH 37 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc
Confidence 578999999999999999993 89999999999764
No 119
>PRK08059 general stress protein 13; Validated
Probab=96.16 E-value=0.0093 Score=50.87 Aligned_cols=38 Identities=11% Similarity=0.157 Sum_probs=34.6
Q ss_pred hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
++.|+++.|+|+++.+.|++|+++ +++||+|.|+++.+
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~ 43 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG 43 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc
Confidence 678999999999999999999994 89999999999654
No 120
>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=96.10 E-value=0.0097 Score=43.50 Aligned_cols=35 Identities=14% Similarity=0.113 Sum_probs=31.4
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|+.+.|+|+++...|++|++ .++.||+|.+++...
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~ 36 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR 36 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc
Confidence 57899999999999999999 479999999999653
No 121
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=96.07 E-value=0.019 Score=48.56 Aligned_cols=50 Identities=14% Similarity=0.132 Sum_probs=41.6
Q ss_pred hhHHHHhhccc---CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 157 KVGEDKVSVEY---YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 157 ~dFa~lLe~~~---~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
+.|+.||..+- -.-..|.+|.|+|..|.++.+|||+|.|..++++..+..
T Consensus 5 ~sFaslLR~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~ 57 (104)
T PF10246_consen 5 ESFASLLRNSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN 57 (104)
T ss_pred ccHHHHhcCChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc
Confidence 78999996542 112369999999999999999999999999999987653
No 122
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=96.01 E-value=0.045 Score=59.15 Aligned_cols=85 Identities=18% Similarity=0.173 Sum_probs=56.7
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS 245 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig 245 (343)
+.+.+.|++++|+|++|+++|+||.+.. ..+|++|++++.... +. .|. .+.. + .+
T Consensus 622 yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~---~~---~d~---------~~~~--------l-~g 677 (709)
T TIGR02063 622 YMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY---YV---FDE---------KGLA--------L-VG 677 (709)
T ss_pred hhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc---EE---Ecc---------cceE--------E-Ee
Confidence 3455789999999999999999999965 799999999997321 10 010 0000 0 01
Q ss_pred CCCCCCCCceeccceEEEEEEeec-CCCceEEeH
Q 019315 246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLST 278 (343)
Q Consensus 246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~ 278 (343)
.. ......+|+.+.++|...+ ..++|.++.
T Consensus 678 ~~---~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l 708 (709)
T TIGR02063 678 ER---TGKVFRLGDRVKVRVVKADLDTGKIDFEL 708 (709)
T ss_pred cc---CCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence 00 0134577888888888766 568888773
No 123
>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=95.97 E-value=0.012 Score=45.55 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=32.0
Q ss_pred CCcEEEEEEEEecCeeEEEEC----CeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe----GlrgFIP~SQl~~r 331 (343)
|++++|+|+++..+|++|+++ |+.||+|.|++..+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~ 39 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE 39 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC
Confidence 578999999999999999997 68999999999765
No 124
>PRK07252 hypothetical protein; Provisional
Probab=95.96 E-value=0.013 Score=50.21 Aligned_cols=37 Identities=11% Similarity=0.263 Sum_probs=33.4
Q ss_pred hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
+.|+++.|+|+++...|++|++ .++.||+|.|++...
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~ 39 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTG 39 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCc
Confidence 3689999999999999999999 579999999999754
No 125
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.94 E-value=0.018 Score=58.35 Aligned_cols=39 Identities=21% Similarity=0.398 Sum_probs=34.2
Q ss_pred CCCCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~-~gv~VDIG~KsEG~IPisEls~ 207 (343)
|.-+.|++|+|+|.+++. +.++||+| +++|+||.+|..+
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip 173 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIK 173 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCC
Confidence 456789999999999996 56999998 7999999999874
No 126
>PHA02945 interferon resistance protein; Provisional
Probab=95.88 E-value=0.012 Score=48.52 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=35.5
Q ss_pred hCCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCcc--ccC-CCChhhh
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL--LSR-VNNFTEL 338 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl--~~r-v~nleel 338 (343)
+.|+.|-|+|++ ...|++|.+ +|++||||.|++ +.+ ++| .++
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~ 57 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDK 57 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeE
Confidence 589999999999 999999988 499999999966 766 666 443
No 127
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.81 E-value=0.0046 Score=59.99 Aligned_cols=90 Identities=19% Similarity=0.117 Sum_probs=61.0
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG 246 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~ 246 (343)
-++.+++|-+.|.+|.+-|+||.+ .| ..||+|.++|++.++ +. .+.
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRR---IR----SI~------------------------- 60 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRR---IR----SIQ------------------------- 60 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHH---HH----HHH-------------------------
Confidence 467899999999999999999999 33 499999999999542 00 000
Q ss_pred CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCC
Q 019315 247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLN 297 (343)
Q Consensus 247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g 297 (343)
.+..+|-...+.|+..+ +.|+|-||+||... ..-.+.++.|++.
T Consensus 61 ------klirVGr~E~vvVlrVDkekGYIDLSkrrVs~-ed~~kC~Er~~ks 105 (304)
T KOG2916|consen 61 ------KLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP-EDKEKCEERFAKS 105 (304)
T ss_pred ------HHHhcCCcceEEEEEEcCCCCceechhccCCH-HHHHHHHHHHHHh
Confidence 01123333345566544 77999999999774 4444555555443
No 128
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=95.80 E-value=0.017 Score=44.44 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=31.4
Q ss_pred CCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS 330 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~ 330 (343)
|++++|+|+++++.|++|+++ |++||+|.|++..
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~ 37 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGD 37 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCC
Confidence 789999999999999999996 7999999999863
No 129
>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=95.75 E-value=0.018 Score=42.43 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=31.6
Q ss_pred CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315 297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR 331 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r 331 (343)
|+++.|+|+++.+.|++|++ .+..||+|.+++..+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~ 36 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDE 36 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCc
Confidence 57899999999999999999 479999999999764
No 130
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=95.69 E-value=0.0065 Score=55.28 Aligned_cols=47 Identities=9% Similarity=0.163 Sum_probs=40.6
Q ss_pred HHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-----------CeEEEEeCCccccC
Q 019315 285 MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-----------GLRAFLPKAELLSR 331 (343)
Q Consensus 285 ~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-----------GlrgFIP~SQl~~r 331 (343)
.||......++.|++|.|+|+++...|++|+|. ++.||||.|++...
T Consensus 53 ~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~ 110 (189)
T PRK09521 53 IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG 110 (189)
T ss_pred ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh
Confidence 478876667789999999999999999999984 57899999999754
No 131
>PRK11642 exoribonuclease R; Provisional
Probab=95.65 E-value=0.048 Score=60.17 Aligned_cols=86 Identities=12% Similarity=0.024 Sum_probs=57.2
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGAD-LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS 245 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~K-sEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig 245 (343)
+.+-+.|++++|+|++|+++|+||.+... .+|+||++++.+. |+..|.. ... + ++
T Consensus 638 ~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d------~y~~d~~----~~~-------------L-~g 693 (813)
T PRK11642 638 FMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDND------YYRFDQV----GQR-------------L-IG 693 (813)
T ss_pred hhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCc------ceEecch----heE-------------E-ec
Confidence 33447899999999999999999999654 9999999998632 1111110 000 0 11
Q ss_pred CCCCCCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315 246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTR 279 (343)
Q Consensus 246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K 279 (343)
.. -.....+|+.+.+.|+..+ ..++|.+++-
T Consensus 694 ~~---~~~~~~lGD~V~VkV~~vD~~~rkI~f~l~ 725 (813)
T PRK11642 694 ES---SGQTYRLGDRVEVRVEAVNMDERKIDFSLI 725 (813)
T ss_pred cc---CCcEECCCCEEEEEEEEeecCCCeEEEEEe
Confidence 00 0134577888888887654 5688888874
No 132
>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=95.63 E-value=0.043 Score=43.64 Aligned_cols=35 Identities=20% Similarity=0.223 Sum_probs=32.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCc
Q 019315 173 GDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLP 207 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~ 207 (343)
|++|+|+|+..+++++.|+++. ...|++|...+++
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD 36 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD 36 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC
Confidence 7899999999999999999955 8999999999985
No 133
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=95.62 E-value=0.027 Score=46.17 Aligned_cols=39 Identities=15% Similarity=0.089 Sum_probs=34.6
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEe-ccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTML-TKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IP-isEls~ 207 (343)
--+++||++. .|+.+.+.++||.+ +|+.||+|. .+|++.
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr 52 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNA 52 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhH
Confidence 3467899999 88899999999998 888999999 999973
No 134
>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=95.57 E-value=0.038 Score=59.77 Aligned_cols=70 Identities=11% Similarity=0.109 Sum_probs=49.3
Q ss_pred ecCCCceEEeH---HHHHHHHH-HHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315 268 RTLSGRPLLST---RRLFRKMA-WHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 268 ~de~G~I~LS~---Krl~~~~a-We~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee 337 (343)
++++|.+.++. ..++.... .+.+....+.|++++|+|+++...|++|++ .|++||||.|+++.+ +.+..+
T Consensus 586 i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~ 661 (684)
T TIGR03591 586 IEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVED 661 (684)
T ss_pred EecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhh
Confidence 35578777753 22222111 122233357899999999999999999999 689999999999765 555554
No 135
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=95.48 E-value=0.13 Score=46.52 Aligned_cols=39 Identities=23% Similarity=0.337 Sum_probs=35.5
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
.++.+|+++.|+|+++++.|++|++|. .+|+++.+++.+
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~ 115 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMD 115 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCC
Confidence 467789999999999999999999984 899999999864
No 136
>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=95.48 E-value=0.028 Score=43.82 Aligned_cols=38 Identities=13% Similarity=0.229 Sum_probs=34.0
Q ss_pred HhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315 293 IKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS 330 (343)
Q Consensus 293 a~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~ 330 (343)
.++.|+.++|+|+++.+.|++|+++ ++.||+|.|++..
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~~ 51 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR 51 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccC
Confidence 3668999999999999999999994 6999999998753
No 137
>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=95.45 E-value=0.017 Score=41.11 Aligned_cols=32 Identities=19% Similarity=0.352 Sum_probs=28.8
Q ss_pred EEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 300 VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
++|+|+++.+.|++|+++ |++||+|.+++..+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~ 33 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK 33 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc
Confidence 479999999999999995 89999999999754
No 138
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.43 E-value=0.051 Score=58.91 Aligned_cols=70 Identities=16% Similarity=0.129 Sum_probs=49.6
Q ss_pred ecCCCceEEeHHHHH-HHHHHHHHH---HHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315 268 RTLSGRPLLSTRRLF-RKMAWHRVR---QIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 268 ~de~G~I~LS~Krl~-~~~aWe~l~---qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee 337 (343)
.+++|.+.++..-.. ...+-+.+. ...+.|++++|+|+++.+.|++|++ .|.+||+|.|+++.+ +++..+
T Consensus 589 i~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~ 664 (693)
T PRK11824 589 IEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVED 664 (693)
T ss_pred cCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccc
Confidence 356788887653221 112222222 2357899999999999999999999 589999999999864 555444
No 139
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.39 E-value=0.05 Score=56.29 Aligned_cols=40 Identities=15% Similarity=0.281 Sum_probs=34.8
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEe----CC-CeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDI----G~-KsEG~IPisEls~ 207 (343)
+.-+.|++|+|+|.+++.+.++||+ |. +++|+||.+|..+
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip 192 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLP 192 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCC
Confidence 4556899999999999999999999 43 4999999999874
No 140
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=95.35 E-value=0.095 Score=39.61 Aligned_cols=35 Identities=23% Similarity=0.056 Sum_probs=22.1
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
.|++.+.+|+.+++.|+|++.|...+-+||.+|+.
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~ 35 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP 35 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC
Confidence 48999999999999999999988789999999974
No 141
>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=95.32 E-value=0.016 Score=47.93 Aligned_cols=36 Identities=14% Similarity=0.233 Sum_probs=33.3
Q ss_pred hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS 330 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~ 330 (343)
+.|++|.|+|+++...|++|.+ +|++||+|.+++..
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~ 38 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISD 38 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhH
Confidence 4799999999999999999999 58999999999974
No 142
>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=95.27 E-value=0.033 Score=45.15 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=32.4
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
.|++|+|+|+++++-|++|.++.+++|++.+|+..
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~ 35 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPS 35 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCc
Confidence 48999999999999999999988999999999953
No 143
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.24 E-value=0.043 Score=61.03 Aligned_cols=71 Identities=10% Similarity=0.096 Sum_probs=50.0
Q ss_pred ecCCCceEEeHHH-HHHHHHHHHHHHH---hhCCCcEE-EEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhhh
Q 019315 268 RTLSGRPLLSTRR-LFRKMAWHRVRQI---KQLNEPIE-VKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTEL 338 (343)
Q Consensus 268 ~de~G~I~LS~Kr-l~~~~aWe~l~qa---~e~g~~Ve-GkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nleel 338 (343)
++++|.+.+...- .....+-+.+.++ .+.|++++ |+|+++..+|++|++ .|++||||.|+++++ +.+.++.
T Consensus 721 i~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv 798 (891)
T PLN00207 721 TQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA 798 (891)
T ss_pred cCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHh
Confidence 3456666654322 2222344445554 36999995 699999999999999 599999999999875 6666553
No 144
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=94.68 E-value=0.22 Score=53.58 Aligned_cols=39 Identities=15% Similarity=0.072 Sum_probs=35.0
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCc
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLP 207 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~ 207 (343)
+-+.|+.++|+|+.|++.|+||.+. ...+|++|++++.+
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~ 608 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN 608 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCC
Confidence 3467999999999999999999996 77999999999863
No 145
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=94.59 E-value=0.032 Score=51.50 Aligned_cols=39 Identities=28% Similarity=0.381 Sum_probs=35.7
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~ 207 (343)
..+..|++|+|+|+++++.|+||.|| -.+|++|.+++.+
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~d 115 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMD 115 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEec-cccccccHhhccC
Confidence 56778999999999999999999999 5799999999974
No 146
>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=94.59 E-value=0.059 Score=43.77 Aligned_cols=33 Identities=21% Similarity=0.279 Sum_probs=30.3
Q ss_pred CcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 298 ~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
++++|+|+++++.|++|++.++.||+|.+++..
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~ 33 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMD 33 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccC
Confidence 468999999999999999988999999999864
No 147
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=94.53 E-value=0.05 Score=55.69 Aligned_cols=40 Identities=18% Similarity=0.198 Sum_probs=36.3
Q ss_pred CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~ 207 (343)
....+|++..|+|.++.+. +||||||.+..||+|++|+.+
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~ 62 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGP 62 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCc
Confidence 4456899999999999998 999999999999999999864
No 148
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.94 E-value=0.086 Score=56.11 Aligned_cols=78 Identities=15% Similarity=0.185 Sum_probs=61.6
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG 247 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ 247 (343)
..+..|-+-+++|.++.+.|+||.+-....|++|.+|++... +. ++
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~-----------------------ia--kp--------- 709 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEK-----------------------IA--KP--------- 709 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEecCCchhhccchhccccc-----------------------cc--Ch---------
Confidence 356678888999999999999999988999999999997321 00 01
Q ss_pred CCCCCCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315 248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR 283 (343)
Q Consensus 248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~ 283 (343)
..+.++|+++.+++++.|..|.+.||.|++..
T Consensus 710 ----sd~levGq~I~vk~ie~d~~g~~~ls~ralLp 741 (760)
T KOG1067|consen 710 ----SDLLEVGQEIQVKYIERDPRGGIMLSSRALLP 741 (760)
T ss_pred ----HHHHhhcceeEEEEEeecCccceeehhhhhcC
Confidence 12247788899999999888888998888775
No 149
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=93.74 E-value=0.057 Score=49.86 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=33.0
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
.|++|+|.|++.++.|++|.+.=+.||+|.||+..
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~d 115 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMD 115 (183)
T ss_pred cccEEEEEEEEEeecceEEEeccccccccHhhccC
Confidence 68999999999999999999977999999999964
No 150
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=93.43 E-value=0.1 Score=47.60 Aligned_cols=35 Identities=20% Similarity=0.383 Sum_probs=32.6
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
.|++|+|+|+++++.|++|.++=+++|+|.+||..
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~ 115 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPP 115 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCC
Confidence 69999999999999999999966899999999963
No 151
>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=93.11 E-value=0.2 Score=40.62 Aligned_cols=34 Identities=24% Similarity=0.203 Sum_probs=30.4
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
+|++|+|+|+++++.|+||.+| ..++|++...+-
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip 34 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIP 34 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecC
Confidence 5899999999999999999997 478999988774
No 152
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=91.58 E-value=0.28 Score=46.37 Aligned_cols=37 Identities=27% Similarity=0.430 Sum_probs=34.3
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR 331 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r 331 (343)
+.|++|.|+|+++...|+.|+++ ++.||||.|++..+
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~ 99 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGR 99 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCC
Confidence 68999999999999999999996 79999999999764
No 153
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=91.48 E-value=0.28 Score=44.68 Aligned_cols=38 Identities=13% Similarity=0.192 Sum_probs=34.3
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
.++-+|++|+|+|+++++.|++|++|. .+++||.+.+.
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~ 114 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIP 114 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCC
Confidence 567789999999999999999999985 56999999984
No 154
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=91.06 E-value=0.37 Score=43.57 Aligned_cols=36 Identities=22% Similarity=0.296 Sum_probs=33.2
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r 331 (343)
.|++++|+|+++++.|++|+++.+.||++.+++..+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~ 116 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDD 116 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCC
Confidence 699999999999999999999779999999998643
No 155
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=90.99 E-value=0.43 Score=45.38 Aligned_cols=87 Identities=20% Similarity=0.299 Sum_probs=58.2
Q ss_pred CCCCC--CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee-cCCcceec
Q 019315 168 YEPKP--GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV-KDDDAIAM 244 (343)
Q Consensus 168 ~~~k~--GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i-~~dgaV~I 244 (343)
++++. |++..|++.+..++|+.||++ +...-+|.+|+.+++. |.+..+ .-+|.|
T Consensus 68 ~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~--------------------g~~~Qi~~rFG~V-- 124 (225)
T PF09883_consen 68 YSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGP--------------------GSPRQIRRRFGLV-- 124 (225)
T ss_pred chhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCC--------------------CCHHHHHHHhCcc--
Confidence 44455 999999999999999999998 7788999999976642 111111 112221
Q ss_pred cCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHH
Q 019315 245 SGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR 289 (343)
Q Consensus 245 g~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~ 289 (343)
+- ..++..++..++....+||.++.++...|.+
T Consensus 125 --------~h----lPvev~~v~~~~~~~~rltd~q~d~l~~W~~ 157 (225)
T PF09883_consen 125 --------QH----LPVEVEFVKVEDGIEARLTDEQVDRLYEWTR 157 (225)
T ss_pred --------cC----CceEEEEEEcccCcccccCHHHHHHHHHHhh
Confidence 10 1123344444444778999999998888875
No 156
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=90.96 E-value=0.34 Score=43.74 Aligned_cols=35 Identities=14% Similarity=0.179 Sum_probs=32.7
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
.|++++|+|+++++.|++|+++.++|+++.+++..
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~ 115 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTD 115 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCC
Confidence 69999999999999999999977999999999864
No 157
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=90.58 E-value=0.58 Score=50.82 Aligned_cols=71 Identities=10% Similarity=0.080 Sum_probs=52.4
Q ss_pred eecCCCceEEeHHHHH---HHH-HHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315 267 GRTLSGRPLLSTRRLF---RKM-AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE 337 (343)
Q Consensus 267 ~~de~G~I~LS~Krl~---~~~-aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee 337 (343)
.++++|.+.++-.... +.+ ..+.+....+.|++.+|+|+++.+.|.+|++ +|-.|+++.||++.. +.+.++
T Consensus 586 dieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~d 662 (692)
T COG1185 586 DIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVED 662 (692)
T ss_pred EecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccc
Confidence 3468898887764422 222 2233444578999999999999999999999 789999999999863 544443
No 158
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=90.53 E-value=1.2 Score=43.88 Aligned_cols=66 Identities=24% Similarity=0.116 Sum_probs=53.9
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCC
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG 251 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~ 251 (343)
.++.|.|+|-+....|.||=+..+.-|+||.+|....
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~------------------------------------------- 191 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE------------------------------------------- 191 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc-------------------------------------------
Confidence 3999999999999999999998899999999997511
Q ss_pred CCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315 252 RPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR 283 (343)
Q Consensus 252 i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~ 283 (343)
..+|+.+.+.|+...++|+|-||.+....
T Consensus 192 ---prlG~~l~~rVi~~reDg~lnLSl~p~~~ 220 (287)
T COG2996 192 ---PRLGERLTARVIGVREDGKLNLSLRPRAH 220 (287)
T ss_pred ---ccCCceEEEEEEEEccCCeeecccccccH
Confidence 13456677788887789999999877554
No 159
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=89.63 E-value=0.86 Score=40.98 Aligned_cols=51 Identities=14% Similarity=0.139 Sum_probs=42.7
Q ss_pred chhHHHHhhccc---CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 156 DKVGEDKVSVEY---YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 156 ~~dFa~lLe~~~---~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
+..|+.||-.+. -..-+|..|.|+|..|..+.+|||.|.|.-.++.+-++.
T Consensus 63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n 116 (173)
T KOG4078|consen 63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN 116 (173)
T ss_pred hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC
Confidence 589999996542 123469999999999999999999999999999887764
No 160
>PRK11642 exoribonuclease R; Provisional
Probab=87.58 E-value=1.2 Score=49.36 Aligned_cols=44 Identities=11% Similarity=0.228 Sum_probs=36.1
Q ss_pred HHHHHHHh-hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315 287 WHRVRQIK-QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS 330 (343)
Q Consensus 287 We~l~qa~-e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~ 330 (343)
|...+-+. ..|++++|+|+++++.|++|+++ +++||+|.|++..
T Consensus 633 ~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~ 679 (813)
T PRK11642 633 WLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDN 679 (813)
T ss_pred HHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCC
Confidence 44443333 58999999999999999999995 4999999998863
No 161
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=87.58 E-value=1.3 Score=45.05 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=31.6
Q ss_pred hCCCcEEEEEEEEec-CeeEEEECCeEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNT-GGLLTRIEGLRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nK-GGliVeIeGlrgFIP~SQl~ 329 (343)
+.|++|+|+|.++.+ ++++|+++++.|+||.++.-
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqi 172 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRI 172 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcC
Confidence 589999999999996 56999999999999999875
No 162
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=87.24 E-value=1.3 Score=48.12 Aligned_cols=35 Identities=17% Similarity=0.276 Sum_probs=32.8
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~ 329 (343)
+.|++++|+|+++.+.|++|+++ |++||+|.|++.
T Consensus 626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~ 662 (709)
T TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK 662 (709)
T ss_pred cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC
Confidence 57999999999999999999995 699999999996
No 163
>PRK11712 ribonuclease G; Provisional
Probab=86.48 E-value=0.85 Score=47.90 Aligned_cols=39 Identities=15% Similarity=0.145 Sum_probs=34.8
Q ss_pred CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccC
Q 019315 168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls 206 (343)
.....|.|..|+|.+|.+. .||||||.+..||+|++++.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~ 74 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIV 74 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhcc
Confidence 3445899999999999884 99999999999999999985
No 164
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=86.38 E-value=2.9 Score=39.03 Aligned_cols=103 Identities=19% Similarity=0.122 Sum_probs=63.5
Q ss_pred CCCCCCCEEEEEEEEEeCCeEEEEeCC----C------eeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeec
Q 019315 168 YEPKPGDFVIGVVVSGNENKLDVNVGA----D------LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVK 237 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~----K------sEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~ 237 (343)
.-+++|++|-|.|+++....+.|.|-. . ..|.+|++.+...+ +
T Consensus 60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~-----------------------~---- 112 (188)
T COG1096 60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGY-----------------------V---- 112 (188)
T ss_pred CCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccc-----------------------c----
Confidence 347889999999999999999999821 1 23555555554211 1
Q ss_pred CCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec--CeeEEE
Q 019315 238 DDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT--GGLLTR 315 (343)
Q Consensus 238 ~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK--GGliVe 315 (343)
.-+.+-+.+||.+-+.|++.. -.+.||.+.=+ -|.|..... ++.++.
T Consensus 113 -----------~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~d------------------lGVI~A~CsrC~~~L~~ 161 (188)
T COG1096 113 -----------EKLSDAFRIGDIVRARVISTG--DPIQLSTKGND------------------LGVIYARCSRCRAPLVK 161 (188)
T ss_pred -----------cccccccccccEEEEEEEecC--CCeEEEecCCc------------------ceEEEEEccCCCcceEE
Confidence 111233466777888887643 45777764422 466666553 233444
Q ss_pred ECCeEEEEeCCccc
Q 019315 316 IEGLRAFLPKAELL 329 (343)
Q Consensus 316 IeGlrgFIP~SQl~ 329 (343)
.|..--+|..+.-
T Consensus 162 -~~~~l~Cp~Cg~t 174 (188)
T COG1096 162 -KGNMLKCPNCGNT 174 (188)
T ss_pred -cCcEEECCCCCCE
Confidence 6777777777653
No 165
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=85.70 E-value=2 Score=46.44 Aligned_cols=36 Identities=11% Similarity=0.318 Sum_probs=33.0
Q ss_pred hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS 330 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~ 330 (343)
+.|+.++|+|++++++|++|+++ |++||+|.|++..
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~ 608 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN 608 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCC
Confidence 57999999999999999999995 7999999999864
No 166
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=84.25 E-value=1.5 Score=42.85 Aligned_cols=41 Identities=22% Similarity=0.441 Sum_probs=38.0
Q ss_pred ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
..|.++.||+|.|+|+.|.....-||++.|.+++++++-+-
T Consensus 79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvN 119 (301)
T KOG3013|consen 79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVN 119 (301)
T ss_pred hhcCCccCCEEEEEeeeeecceeEEecccccceEEEeeccc
Confidence 45788999999999999999999999999999999998875
No 167
>PRK10811 rne ribonuclease E; Reviewed
Probab=83.34 E-value=1.4 Score=49.87 Aligned_cols=37 Identities=22% Similarity=0.234 Sum_probs=33.9
Q ss_pred CCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccC
Q 019315 170 PKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls 206 (343)
..+|+|..|+|.+|.++ ++|||||.+..|||+++++.
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~ 74 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA 74 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcc
Confidence 45899999999999874 99999999999999999985
No 168
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=83.33 E-value=1.9 Score=32.49 Aligned_cols=34 Identities=21% Similarity=0.204 Sum_probs=21.4
Q ss_pred CCcEEEEEEEEecCeeEEEECC-eEEEEeCCcccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELLS 330 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIeG-lrgFIP~SQl~~ 330 (343)
|++.+.+|++.++.|++++.++ -+.|||.+++..
T Consensus 2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~ 36 (61)
T PF13509_consen 2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE 36 (61)
T ss_dssp -------EEEE-SSEEEEEETT-EEEEEEGGG---
T ss_pred CCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC
Confidence 7788999999999999999864 899999999854
No 169
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=81.87 E-value=2.1 Score=34.76 Aligned_cols=23 Identities=39% Similarity=0.564 Sum_probs=18.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEe
Q 019315 170 PKPGDFVIGVVVSGNENKLDVNV 192 (343)
Q Consensus 170 ~k~GdiVeG~VVsI~~~gv~VDI 192 (343)
+++|++|.|+|++++...++++|
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~I 24 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEI 24 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEE
Confidence 57899999999999999999998
No 170
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=79.81 E-value=2.5 Score=41.28 Aligned_cols=64 Identities=16% Similarity=0.163 Sum_probs=44.9
Q ss_pred hhhcceeeeecCCcc-eec--cCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHH-HHHHHhhCCCcEEE
Q 019315 227 FMVRGKMGIVKDDDA-IAM--SGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH-RVRQIKQLNEPIEV 302 (343)
Q Consensus 227 ~~VeGkV~~i~~dga-V~I--g~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe-~l~qa~e~g~~VeG 302 (343)
..|-|+|..|.++|+ +.+ -++++||+|++++ ...|- .+++..++|..+-+
T Consensus 13 EiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEv--------------------------as~wVknIrd~vkegqkvV~ 66 (269)
T COG1093 13 EIVVGTVKQVADYGAYVELDEYPGKEGFIHISEV--------------------------ASGWVKNIRDYVKEGQKVVA 66 (269)
T ss_pred cEEEEEEEEeeccccEEEeeccCCeeeeEEHHHH--------------------------HHHHHHHHHHHhhcCCeEEE
Confidence 467799999999998 655 3345555555544 24554 47777899999999
Q ss_pred EEEEEecCeeEEEE
Q 019315 303 KFTEWNTGGLLTRI 316 (343)
Q Consensus 303 kVve~nKGGliVeI 316 (343)
+|.++++.==.|++
T Consensus 67 kVlrVd~~rg~IDL 80 (269)
T COG1093 67 KVLRVDPKRGHIDL 80 (269)
T ss_pred EEEEEcCCCCeEee
Confidence 99999975333454
No 171
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=79.71 E-value=4.5 Score=35.03 Aligned_cols=35 Identities=14% Similarity=0.086 Sum_probs=31.1
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
+|++++|+|.+-+.+|+.|.+|.--+=+||..-|.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~ 37 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLP 37 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCC
Confidence 69999999999999999999998889999988875
No 172
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=79.11 E-value=2.2 Score=43.95 Aligned_cols=35 Identities=11% Similarity=0.054 Sum_probs=31.9
Q ss_pred hCCCcEEEEEEEEecC--eeEEEE-CCeEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNTG--GLLTRI-EGLRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nKG--GliVeI-eGlrgFIP~SQl~ 329 (343)
..|.+..|+|+++.+| |++|+| .|-.||||.+++.
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~ 61 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG 61 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC
Confidence 4799999999999999 999999 4789999999975
No 173
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=77.89 E-value=1.9 Score=47.55 Aligned_cols=55 Identities=11% Similarity=0.035 Sum_probs=44.1
Q ss_pred HHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhhhc
Q 019315 284 KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTELK 339 (343)
Q Consensus 284 ~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel~ 339 (343)
......+. .++.|.+++|+|.++...|.+|+|+ ...|.++.|+++.+ ++++.+++
T Consensus 647 ~~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv 703 (780)
T COG2183 647 DEGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVV 703 (780)
T ss_pred hhhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhc
Confidence 34444444 4678999999999999999999995 56899999999987 77776553
No 174
>PRK05054 exoribonuclease II; Provisional
Probab=77.83 E-value=5.4 Score=43.20 Aligned_cols=33 Identities=24% Similarity=0.467 Sum_probs=30.0
Q ss_pred CCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL 329 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~ 329 (343)
|+..+|.|+++...|++|+++ |++||+|.|.+.
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~ 596 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLH 596 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccC
Confidence 459999999999999999994 899999999884
No 175
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=77.45 E-value=5.7 Score=41.50 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=31.2
Q ss_pred hCCCcEEEEEEEEecCeeEEEE----C--CeEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI----E--GLRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI----e--GlrgFIP~SQl~ 329 (343)
..|++|+|+|.++.+++++|++ + +++|+||.++.-
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi 191 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL 191 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC
Confidence 5899999999999999999998 3 299999998874
No 176
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=76.67 E-value=3.7 Score=44.39 Aligned_cols=41 Identities=12% Similarity=0.246 Sum_probs=38.3
Q ss_pred ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
.++.++.|..-.|+|.++...|+||+++..+-|+|+.+.++
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~ 156 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLG 156 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccC
Confidence 46778899999999999999999999999999999999987
No 177
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=75.07 E-value=2.6 Score=34.72 Aligned_cols=44 Identities=11% Similarity=0.197 Sum_probs=34.4
Q ss_pred hCCCcEEEEEEEEecCeeEEEE-C-CeEEEEe-CCccccC-CCChhhhc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI-E-GLRAFLP-KAELLSR-VNNFTELK 339 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI-e-GlrgFIP-~SQl~~r-v~nleel~ 339 (343)
+.|+.+. .|+.+...|+.|.+ + |++|+|+ -|++..+ .+++.++.
T Consensus 15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll 62 (86)
T PHA02858 15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL 62 (86)
T ss_pred CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh
Confidence 4677787 99999999999998 3 7999998 8988765 55555443
No 178
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=73.56 E-value=9.3 Score=33.08 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.0
Q ss_pred CCCcEEEEEEEEecCeeEEEECC-eEEEEeCCccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELL 329 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeG-lrgFIP~SQl~ 329 (343)
.|++++|+|++.++-|+.|.++= =.-|||.+.|.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~ 37 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLP 37 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCC
Confidence 58999999999999999999942 35799999885
No 179
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=72.33 E-value=2.6 Score=44.25 Aligned_cols=40 Identities=23% Similarity=0.265 Sum_probs=36.0
Q ss_pred CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315 168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~ 207 (343)
....+|.|..|+|..|.+. .+|||||...-||+|.+|+.+
T Consensus 33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~ 74 (487)
T COG1530 33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP 74 (487)
T ss_pred cEeeecCceEEEecccCccchhheeeccCCccceEEecccch
Confidence 4556899999999999885 999999999999999999985
No 180
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=71.07 E-value=4.9 Score=36.84 Aligned_cols=32 Identities=28% Similarity=0.239 Sum_probs=26.6
Q ss_pred CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEe
Q 019315 169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTML 201 (343)
Q Consensus 169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IP 201 (343)
++=+|++|.|+|++++..|+|+++|. .+-++.
T Consensus 78 kpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~s 109 (170)
T KOG3298|consen 78 KPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYS 109 (170)
T ss_pred eecCCcEEEEEEEEEeeeeEEEeccc-eEeeee
Confidence 45579999999999999999999985 455544
No 181
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=69.82 E-value=2.5 Score=40.99 Aligned_cols=60 Identities=17% Similarity=0.126 Sum_probs=43.7
Q ss_pred HhhhcceeeeecCCcc-eeccC--CCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEE
Q 019315 226 EFMVRGKMGIVKDDDA-IAMSG--GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEV 302 (343)
Q Consensus 226 e~~VeGkV~~i~~dga-V~Ig~--~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeG 302 (343)
+..+.|+|+.+.++|+ |.+.+ +++|++|+++++.. ....+.+.++.|+.|.+
T Consensus 9 GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~-------------------------~i~~i~~~~kvGd~V~v 63 (262)
T PRK03987 9 GELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASG-------------------------WVKNIRDHVKEGQKVVC 63 (262)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcc-------------------------cccCHHHhCCCCCEEEE
Confidence 4578899999999999 88864 57777777665211 01123456789999999
Q ss_pred EEEEEecC
Q 019315 303 KFTEWNTG 310 (343)
Q Consensus 303 kVve~nKG 310 (343)
+|.++.+.
T Consensus 64 kVi~VD~~ 71 (262)
T PRK03987 64 KVIRVDPR 71 (262)
T ss_pred EEEEEecc
Confidence 99999863
No 182
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=68.54 E-value=15 Score=39.73 Aligned_cols=33 Identities=30% Similarity=0.535 Sum_probs=29.7
Q ss_pred CCcEEEEEEEEecCeeEEEE--CCeEEEEeCCccc
Q 019315 297 NEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL 329 (343)
Q Consensus 297 g~~VeGkVve~nKGGliVeI--eGlrgFIP~SQl~ 329 (343)
++..+|.|+.+++.|++|++ .|+.||+|.+.+.
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~ 592 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLH 592 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcC
Confidence 45899999999999999999 4899999999884
No 183
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=62.87 E-value=13 Score=34.11 Aligned_cols=34 Identities=21% Similarity=0.178 Sum_probs=29.6
Q ss_pred CCCcEEEEEEEEecCeeEEEECCeEEEEeCCccc
Q 019315 296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL 329 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~ 329 (343)
+|++|.|.|++++|-|++++++=++.|+-.-++.
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~p 114 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKP 114 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeecccCC
Confidence 6999999999999999999997799998655443
No 184
>PRK05054 exoribonuclease II; Provisional
Probab=62.18 E-value=14 Score=40.13 Aligned_cols=36 Identities=8% Similarity=0.098 Sum_probs=31.4
Q ss_pred CCC--CEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccC
Q 019315 171 KPG--DFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVL 206 (343)
Q Consensus 171 k~G--diVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls 206 (343)
+.| +...|.|+.++.+|+||.| ....+|+||.+.+.
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~ 596 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLH 596 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccC
Confidence 455 5999999999999999999 45699999998875
No 185
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=61.55 E-value=38 Score=31.61 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=33.0
Q ss_pred hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEe---CC-----CeeEEEeccccC
Q 019315 157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV---GA-----DLLGTMLTKEVL 206 (343)
Q Consensus 157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDI---G~-----KsEG~IPisEls 206 (343)
..|.++| +..|+||+.+|.+++...+-|+| |. -.-|+|+..++.
T Consensus 59 ~~~~~~L------P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR 110 (193)
T KOG3409|consen 59 QLFNELL------PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVR 110 (193)
T ss_pred cchhhcC------CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcc
Confidence 4555555 45799999999999999999998 32 245777777665
No 186
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=61.10 E-value=45 Score=32.05 Aligned_cols=40 Identities=28% Similarity=0.412 Sum_probs=34.4
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
.|-+.+||.|-|.|++...+...||||.-.-+.+|.--|.
T Consensus 60 RYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe 99 (230)
T KOG1004|consen 60 RYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE 99 (230)
T ss_pred eecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeecccc
Confidence 4667899999999999999999999998777888776554
No 187
>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=59.84 E-value=11 Score=30.69 Aligned_cols=32 Identities=25% Similarity=0.338 Sum_probs=23.8
Q ss_pred CCCCCCCEEEEEEEEEeC-CeEEEEeCCCeeEE
Q 019315 168 YEPKPGDFVIGVVVSGNE-NKLDVNVGADLLGT 199 (343)
Q Consensus 168 ~~~k~GdiVeG~VVsI~~-~gv~VDIG~KsEG~ 199 (343)
..|++||+|.++|++..+ ..+++.+-.+--|+
T Consensus 59 ~~f~~GDiV~AkVis~~~~~~~~Lst~~~~lGV 91 (92)
T cd05791 59 KCFRPGDIVRAKVISLGDASSYYLSTAENELGV 91 (92)
T ss_pred hhcCCCCEEEEEEEEcCCCCCcEEEecCCCCcc
Confidence 347899999999999976 56777775444444
No 188
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=59.53 E-value=28 Score=40.46 Aligned_cols=43 Identities=16% Similarity=0.137 Sum_probs=35.5
Q ss_pred cccCCCCCCCEEEEEEEEEeCCe---EEEEeCCCeeEEEeccccCc
Q 019315 165 VEYYEPKPGDFVIGVVVSGNENK---LDVNVGADLLGTMLTKEVLP 207 (343)
Q Consensus 165 ~~~~~~k~GdiVeG~VVsI~~~g---v~VDIG~KsEG~IPisEls~ 207 (343)
+....+..|.+|.++|.+++.+. |-|-+.-+.+|+|+.+.+++
T Consensus 978 et~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd 1023 (1299)
T KOG1856|consen 978 ETPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSD 1023 (1299)
T ss_pred CChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccCh
Confidence 33355889999999999999876 55666777999999999985
No 189
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=50.73 E-value=25 Score=40.91 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=35.3
Q ss_pred hCCCcEEEEEEEEecCe---eEEEE-CCeEEEEeCCccccC-CCChhhhc
Q 019315 295 QLNEPIEVKFTEWNTGG---LLTRI-EGLRAFLPKAELLSR-VNNFTELK 339 (343)
Q Consensus 295 e~g~~VeGkVve~nKGG---liVeI-eGlrgFIP~SQl~~r-v~nleel~ 339 (343)
.+|.+|.|.|+++.-+= +-|.+ .|+.||||++.++.+ ++++...+
T Consensus 984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v 1033 (1299)
T KOG1856|consen 984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRV 1033 (1299)
T ss_pred ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhh
Confidence 47889999999998654 44566 499999999999886 66766543
No 190
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=49.83 E-value=27 Score=37.95 Aligned_cols=34 Identities=6% Similarity=0.017 Sum_probs=30.7
Q ss_pred CCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccC
Q 019315 173 GDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVL 206 (343)
Q Consensus 173 GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls 206 (343)
|+.-.|+|+.++.+|+||.+ ..+.+|+||...+.
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~ 592 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLH 592 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcC
Confidence 45899999999999999999 67799999998885
No 191
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=48.62 E-value=16 Score=39.58 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=36.4
Q ss_pred CCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhhh
Q 019315 296 LNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTEL 338 (343)
Q Consensus 296 ~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nleel 338 (343)
-|-+.+++|+++-..|++|++ .+..|+|+.||++.+ +..++++
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~ 712 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDL 712 (760)
T ss_pred eeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHH
Confidence 466679999999999999999 678999999999977 5556655
No 192
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=48.02 E-value=71 Score=27.00 Aligned_cols=35 Identities=23% Similarity=0.187 Sum_probs=26.9
Q ss_pred CCCCCCCEE------EEEEEEEeCCeEEEEeCCCeeEEEec
Q 019315 168 YEPKPGDFV------IGVVVSGNENKLDVNVGADLLGTMLT 202 (343)
Q Consensus 168 ~~~k~GdiV------eG~VVsI~~~gv~VDIG~KsEG~IPi 202 (343)
.++++||.| -|+|++++++.+.|+++.+..=-+.+
T Consensus 51 ~~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r 91 (106)
T PRK05585 51 SSLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQK 91 (106)
T ss_pred HhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 458899997 69999999999999997654333333
No 193
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=47.25 E-value=48 Score=31.85 Aligned_cols=53 Identities=15% Similarity=0.220 Sum_probs=39.3
Q ss_pred HHHHHHHHHhhC--CCcEEEEEEEEecCeeEEEECCeEEEEeCCcc-ccCCCChhh
Q 019315 285 MAWHRVRQIKQL--NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTE 337 (343)
Q Consensus 285 ~aWe~l~qa~e~--g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl-~~rv~nlee 337 (343)
.-|-++....+. |++..|++.++.+-|+.++++|+..=+|+.++ .+....+.+
T Consensus 61 eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~G~~~~ip~d~L~~Lg~g~~~Q 116 (225)
T PF09883_consen 61 EEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVDGIFVPIPKDELKPLGPGSPRQ 116 (225)
T ss_pred HHhCCCCchhcccCCceEEEEEEeecccceEEEeecccccCcHHHhcccCCCCHHH
Confidence 345444333455 99999999999999999999888888999888 443333333
No 194
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.18 E-value=39 Score=32.51 Aligned_cols=41 Identities=15% Similarity=0.127 Sum_probs=31.4
Q ss_pred ccCCCCCCCEEEEEEEEEeCC--eEEEEeCCC----eeEEEeccccC
Q 019315 166 EYYEPKPGDFVIGVVVSGNEN--KLDVNVGAD----LLGTMLTKEVL 206 (343)
Q Consensus 166 ~~~~~k~GdiVeG~VVsI~~~--gv~VDIG~K----sEG~IPisEls 206 (343)
+..+++.||+.-|+.+...+. ++|||||-- .++++|+.++.
T Consensus 69 sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk 115 (247)
T COG4044 69 SLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELK 115 (247)
T ss_pred ccccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHH
Confidence 457889999999999999876 566666432 56778887775
No 195
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=46.38 E-value=92 Score=25.18 Aligned_cols=36 Identities=25% Similarity=0.318 Sum_probs=27.1
Q ss_pred hHHHHhhcccCCCCCCCEE------EEEEEEEeCCeEEEEeCCCee
Q 019315 158 VGEDKVSVEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLL 197 (343)
Q Consensus 158 dFa~lLe~~~~~~k~GdiV------eG~VVsI~~~gv~VDIG~KsE 197 (343)
...+|++ ++++||.| -|+|++++++.+.|.+..+..
T Consensus 30 ~~~~m~~----~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~ 71 (84)
T TIGR00739 30 AHKKLIE----SLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTE 71 (84)
T ss_pred HHHHHHH----hCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeE
Confidence 4445553 58899985 699999999999998865443
No 196
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=45.96 E-value=83 Score=26.97 Aligned_cols=46 Identities=20% Similarity=0.312 Sum_probs=33.2
Q ss_pred hhHHHHhhcccCCCCCCCEE------EEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315 157 KVGEDKVSVEYYEPKPGDFV------IGVVVSGNENKLDVNVGADLLGTMLTKEVL 206 (343)
Q Consensus 157 ~dFa~lLe~~~~~~k~GdiV------eG~VVsI~~~gv~VDIG~KsEG~IPisEls 206 (343)
....+|++ ++++||.| -|+|++|+++.+.|+++.+..=-+.++-++
T Consensus 30 K~~~~m~~----~Lk~GD~VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~r~AI~ 81 (109)
T PRK05886 30 QATIDLHE----SLQPGDRVHTTSGLQATIVGITDDTVDLEIAPGVVTTWMKLAVR 81 (109)
T ss_pred HHHHHHHH----hcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhhhee
Confidence 34455554 58899986 599999999999999976655555555444
No 197
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=44.65 E-value=38 Score=24.34 Aligned_cols=34 Identities=24% Similarity=0.285 Sum_probs=22.5
Q ss_pred hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl 328 (343)
+.|++|++.=.....+-+.+...|-+||+|.+.+
T Consensus 19 ~~Gd~i~v~~~~~~~~ww~~~~~g~~G~~P~~~v 52 (55)
T PF07653_consen 19 KKGDVIEVLGEKDDDGWWLGENNGRRGWFPSSYV 52 (55)
T ss_dssp -TTEEEEEEEEECSTSEEEEEETTEEEEEEGGGE
T ss_pred ecCCEEEEEEeecCCCEEEEEECCcEEEEcHHHE
Confidence 3577776541123344566777899999999876
No 198
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=42.93 E-value=25 Score=26.97 Aligned_cols=19 Identities=26% Similarity=0.324 Sum_probs=17.5
Q ss_pred EEEEEEEEeCCeEEEEeCC
Q 019315 176 VIGVVVSGNENKLDVNVGA 194 (343)
Q Consensus 176 VeG~VVsI~~~gv~VDIG~ 194 (343)
.+|+|.++.++.++|||..
T Consensus 16 ~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cEEEEEEEecCcEEEEEEe
Confidence 6899999999999999964
No 199
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=42.20 E-value=42 Score=25.05 Aligned_cols=31 Identities=16% Similarity=0.245 Sum_probs=22.9
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeeEEEecccc
Q 019315 175 FVIGVVVSGNENKLDVNVGA-DLLGTMLTKEV 205 (343)
Q Consensus 175 iVeG~VVsI~~~gv~VDIG~-KsEG~IPisEl 205 (343)
-++|+|+.++++.+.||+++ +.+=++|.+.+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~ 35 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL 35 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHH
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchH
Confidence 47999999999999999963 25555665544
No 200
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=40.63 E-value=1e+02 Score=25.95 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=28.3
Q ss_pred CCCCCCCEE------EEEEEEEeCCeEEEEeCCCeeEEEeccc
Q 019315 168 YEPKPGDFV------IGVVVSGNENKLDVNVGADLLGTMLTKE 204 (343)
Q Consensus 168 ~~~k~GdiV------eG~VVsI~~~gv~VDIG~KsEG~IPisE 204 (343)
.++++||.| .|+|++|.++.+-|.+|...+-.+-++-
T Consensus 42 ~sL~kGD~VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~~~k~a 84 (97)
T COG1862 42 NSLKKGDEVVTIGGIVGTVTKVGDDTVEIELGDGTKIKFEKEA 84 (97)
T ss_pred HhccCCCEEEEcCCeEEEEEEEecCcEEEEECCCeEEEEEHHH
Confidence 358899984 6999999999999999866655544433
No 201
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=37.39 E-value=38 Score=37.10 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=38.2
Q ss_pred HHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEeccccC
Q 019315 159 GEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGAD-LLGTMLTKEVL 206 (343)
Q Consensus 159 Fa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~K-sEG~IPisEls 206 (343)
+.+++...+.+-+.|+.-+|+|++++.+|++|-+-.. .+|+++++-+.
T Consensus 609 ~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~ 657 (706)
T COG0557 609 VIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLP 657 (706)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCC
Confidence 3344444445566899999999999999999999444 99999999986
No 202
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=37.36 E-value=13 Score=39.49 Aligned_cols=35 Identities=23% Similarity=0.462 Sum_probs=31.9
Q ss_pred hCCCcEEEEEEEEecCeeEEEE--CCeEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeI--eGlrgFIP~SQl~ 329 (343)
..+....+.|..+++||+-|++ +|--+|||++.+-
T Consensus 560 ~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih 596 (645)
T COG4776 560 GTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIH 596 (645)
T ss_pred ccCchhhhhhhhhccCceEEEeccCCcceecchhhhc
Confidence 4788899999999999999998 6999999999884
No 203
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.17 E-value=51 Score=30.91 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=29.6
Q ss_pred cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEec
Q 019315 167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLT 202 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPi 202 (343)
...|++||+|.++|++.. +.+++.+-.+--|+|-.
T Consensus 116 ~d~f~~GDivrA~Vis~~-~~~~Lst~~~dlGVI~A 150 (188)
T COG1096 116 SDAFRIGDIVRARVISTG-DPIQLSTKGNDLGVIYA 150 (188)
T ss_pred ccccccccEEEEEEEecC-CCeEEEecCCcceEEEE
Confidence 357999999999999998 77888887777888765
No 204
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=36.77 E-value=81 Score=23.50 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=25.3
Q ss_pred cEEEEEEEEecCeeEEEECC--eEEEEeCCccc
Q 019315 299 PIEVKFTEWNTGGLLTRIEG--LRAFLPKAELL 329 (343)
Q Consensus 299 ~VeGkVve~nKGGliVeIeG--lrgFIP~SQl~ 329 (343)
-++|+|+++.+.-++++.+| .+-|+|.+.+.
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~ 36 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLS 36 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHH
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHH
Confidence 37899999999999999975 68899987554
No 205
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=36.16 E-value=34 Score=27.74 Aligned_cols=17 Identities=41% Similarity=0.483 Sum_probs=12.6
Q ss_pred cCCCCCCCEEEEEEEEE
Q 019315 167 YYEPKPGDFVIGVVVSG 183 (343)
Q Consensus 167 ~~~~k~GdiVeG~VVsI 183 (343)
+..|++||+|.++|++.
T Consensus 66 ~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 66 YDCFRPGDIVRARVISL 82 (82)
T ss_dssp GGT--SSSEEEEEEEEE
T ss_pred HhccCCCCEEEEEEeeC
Confidence 35689999999999874
No 206
>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=33.43 E-value=63 Score=26.38 Aligned_cols=35 Identities=11% Similarity=-0.088 Sum_probs=30.6
Q ss_pred hCCCcEEEEEEEEecCeeEEEECC-eEEEEeCCccc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELL 329 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIeG-lrgFIP~SQl~ 329 (343)
+.|+.|=|+|+++...++.|+|.+ ..|+||.+...
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ 40 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFE 40 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcc
Confidence 479999999999999999999954 68999988764
No 207
>PRK10811 rne ribonuclease E; Reviewed
Probab=30.32 E-value=50 Score=38.00 Aligned_cols=34 Identities=18% Similarity=0.193 Sum_probs=30.3
Q ss_pred CCCcEEEEEEEEecC--eeEEEE-CCeEEEEeCCccc
Q 019315 296 LNEPIEVKFTEWNTG--GLLTRI-EGLRAFLPKAELL 329 (343)
Q Consensus 296 ~g~~VeGkVve~nKG--GliVeI-eGlrgFIP~SQl~ 329 (343)
.|.+..|+|.++.+| +++|+| .|-.||||.+.+.
T Consensus 38 vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~ 74 (1068)
T PRK10811 38 KANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA 74 (1068)
T ss_pred ccceEEEEEecccCCcceeEEEecCCcceEEEhhhcc
Confidence 599999999999997 899999 4789999988774
No 208
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=29.16 E-value=1.1e+02 Score=33.59 Aligned_cols=37 Identities=19% Similarity=0.304 Sum_probs=33.1
Q ss_pred hhCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315 294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS 330 (343)
Q Consensus 294 ~e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~ 330 (343)
...|+..+|.|+++.+.|++|.+. |++|+++.|.+..
T Consensus 620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~ 658 (706)
T COG0557 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPD 658 (706)
T ss_pred HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCC
Confidence 358899999999999999999994 5899999999873
No 209
>PRK11712 ribonuclease G; Provisional
Probab=27.31 E-value=64 Score=34.21 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=29.8
Q ss_pred CCCcEEEEEEEEecC--eeEEEE-CCeEEEEeCCcc
Q 019315 296 LNEPIEVKFTEWNTG--GLLTRI-EGLRAFLPKAEL 328 (343)
Q Consensus 296 ~g~~VeGkVve~nKG--GliVeI-eGlrgFIP~SQl 328 (343)
.|.+..|+|.++.+| +++|+| .+-.||||.+.+
T Consensus 38 vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~ 73 (489)
T PRK11712 38 VGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI 73 (489)
T ss_pred cccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc
Confidence 699999999999997 799999 478999999976
No 210
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=27.30 E-value=97 Score=22.07 Aligned_cols=19 Identities=5% Similarity=0.029 Sum_probs=16.1
Q ss_pred CCCEEEEEEEEEeCCeEEE
Q 019315 172 PGDFVIGVVVSGNENKLDV 190 (343)
Q Consensus 172 ~GdiVeG~VVsI~~~gv~V 190 (343)
.++.++|++..|+++|.++
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 5889999999999987654
No 211
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=24.72 E-value=1.1e+02 Score=21.85 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.1
Q ss_pred hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315 295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328 (343)
Q Consensus 295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl 328 (343)
+.|++|.+. .+...+=..++..|-+|++|++-+
T Consensus 16 ~~Gd~i~v~-~~~~~~W~~g~~~g~~G~~P~~yV 48 (49)
T PF14604_consen 16 KKGDVITVL-EKSDDGWWYGRNTGRTGLFPANYV 48 (49)
T ss_dssp -TTEEEEEE-EESSTSEEEEEETTEEEEEEGGGE
T ss_pred cCCCEEEEE-EeCCCCEEEEEECCEEEEECHHhC
Confidence 467777765 333333355777899999998754
No 212
>PF05339 DUF739: Protein of unknown function (DUF739); InterPro: IPR008003 This entry is represented by Bacteriophage bIL285, Orf5. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several bacteriophage proteins. Three of the proteins in this family have been labelled putative cro repressor proteins.; PDB: 2PH7_A.
Probab=23.57 E-value=20 Score=31.97 Aligned_cols=16 Identities=38% Similarity=0.808 Sum_probs=11.9
Q ss_pred ChhhhhhhhhhccCCC
Q 019315 117 DEEEALAPFLKFFKPR 132 (343)
Q Consensus 117 ~~~~~~~~~~~~~~~~ 132 (343)
.+++-++||++||+-.
T Consensus 75 pte~~~~pfm~ff~~~ 90 (138)
T PF05339_consen 75 PTEKNPAPFMNFFREH 90 (138)
T ss_dssp E--SSSHHHHHHHHHH
T ss_pred cccccccHHHHHHHHh
Confidence 3577899999999964
No 213
>PF04270 Strep_his_triad: Streptococcal histidine triad protein ; InterPro: IPR006270 This entry represents a repeated sequence region that includes a His-X-X-His-X-His (histidine triad) motif, which is found in family of Streptococcal proteins. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice []. ; PDB: 2CS7_C.
Probab=23.08 E-value=1.3e+02 Score=22.78 Aligned_cols=27 Identities=15% Similarity=0.249 Sum_probs=20.4
Q ss_pred EEEEecCeeEEEECCeEEEEeCCcccc
Q 019315 304 FTEWNTGGLLTRIEGLRAFLPKAELLS 330 (343)
Q Consensus 304 Vve~nKGGliVeIeGlrgFIP~SQl~~ 330 (343)
|++....|++|.-++--=|||+++|+.
T Consensus 14 I~~~~~~gy~vpHgdH~HyI~k~dLs~ 40 (53)
T PF04270_consen 14 IISETGDGYVVPHGDHFHYIPKSDLSA 40 (53)
T ss_dssp --EE-SSEEEEEETTEEEEEEGGGS-H
T ss_pred ccccCCCeEEeeCCCcccCCchhhCCH
Confidence 677889999999988788999999863
No 214
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.31 E-value=1.1e+02 Score=24.63 Aligned_cols=26 Identities=35% Similarity=0.442 Sum_probs=21.0
Q ss_pred CCCCCCEE------EEEEEEEeCCeEEEEeCC
Q 019315 169 EPKPGDFV------IGVVVSGNENKLDVNVGA 194 (343)
Q Consensus 169 ~~k~GdiV------eG~VVsI~~~gv~VDIG~ 194 (343)
.-+.|++| +|.|-+++++.+.||+..
T Consensus 23 ~a~vgniief~dgl~g~vek~nensvivdlt~ 54 (81)
T COG4873 23 IAKVGNIIEFKDGLTGVVEKVNENSVIVDLTI 54 (81)
T ss_pred eeeccceEEEcccceeeeeeecCCcEEEEEEe
Confidence 34567775 699999999999999854
No 215
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=22.09 E-value=42 Score=26.85 Aligned_cols=29 Identities=28% Similarity=0.464 Sum_probs=0.5
Q ss_pred CCCCCCCEE------EEEEEEEeCCeEEEEeCCCe
Q 019315 168 YEPKPGDFV------IGVVVSGNENKLDVNVGADL 196 (343)
Q Consensus 168 ~~~k~GdiV------eG~VVsI~~~gv~VDIG~Ks 196 (343)
.++++||.| -|+|++++++.+.|+++.++
T Consensus 35 ~~Lk~Gd~VvT~gGi~G~V~~i~~~~v~lei~~g~ 69 (82)
T PF02699_consen 35 ASLKPGDEVVTIGGIYGTVVEIDDDTVVLEIAPGV 69 (82)
T ss_dssp G----------------------------------
T ss_pred HcCCCCCEEEECCcEEEEEEEEeCCEEEEEECCCe
Confidence 568899985 59999999999999997643
Done!