Query 021034
Match_columns 318
No_of_seqs 349 out of 1898
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 07:05:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021034.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021034hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07400 30S ribosomal protein 100.0 3.6E-48 7.9E-53 361.4 29.1 245 73-318 5-250 (318)
2 COG0539 RpsA Ribosomal protein 100.0 1.4E-45 3E-50 357.8 23.0 282 6-318 126-418 (541)
3 COG0539 RpsA Ribosomal protein 100.0 1.4E-44 3.1E-49 350.7 19.0 272 7-318 214-497 (541)
4 PRK07899 rpsA 30S ribosomal pr 100.0 6E-43 1.3E-47 341.0 28.5 235 82-318 18-262 (486)
5 PRK13806 rpsA 30S ribosomal pr 100.0 1.3E-43 2.8E-48 349.4 22.4 282 6-318 136-434 (491)
6 PRK07899 rpsA 30S ribosomal pr 100.0 4.6E-43 9.9E-48 341.8 24.2 278 6-318 57-348 (486)
7 PRK12269 bifunctional cytidyla 100.0 1.7E-42 3.6E-47 356.4 22.9 280 6-318 514-810 (863)
8 PRK06676 rpsA 30S ribosomal pr 100.0 2.4E-41 5.2E-46 325.6 25.6 279 6-318 40-332 (390)
9 PRK06299 rpsA 30S ribosomal pr 100.0 3.2E-40 7E-45 331.7 25.7 283 6-318 135-429 (565)
10 PRK06299 rpsA 30S ribosomal pr 100.0 1.4E-39 3.1E-44 326.9 29.8 236 79-318 8-255 (565)
11 PRK06676 rpsA 30S ribosomal pr 100.0 1.8E-39 3.8E-44 312.7 28.3 234 83-318 2-246 (390)
12 TIGR00717 rpsA ribosomal prote 100.0 2E-40 4.4E-45 329.9 21.8 280 6-318 208-501 (516)
13 PRK12269 bifunctional cytidyla 100.0 6E-40 1.3E-44 337.5 25.1 281 7-318 423-721 (863)
14 TIGR00717 rpsA ribosomal prote 100.0 2.1E-38 4.6E-43 315.4 25.8 281 7-318 122-415 (516)
15 PRK00087 4-hydroxy-3-methylbut 100.0 1.2E-37 2.5E-42 316.4 30.5 256 61-318 265-531 (647)
16 PRK00087 4-hydroxy-3-methylbut 100.0 2.7E-38 5.9E-43 321.0 23.9 279 6-318 324-617 (647)
17 PRK13806 rpsA 30S ribosomal pr 100.0 1.5E-37 3.2E-42 306.4 24.8 274 7-318 57-348 (491)
18 KOG1070 rRNA processing protei 100.0 1.6E-28 3.5E-33 252.3 12.9 284 6-318 532-942 (1710)
19 PRK07400 30S ribosomal protein 99.9 1.1E-26 2.3E-31 217.1 17.5 212 7-258 54-271 (318)
20 KOG1070 rRNA processing protei 99.8 8.9E-20 1.9E-24 188.5 17.5 259 20-318 1026-1308(1710)
21 COG2996 Predicted RNA-bindinin 99.7 2.7E-15 5.9E-20 133.2 20.9 192 96-318 2-202 (287)
22 PTZ00248 eukaryotic translatio 99.7 3.1E-17 6.8E-22 151.4 8.3 121 98-220 16-146 (319)
23 PTZ00248 eukaryotic translatio 99.7 2.9E-17 6.2E-22 151.6 2.5 128 187-314 17-166 (319)
24 COG1098 VacB Predicted RNA bin 99.5 7.1E-15 1.5E-19 115.7 5.8 77 96-174 2-78 (129)
25 PF00575 S1: S1 RNA binding do 99.5 8.5E-14 1.8E-18 102.5 10.6 73 97-170 2-74 (74)
26 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 5.6E-14 1.2E-18 103.7 9.0 71 97-168 1-74 (74)
27 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 1.2E-13 2.6E-18 104.2 8.6 79 89-169 5-83 (83)
28 cd05694 S1_Rrp5_repeat_hs2_sc2 99.5 6.1E-13 1.3E-17 98.1 10.4 71 96-173 1-72 (74)
29 cd05698 S1_Rrp5_repeat_hs6_sc5 99.5 3.9E-13 8.5E-18 97.9 8.9 70 100-170 1-70 (70)
30 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 6.7E-13 1.4E-17 97.7 9.3 70 100-170 1-72 (73)
31 COG1098 VacB Predicted RNA bin 99.4 7.4E-14 1.6E-18 110.0 4.2 58 261-318 2-60 (129)
32 cd05705 S1_Rrp5_repeat_hs14 S1 99.4 3E-13 6.5E-18 99.8 6.2 57 262-318 1-61 (74)
33 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 2.2E-12 4.7E-17 94.0 9.4 70 100-170 1-70 (70)
34 cd04465 S1_RPS1_repeat_ec2_hs2 99.4 2.3E-12 4.9E-17 93.1 9.1 65 188-252 1-67 (67)
35 PRK07252 hypothetical protein; 99.4 2.5E-12 5.4E-17 103.6 10.0 81 98-179 2-82 (120)
36 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 2.7E-12 6E-17 93.2 9.2 69 100-169 1-69 (69)
37 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 5.5E-12 1.2E-16 92.6 10.6 73 97-170 1-73 (73)
38 cd05704 S1_Rrp5_repeat_hs13 S1 99.4 3.4E-12 7.3E-17 93.7 8.9 71 97-170 1-72 (72)
39 PF00575 S1: S1 RNA binding do 99.4 7.6E-12 1.7E-16 92.0 10.3 68 185-252 2-74 (74)
40 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 4.7E-12 1E-16 92.6 9.1 69 100-169 1-71 (71)
41 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 4.3E-12 9.3E-17 93.6 8.8 67 186-255 3-72 (74)
42 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 4E-12 8.6E-17 92.1 8.3 68 100-168 1-68 (68)
43 cd04452 S1_IF2_alpha S1_IF2_al 99.3 9E-12 2E-16 92.0 10.2 73 98-171 2-76 (76)
44 cd05691 S1_RPS1_repeat_ec6 S1_ 99.3 1.1E-11 2.3E-16 90.8 9.7 72 100-172 1-72 (73)
45 PRK08582 hypothetical protein; 99.3 1.3E-11 2.8E-16 102.0 10.8 82 96-180 2-83 (139)
46 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 3.8E-12 8.3E-17 95.9 6.2 64 255-318 5-69 (83)
47 cd04465 S1_RPS1_repeat_ec2_hs2 99.3 1.8E-11 4E-16 88.4 9.3 67 100-170 1-67 (67)
48 cd05708 S1_Rrp5_repeat_sc12 S1 99.3 2.4E-11 5.1E-16 89.8 10.0 74 98-172 1-75 (77)
49 cd05703 S1_Rrp5_repeat_hs12_sc 99.3 1.4E-11 2.9E-16 90.7 8.5 65 188-252 1-72 (73)
50 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 3.8E-12 8.3E-17 93.4 5.5 57 262-318 1-59 (72)
51 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 3.6E-11 7.7E-16 88.4 9.6 70 98-169 2-72 (73)
52 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.3 2.5E-11 5.5E-16 87.5 8.6 66 100-168 1-66 (66)
53 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 3E-11 6.6E-16 86.9 9.0 69 100-170 1-69 (69)
54 PHA02945 interferon resistance 99.3 4.1E-11 8.9E-16 89.1 9.4 74 97-174 9-86 (88)
55 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 1.5E-11 3.3E-16 90.4 7.0 56 263-318 2-59 (73)
56 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 2.6E-11 5.6E-16 94.7 7.6 76 97-173 1-98 (100)
57 PRK08059 general stress protei 99.2 1.1E-10 2.4E-15 94.7 10.4 78 96-174 4-81 (123)
58 COG1093 SUI2 Translation initi 99.2 2.8E-11 6.1E-16 107.3 7.3 77 97-174 9-87 (269)
59 PRK05807 hypothetical protein; 99.2 1.2E-10 2.7E-15 95.9 10.7 75 96-173 2-76 (136)
60 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 7.5E-11 1.6E-15 89.4 8.7 76 96-173 3-82 (86)
61 cd04454 S1_Rrp4_like S1_Rrp4_l 99.2 9.2E-11 2E-15 88.2 9.1 75 96-172 3-77 (82)
62 cd05707 S1_Rrp5_repeat_sc11 S1 99.2 2.6E-11 5.7E-16 87.8 5.8 54 265-318 1-55 (68)
63 smart00316 S1 Ribosomal protei 99.2 1.2E-10 2.7E-15 83.9 9.4 72 98-170 1-72 (72)
64 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 7.9E-11 1.7E-15 85.3 8.2 68 100-168 1-69 (69)
65 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 4.8E-11 1E-15 87.5 7.1 57 262-318 1-58 (73)
66 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 7.5E-11 1.6E-15 85.7 8.0 65 188-252 1-70 (70)
67 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 9.1E-11 2E-15 84.6 8.2 63 188-250 1-66 (66)
68 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 1.1E-10 2.3E-15 84.8 8.6 64 188-251 1-69 (69)
69 PLN00207 polyribonucleotide nu 99.2 6.1E-11 1.3E-15 122.4 10.0 125 58-185 705-837 (891)
70 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 3.7E-11 8.1E-16 87.0 5.9 54 265-318 1-56 (69)
71 PRK08582 hypothetical protein; 99.2 5E-11 1.1E-15 98.5 7.4 57 262-318 3-60 (139)
72 cd04453 S1_RNase_E S1_RNase_E: 99.2 4.1E-11 8.8E-16 91.4 6.2 58 261-318 4-67 (88)
73 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.2 1.3E-10 2.8E-15 85.0 8.1 64 188-251 1-71 (71)
74 cd05685 S1_Tex S1_Tex: The C-t 99.2 1.5E-10 3.3E-15 83.1 8.1 68 100-168 1-68 (68)
75 cd05688 S1_RPS1_repeat_ec3 S1_ 99.2 1.9E-10 4.2E-15 82.7 8.6 68 99-168 1-68 (68)
76 PRK09202 nusA transcription el 99.2 4.4E-10 9.6E-15 110.0 13.7 122 123-254 71-201 (470)
77 cd05689 S1_RPS1_repeat_ec4 S1_ 99.2 1E-10 2.2E-15 85.6 6.8 57 262-318 1-59 (72)
78 cd04472 S1_PNPase S1_PNPase: P 99.1 2.6E-10 5.6E-15 82.0 8.6 68 100-169 1-68 (68)
79 cd05684 S1_DHX8_helicase S1_DH 99.1 3.9E-10 8.4E-15 84.1 9.7 72 100-174 1-76 (79)
80 PRK03987 translation initiatio 99.1 3.5E-10 7.5E-15 103.0 11.0 84 97-181 6-91 (262)
81 COG2996 Predicted RNA-bindinin 99.1 3.8E-09 8.2E-14 94.4 16.6 146 96-256 70-220 (287)
82 cd04452 S1_IF2_alpha S1_IF2_al 99.1 2.1E-10 4.5E-15 84.7 6.6 56 263-318 2-60 (76)
83 cd04453 S1_RNase_E S1_RNase_E: 99.1 5.6E-10 1.2E-14 85.1 9.2 75 96-171 4-83 (88)
84 cd05689 S1_RPS1_repeat_ec4 S1_ 99.1 6.3E-10 1.4E-14 81.3 9.1 70 98-168 2-72 (72)
85 PRK07252 hypothetical protein; 99.1 2.8E-10 6E-15 91.7 6.8 56 263-318 2-58 (120)
86 COG2183 Tex Transcriptional ac 99.1 4.1E-10 8.9E-15 113.5 9.4 112 59-175 622-733 (780)
87 PRK05807 hypothetical protein; 99.1 3.9E-10 8.4E-15 92.9 7.5 57 262-318 3-59 (136)
88 cd05692 S1_RPS1_repeat_hs4 S1_ 99.1 3.7E-10 8.1E-15 81.2 6.2 54 265-318 1-55 (69)
89 TIGR02696 pppGpp_PNP guanosine 99.1 2.3E-10 5.1E-15 115.8 6.9 120 43-168 587-718 (719)
90 PRK11824 polynucleotide phosph 99.1 8.7E-10 1.9E-14 113.3 11.2 113 58-172 574-692 (693)
91 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 1.1E-09 2.5E-14 79.5 8.5 65 188-252 1-70 (70)
92 cd04455 S1_NusA S1_NusA: N-uti 99.0 1.4E-09 3.1E-14 78.5 8.8 64 98-169 2-67 (67)
93 cd05693 S1_Rrp5_repeat_hs1_sc1 99.0 5.9E-10 1.3E-14 87.0 7.0 71 186-256 2-99 (100)
94 PRK09202 nusA transcription el 99.0 7E-09 1.5E-13 101.6 15.5 117 36-175 86-204 (470)
95 cd05691 S1_RPS1_repeat_ec6 S1_ 99.0 1.6E-09 3.4E-14 79.2 8.2 67 188-254 1-72 (73)
96 cd05708 S1_Rrp5_repeat_sc12 S1 99.0 2.1E-09 4.5E-14 79.3 8.8 68 187-254 2-75 (77)
97 cd05684 S1_DHX8_helicase S1_DH 99.0 7.8E-10 1.7E-14 82.4 6.5 54 265-318 1-59 (79)
98 cd05685 S1_Tex S1_Tex: The C-t 99.0 5.8E-10 1.3E-14 80.0 5.5 54 265-318 1-55 (68)
99 cd05688 S1_RPS1_repeat_ec3 S1_ 99.0 1.2E-09 2.5E-14 78.5 6.3 55 264-318 1-55 (68)
100 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 2.9E-09 6.2E-14 77.5 8.2 63 100-163 1-65 (70)
101 cd00164 S1_like S1_like: Ribos 99.0 2E-09 4.3E-14 76.0 7.1 65 103-168 1-65 (65)
102 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 1.3E-09 2.8E-14 79.4 6.3 54 265-318 1-57 (70)
103 cd04472 S1_PNPase S1_PNPase: P 99.0 1.8E-09 3.9E-14 77.6 6.4 54 265-318 1-55 (68)
104 PHA02945 interferon resistance 99.0 3.3E-09 7.3E-14 79.0 7.7 69 185-255 9-85 (88)
105 PRK08059 general stress protei 98.9 2E-09 4.3E-14 87.3 6.2 59 260-318 3-62 (123)
106 TIGR02696 pppGpp_PNP guanosine 98.9 4.4E-09 9.5E-14 106.7 8.9 58 261-318 644-706 (719)
107 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.9 7.4E-09 1.6E-13 74.9 7.6 63 188-252 1-72 (72)
108 smart00316 S1 Ribosomal protei 98.9 1.4E-08 3.1E-13 72.9 8.6 66 187-252 2-72 (72)
109 TIGR01953 NusA transcription t 98.9 8.1E-08 1.8E-12 90.6 15.7 116 36-175 83-202 (341)
110 cd04471 S1_RNase_R S1_RNase_R: 98.8 2.6E-08 5.7E-13 74.5 9.5 70 99-169 1-82 (83)
111 TIGR01953 NusA transcription t 98.8 1.2E-08 2.6E-13 96.2 9.1 105 145-254 84-199 (341)
112 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.8 5.5E-09 1.2E-13 79.1 5.6 57 262-318 4-65 (86)
113 cd04473 S1_RecJ_like S1_RecJ_l 98.8 4.8E-08 1E-12 72.5 10.2 64 96-169 13-76 (77)
114 PRK12327 nusA transcription el 98.8 1.8E-07 3.8E-12 88.9 15.1 117 36-175 86-204 (362)
115 PLN00207 polyribonucleotide nu 98.8 2.5E-08 5.3E-13 103.4 9.6 100 162-262 724-833 (891)
116 cd04471 S1_RNase_R S1_RNase_R: 98.8 2.2E-08 4.7E-13 74.9 6.9 55 264-318 1-68 (83)
117 cd04455 S1_NusA S1_NusA: N-uti 98.8 5.1E-08 1.1E-12 70.4 8.4 63 187-251 3-67 (67)
118 PRK09521 exosome complex RNA-b 98.8 1.9E-08 4.1E-13 87.6 7.1 79 237-318 40-129 (189)
119 TIGR03591 polynuc_phos polyrib 98.7 2.4E-08 5.2E-13 102.6 8.2 107 58-166 571-683 (684)
120 COG1093 SUI2 Translation initi 98.7 2.2E-08 4.7E-13 89.1 6.4 71 185-255 9-86 (269)
121 cd04473 S1_RecJ_like S1_RecJ_l 98.7 4.7E-08 1E-12 72.6 7.0 51 260-318 12-63 (77)
122 PRK09521 exosome complex RNA-b 98.7 4.3E-08 9.3E-13 85.4 7.8 80 89-172 54-143 (189)
123 cd04454 S1_Rrp4_like S1_Rrp4_l 98.7 7.7E-08 1.7E-12 72.2 8.0 67 186-253 5-76 (82)
124 COG2183 Tex Transcriptional ac 98.7 1.4E-08 3.1E-13 102.6 4.4 59 260-318 654-713 (780)
125 PRK04163 exosome complex RNA-b 98.7 1.3E-07 2.8E-12 85.1 10.1 75 96-172 60-138 (235)
126 PRK12327 nusA transcription el 98.7 4.7E-08 1E-12 92.7 7.6 106 145-254 87-201 (362)
127 PRK11824 polynucleotide phosph 98.7 4.5E-08 9.7E-13 100.8 7.7 59 260-318 617-676 (693)
128 COG1185 Pnp Polyribonucleotide 98.6 2.4E-08 5.1E-13 99.6 4.9 123 44-172 562-690 (692)
129 PRK03987 translation initiatio 98.6 1E-07 2.2E-12 86.9 8.5 70 185-254 6-82 (262)
130 cd00164 S1_like S1_like: Ribos 98.6 5.7E-08 1.2E-12 68.4 5.1 51 268-318 1-52 (65)
131 TIGR03591 polynuc_phos polyrib 98.6 1.2E-07 2.5E-12 97.5 8.8 59 260-318 614-673 (684)
132 COG1185 Pnp Polyribonucleotide 98.5 1.8E-07 3.8E-12 93.5 7.7 80 238-318 585-674 (692)
133 cd04460 S1_RpoE S1_RpoE: RpoE, 98.5 5.5E-07 1.2E-11 70.0 8.7 78 101-181 1-94 (99)
134 KOG1067 Predicted RNA-binding 98.4 4.1E-07 8.8E-12 88.5 6.4 78 95-174 664-741 (760)
135 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.4 1.4E-06 3.1E-11 63.1 7.1 69 100-170 1-72 (72)
136 cd04460 S1_RpoE S1_RpoE: RpoE, 98.4 1E-06 2.3E-11 68.5 6.4 53 266-318 1-64 (99)
137 KOG1067 Predicted RNA-binding 98.3 7E-07 1.5E-11 86.9 5.9 58 260-317 664-722 (760)
138 PF13509 S1_2: S1 domain; PDB: 98.3 3.4E-06 7.3E-11 59.7 7.7 61 99-170 1-61 (61)
139 PRK12328 nusA transcription el 98.3 1.7E-05 3.7E-10 75.2 14.7 116 36-175 90-210 (374)
140 PRK04163 exosome complex RNA-b 98.3 1E-06 2.2E-11 79.3 5.9 58 261-318 60-122 (235)
141 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.3 3.7E-06 8E-11 64.6 7.9 74 97-172 4-87 (92)
142 TIGR00448 rpoE DNA-directed RN 98.3 5.6E-06 1.2E-10 71.5 9.7 77 96-174 78-170 (179)
143 PHA02858 EIF2a-like PKR inhibi 98.2 5.1E-06 1.1E-10 61.4 7.0 70 97-169 14-85 (86)
144 TIGR00448 rpoE DNA-directed RN 98.2 9.1E-06 2E-10 70.2 8.6 68 187-254 81-168 (179)
145 TIGR02063 RNase_R ribonuclease 98.2 1.4E-05 3E-10 83.1 11.4 73 96-169 624-708 (709)
146 COG1095 RPB7 DNA-directed RNA 98.1 1.2E-05 2.5E-10 68.6 8.0 85 96-181 78-178 (183)
147 COG1095 RPB7 DNA-directed RNA 98.1 4.5E-06 9.8E-11 71.1 5.1 55 264-318 81-146 (183)
148 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.1 8.2E-06 1.8E-10 62.6 5.4 56 263-318 5-71 (92)
149 PRK12329 nusA transcription el 98.0 0.00019 4.1E-09 69.3 14.8 79 87-174 142-228 (449)
150 PRK08563 DNA-directed RNA poly 98.0 9.1E-05 2E-09 64.3 11.1 77 96-174 78-170 (187)
151 PRK12328 nusA transcription el 97.9 9.8E-05 2.1E-09 70.1 11.4 103 145-254 91-207 (374)
152 TIGR02063 RNase_R ribonuclease 97.9 1.9E-05 4.1E-10 82.1 7.1 58 261-318 624-694 (709)
153 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.9 9.4E-05 2E-09 55.9 9.0 74 96-172 3-76 (86)
154 PRK11642 exoribonuclease R; Pr 97.9 9.1E-05 2E-09 77.7 11.0 73 98-171 642-726 (813)
155 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.9 5.3E-05 1.1E-09 57.7 6.8 55 264-318 1-66 (88)
156 PRK11642 exoribonuclease R; Pr 97.9 7E-05 1.5E-09 78.6 10.0 67 186-252 642-725 (813)
157 KOG2916 Translation initiation 97.9 1.6E-05 3.6E-10 70.8 4.5 79 96-175 13-93 (304)
158 PRK08563 DNA-directed RNA poly 97.9 3.7E-05 8E-10 66.8 6.7 55 264-318 81-146 (187)
159 TIGR00358 3_prime_RNase VacB a 97.8 0.00014 3E-09 74.9 11.1 72 97-169 570-653 (654)
160 TIGR00757 RNaseEG ribonuclease 97.7 4.7E-05 1E-09 73.9 5.7 59 260-318 21-94 (414)
161 TIGR00757 RNaseEG ribonuclease 97.7 0.00014 3.1E-09 70.6 8.0 61 96-157 22-96 (414)
162 TIGR00358 3_prime_RNase VacB a 97.6 0.0002 4.3E-09 73.8 9.1 66 186-251 571-653 (654)
163 KOG1856 Transcription elongati 97.6 0.00018 3.9E-09 75.5 8.5 95 79-174 964-1062(1299)
164 PHA02858 EIF2a-like PKR inhibi 97.6 0.00022 4.8E-09 52.8 6.3 65 186-251 15-85 (86)
165 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.6 0.00065 1.4E-08 51.6 8.9 64 99-163 1-74 (88)
166 COG1097 RRP4 RNA-binding prote 97.5 0.00064 1.4E-08 60.4 9.7 75 96-172 61-139 (239)
167 PRK12329 nusA transcription el 97.4 0.00078 1.7E-08 65.1 8.4 66 186-254 151-226 (449)
168 PTZ00162 DNA-directed RNA poly 97.3 0.0015 3.2E-08 56.3 8.8 77 96-173 78-167 (176)
169 PTZ00162 DNA-directed RNA poly 97.2 0.00075 1.6E-08 58.0 6.1 55 264-318 81-147 (176)
170 PF13509 S1_2: S1 domain; PDB: 97.1 0.0012 2.5E-08 46.6 5.3 47 264-318 1-48 (61)
171 PF10447 EXOSC1: Exosome compo 97.1 0.00084 1.8E-08 50.2 4.2 56 263-318 3-79 (82)
172 PRK05054 exoribonuclease II; P 96.9 0.0045 9.7E-08 63.7 9.8 63 188-250 562-642 (644)
173 COG1096 Predicted RNA-binding 96.9 0.0028 6E-08 54.3 6.6 73 245-318 46-129 (188)
174 COG1096 Predicted RNA-binding 96.9 0.0057 1.2E-07 52.4 8.1 74 96-173 61-144 (188)
175 PF10447 EXOSC1: Exosome compo 96.7 0.0057 1.2E-07 45.8 6.5 61 97-158 2-82 (82)
176 PRK10811 rne ribonuclease E; R 96.6 0.0053 1.1E-07 64.4 7.6 59 98-157 37-106 (1068)
177 COG1107 Archaea-specific RecJ- 96.5 0.021 4.5E-07 56.8 10.3 145 95-249 118-280 (715)
178 PRK11712 ribonuclease G; Provi 96.4 0.0088 1.9E-07 59.3 7.5 61 96-157 35-109 (489)
179 PF10246 MRP-S35: Mitochondria 96.4 0.027 5.8E-07 43.5 8.2 67 84-158 5-74 (104)
180 PRK05054 exoribonuclease II; P 96.4 0.022 4.8E-07 58.7 10.3 72 98-169 558-643 (644)
181 COG1107 Archaea-specific RecJ- 96.3 0.0026 5.6E-08 63.0 2.6 54 259-318 117-171 (715)
182 COG1097 RRP4 RNA-binding prote 96.2 0.01 2.3E-07 52.8 5.7 57 262-318 62-123 (239)
183 KOG1856 Transcription elongati 96.2 0.0079 1.7E-07 63.7 5.7 59 260-318 981-1043(1299)
184 TIGR02062 RNase_B exoribonucle 96.1 0.027 5.8E-07 58.0 9.2 63 188-250 558-638 (639)
185 PRK11712 ribonuclease G; Provi 96.1 0.0087 1.9E-07 59.4 5.3 58 261-318 35-107 (489)
186 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.1 0.02 4.2E-07 43.3 6.0 55 263-318 5-60 (86)
187 PRK10811 rne ribonuclease E; R 96.1 0.0097 2.1E-07 62.5 5.8 56 263-318 37-104 (1068)
188 KOG2916 Translation initiation 96.1 0.0067 1.4E-07 54.5 4.0 71 186-256 15-92 (304)
189 COG0557 VacB Exoribonuclease R 95.9 0.015 3.2E-07 60.7 6.1 58 261-318 619-689 (706)
190 COG0557 VacB Exoribonuclease R 95.8 0.027 5.8E-07 58.7 7.6 74 96-169 619-703 (706)
191 TIGR02062 RNase_B exoribonucle 95.7 0.1 2.3E-06 53.7 11.4 69 100-168 558-638 (639)
192 PF08292 RNA_pol_Rbc25: RNA po 94.7 0.25 5.4E-06 39.8 8.6 62 99-160 3-76 (122)
193 KOG3298 DNA-directed RNA polym 94.1 0.19 4.1E-06 42.1 6.6 55 264-318 81-146 (170)
194 PF10246 MRP-S35: Mitochondria 93.9 0.29 6.2E-06 37.9 6.8 49 263-318 22-71 (104)
195 KOG3298 DNA-directed RNA polym 93.6 0.53 1.1E-05 39.5 8.4 66 97-163 79-154 (170)
196 KOG3409 Exosomal 3'-5' exoribo 93.5 0.44 9.5E-06 40.4 7.7 72 97-170 66-147 (193)
197 PF08292 RNA_pol_Rbc25: RNA po 93.0 0.55 1.2E-05 37.9 7.5 56 187-242 3-76 (122)
198 COG1530 CafA Ribonucleases G a 92.0 0.26 5.7E-06 49.1 5.4 63 96-159 34-102 (487)
199 KOG3409 Exosomal 3'-5' exoribo 91.6 0.38 8.3E-06 40.7 5.1 55 264-318 68-133 (193)
200 KOG4078 Putative mitochondrial 91.5 2 4.4E-05 35.1 8.9 69 83-159 63-134 (173)
201 COG1530 CafA Ribonucleases G a 90.9 0.21 4.6E-06 49.8 3.5 58 260-318 33-98 (487)
202 KOG1004 Exosomal 3'-5' exoribo 86.9 3.4 7.3E-05 36.3 7.5 63 96-160 62-124 (230)
203 PRK12442 translation initiatio 86.8 3.2 7E-05 31.2 6.5 65 189-253 7-73 (87)
204 TIGR00008 infA translation ini 86.6 4.8 0.0001 29.0 7.0 60 102-166 6-66 (68)
205 PRK12442 translation initiatio 86.3 5.7 0.00012 29.9 7.5 64 102-171 8-73 (87)
206 TIGR00008 infA translation ini 85.3 5.1 0.00011 28.8 6.6 59 190-248 6-66 (68)
207 PRK15464 cold shock-like prote 85.0 8.6 0.00019 27.7 7.8 50 103-157 5-57 (70)
208 PF00313 CSD: 'Cold-shock' DNA 84.1 12 0.00026 26.1 9.3 50 103-157 1-53 (66)
209 PRK10943 cold shock-like prote 83.4 13 0.00029 26.6 8.3 51 102-157 3-56 (69)
210 PRK09937 stationary phase/star 82.9 12 0.00025 27.4 7.8 60 104-170 3-65 (74)
211 PRK09507 cspE cold shock prote 81.2 9.3 0.0002 27.4 6.8 51 102-157 3-56 (69)
212 COG4044 Uncharacterized protei 80.7 5.5 0.00012 34.9 6.2 73 95-167 71-154 (247)
213 PRK15463 cold shock-like prote 79.8 18 0.00039 26.0 7.9 50 103-157 5-57 (70)
214 PRK14998 cold shock-like prote 79.5 17 0.00037 26.4 7.8 58 104-168 3-63 (73)
215 PF03459 TOBE: TOBE domain; I 76.5 9.4 0.0002 26.3 5.6 47 101-155 5-57 (64)
216 PRK09890 cold shock protein Cs 75.9 26 0.00057 25.1 8.5 50 103-157 5-57 (70)
217 TIGR02381 cspD cold shock doma 75.4 21 0.00045 25.4 7.1 49 104-157 3-54 (68)
218 PF00313 CSD: 'Cold-shock' DNA 75.4 12 0.00027 26.0 6.0 45 268-317 1-50 (66)
219 PRK10354 RNA chaperone/anti-te 74.3 29 0.00063 24.8 8.3 50 103-157 5-57 (70)
220 PF09883 DUF2110: Uncharacteri 74.3 7.2 0.00016 34.4 5.2 75 96-172 69-149 (225)
221 cd05701 S1_Rrp5_repeat_hs10 S1 74.0 6.6 0.00014 27.8 4.0 58 101-160 2-61 (69)
222 COG0361 InfA Translation initi 72.7 34 0.00074 25.1 7.6 66 100-170 6-72 (75)
223 cd04322 LysRS_N LysRS_N: N-ter 72.0 11 0.00025 29.1 5.6 51 267-317 3-59 (108)
224 PF01330 RuvA_N: RuvA N termin 72.0 19 0.00041 24.9 6.1 51 102-162 4-55 (61)
225 cd05700 S1_Rrp5_repeat_hs9 S1_ 71.3 21 0.00045 25.0 5.9 63 100-168 1-64 (65)
226 KOG1999 RNA polymerase II tran 70.1 1.7E+02 0.0036 31.8 15.8 26 42-73 169-194 (1024)
227 TIGR00084 ruvA Holliday juncti 68.6 40 0.00087 29.3 8.7 70 102-181 4-74 (191)
228 TIGR00638 Mop molybdenum-pteri 68.6 5.3 0.00012 28.0 2.8 51 266-318 7-59 (69)
229 PRK14603 ruvA Holliday junctio 66.3 46 0.001 29.0 8.7 70 102-181 4-74 (197)
230 PF03459 TOBE: TOBE domain; I 64.6 14 0.00031 25.4 4.3 46 266-318 5-57 (64)
231 PRK14600 ruvA Holliday junctio 64.1 55 0.0012 28.3 8.6 63 102-174 4-68 (186)
232 KOG4078 Putative mitochondrial 64.0 20 0.00044 29.4 5.4 48 264-318 82-130 (173)
233 PRK14601 ruvA Holliday junctio 61.7 60 0.0013 28.0 8.4 70 102-181 4-75 (183)
234 cd04458 CSP_CDS Cold-Shock Pro 61.6 51 0.0011 22.8 7.5 49 104-157 2-53 (65)
235 PRK10676 DNA-binding transcrip 61.2 1.3E+02 0.0028 27.5 11.0 129 84-238 111-253 (263)
236 PRK15464 cold shock-like prote 60.2 32 0.00069 24.8 5.5 48 191-239 5-57 (70)
237 PRK13901 ruvA Holliday junctio 60.1 73 0.0016 27.9 8.7 70 102-181 4-74 (196)
238 PRK14604 ruvA Holliday junctio 59.0 76 0.0017 27.6 8.7 71 102-181 4-75 (195)
239 PF08206 OB_RNB: Ribonuclease 58.4 29 0.00063 23.8 4.8 43 105-157 1-44 (58)
240 PRK14605 ruvA Holliday junctio 58.1 83 0.0018 27.4 8.8 71 102-181 4-75 (194)
241 COG1278 CspC Cold shock protei 58.0 54 0.0012 23.5 6.2 49 104-157 3-54 (67)
242 KOG3297 DNA-directed RNA polym 57.6 25 0.00054 30.3 5.1 62 97-158 79-156 (202)
243 KOG3013 Exosomal 3'-5' exoribo 57.5 19 0.00042 32.7 4.7 78 90-171 78-165 (301)
244 PF01938 TRAM: TRAM domain; I 56.3 52 0.0011 22.4 5.9 55 227-283 2-59 (61)
245 KOG1004 Exosomal 3'-5' exoribo 56.0 47 0.001 29.3 6.7 57 186-242 64-124 (230)
246 PRK10943 cold shock-like prote 55.9 55 0.0012 23.3 6.1 49 190-239 3-56 (69)
247 PRK04012 translation initiatio 54.3 1E+02 0.0022 23.9 8.0 67 99-171 19-86 (100)
248 PRK09507 cspE cold shock prote 53.7 66 0.0014 22.9 6.2 49 190-239 3-56 (69)
249 PRK14606 ruvA Holliday junctio 52.9 85 0.0018 27.2 7.9 70 102-181 4-75 (188)
250 cd05793 S1_IF1A S1_IF1A: Trans 52.1 92 0.002 22.8 7.0 60 103-170 2-64 (77)
251 COG0361 InfA Translation initi 49.9 91 0.002 22.9 6.4 59 190-251 8-71 (75)
252 PF08206 OB_RNB: Ribonuclease 49.1 51 0.0011 22.5 4.9 42 193-239 1-44 (58)
253 PRK15463 cold shock-like prote 48.8 70 0.0015 22.9 5.7 48 191-239 5-57 (70)
254 COG0195 NusA Transcription elo 46.1 57 0.0012 28.4 5.8 48 123-177 2-50 (190)
255 PF07076 DUF1344: Protein of u 45.9 1E+02 0.0022 21.6 6.8 45 102-155 4-48 (61)
256 cd05700 S1_Rrp5_repeat_hs9 S1_ 45.8 75 0.0016 22.3 5.1 61 188-250 1-64 (65)
257 PF01330 RuvA_N: RuvA N termin 45.0 58 0.0012 22.4 4.7 31 190-220 4-36 (61)
258 PF09883 DUF2110: Uncharacteri 44.7 51 0.0011 29.2 5.2 92 161-253 39-148 (225)
259 cd05701 S1_Rrp5_repeat_hs10 S1 43.2 43 0.00094 23.8 3.6 53 191-243 4-62 (69)
260 COG4148 ModC ABC-type molybdat 43.0 2.9E+02 0.0063 26.0 10.4 114 98-240 230-348 (352)
261 PF09953 DUF2187: Uncharacteri 42.9 54 0.0012 22.7 4.0 19 103-121 16-34 (57)
262 PRK10676 DNA-binding transcrip 42.8 61 0.0013 29.6 5.7 110 189-318 128-252 (263)
263 PRK09937 stationary phase/star 42.6 96 0.0021 22.5 5.7 48 192-240 3-55 (74)
264 KOG3297 DNA-directed RNA polym 41.8 49 0.0011 28.6 4.5 54 187-240 81-156 (202)
265 COG4044 Uncharacterized protei 40.6 29 0.00062 30.6 3.0 45 260-304 71-122 (247)
266 COG4776 Rnb Exoribonuclease II 39.6 8.8 0.00019 37.7 -0.3 62 187-248 561-640 (645)
267 PRK09838 periplasmic copper-bi 39.5 1.8E+02 0.0039 23.1 7.2 68 101-171 43-113 (115)
268 TIGR00638 Mop molybdenum-pteri 39.3 34 0.00073 23.7 2.8 48 100-155 6-59 (69)
269 PRK14602 ruvA Holliday junctio 38.3 1.9E+02 0.0041 25.3 7.9 70 102-180 4-75 (203)
270 COG1545 Predicted nucleic-acid 36.9 1.9E+02 0.0041 23.7 7.3 57 98-162 62-127 (140)
271 PRK14998 cold shock-like prote 36.6 1.3E+02 0.0028 21.7 5.6 48 192-240 3-55 (73)
272 cd04320 AspRS_cyto_N AspRS_cyt 36.1 1.1E+02 0.0025 23.1 5.6 49 267-316 3-60 (102)
273 PRK00116 ruvA Holliday junctio 36.0 1.5E+02 0.0032 25.7 6.8 60 102-171 4-65 (192)
274 cd04319 PhAsnRS_like_N PhAsnRS 35.8 1.2E+02 0.0025 23.1 5.6 48 267-316 3-56 (103)
275 PRK09890 cold shock protein Cs 35.5 1.6E+02 0.0035 20.9 6.3 48 191-239 5-57 (70)
276 TIGR00739 yajC preprotein tran 35.2 1.9E+02 0.0041 21.5 7.2 30 96-125 37-72 (84)
277 cd04323 AsnRS_cyto_like_N AsnR 35.1 1.4E+02 0.0031 21.6 5.8 48 267-317 3-56 (84)
278 PF01176 eIF-1a: Translation i 35.0 86 0.0019 22.0 4.3 56 102-165 4-62 (65)
279 COG1862 YajC Preprotein transl 34.9 2.1E+02 0.0046 22.0 6.8 37 96-132 43-85 (97)
280 COG2106 Uncharacterized conser 34.9 1E+02 0.0022 28.4 5.7 49 96-158 102-150 (272)
281 CHL00010 infA translation init 34.7 1.8E+02 0.0039 21.2 6.5 62 190-251 8-71 (78)
282 PTZ00329 eukaryotic translatio 33.7 2.4E+02 0.0053 23.7 7.4 69 98-173 30-99 (155)
283 PF11813 DUF3334: Protein of u 33.0 30 0.00066 30.4 2.0 18 277-294 49-67 (229)
284 smart00357 CSP Cold shock prot 32.9 1.5E+02 0.0032 19.6 7.2 48 105-158 2-50 (64)
285 PF11213 DUF3006: Protein of u 32.6 1.8E+02 0.004 20.7 7.1 40 105-153 2-42 (71)
286 PF14604 SH3_9: Variant SH3 do 32.3 81 0.0017 20.6 3.6 34 96-131 14-47 (49)
287 KOG4134 DNA-dependent RNA poly 32.0 38 0.00082 30.2 2.4 58 95-160 103-162 (253)
288 COG0298 HypC Hydrogenase matur 32.0 1.7E+02 0.0037 21.7 5.4 43 103-155 5-49 (82)
289 cd04318 EcAsnRS_like_N EcAsnRS 31.5 2E+02 0.0043 20.7 6.0 47 267-317 3-57 (82)
290 COG2106 Uncharacterized conser 31.4 84 0.0018 28.9 4.6 46 260-318 101-147 (272)
291 PRK05886 yajC preprotein trans 31.1 2.6E+02 0.0057 22.0 7.6 37 96-132 38-80 (109)
292 PLN00208 translation initiatio 31.0 3.1E+02 0.0067 22.8 7.5 65 98-171 30-97 (145)
293 smart00652 eIF1a eukaryotic tr 30.5 2.3E+02 0.0049 21.0 6.3 63 99-170 4-69 (83)
294 cd04316 ND_PkAspRS_like_N ND_P 30.1 1.6E+02 0.0034 22.6 5.5 50 266-316 15-70 (108)
295 PF10844 DUF2577: Protein of u 30.0 1.5E+02 0.0032 22.7 5.3 25 260-286 12-36 (100)
296 COG3269 Predicted RNA-binding 28.5 2.4E+02 0.0051 20.6 6.5 48 185-242 13-61 (73)
297 PF12857 TOBE_3: TOBE-like dom 27.3 85 0.0018 21.3 3.1 49 266-317 5-56 (58)
298 TIGR00074 hypC_hupF hydrogenas 27.0 2.1E+02 0.0045 20.9 5.3 40 268-316 5-44 (76)
299 TIGR02760 TraI_TIGR conjugativ 26.7 6.6E+02 0.014 30.0 11.8 142 51-218 633-796 (1960)
300 PRK00276 infA translation init 26.0 2.5E+02 0.0054 20.0 7.2 61 189-249 7-69 (72)
301 PRK00484 lysS lysyl-tRNA synth 25.7 1.4E+02 0.0031 29.8 5.7 51 266-317 57-113 (491)
302 PF07653 SH3_2: Variant SH3 do 25.5 1.9E+02 0.004 19.1 4.6 35 261-296 17-52 (55)
303 cd04317 EcAspRS_like_N EcAspRS 25.4 1.4E+02 0.0031 23.9 4.7 48 266-316 17-70 (135)
304 PRK14605 ruvA Holliday junctio 24.8 2.1E+02 0.0045 24.9 5.8 47 190-240 4-52 (194)
305 PRK13605 endoribonuclease SymE 24.4 1.5E+02 0.0032 23.5 4.3 49 127-183 37-87 (113)
306 PRK14604 ruvA Holliday junctio 24.3 2.1E+02 0.0045 24.9 5.8 47 190-240 4-52 (195)
307 cd04100 Asp_Lys_Asn_RS_N Asp_L 23.9 1.7E+02 0.0037 21.2 4.5 48 267-316 3-56 (85)
308 PRK04950 ProP expression regul 23.6 82 0.0018 27.9 3.0 31 189-219 180-211 (213)
309 cd04456 S1_IF1A_like S1_IF1A_l 23.5 3E+02 0.0066 20.1 6.9 64 103-172 2-67 (78)
310 COG0632 RuvA Holliday junction 23.4 2.6E+02 0.0057 24.5 6.2 54 102-164 4-58 (201)
311 COG3109 ProQ Activator of osmo 23.3 97 0.0021 26.5 3.2 30 190-219 176-206 (208)
312 TIGR00458 aspS_arch aspartyl-t 23.1 1.7E+02 0.0038 28.7 5.6 51 266-317 15-71 (428)
313 cd04486 YhcR_OBF_like YhcR_OBF 23.0 1.5E+02 0.0033 21.5 4.0 42 268-317 2-54 (78)
314 COG4148 ModC ABC-type molybdat 22.6 6.6E+02 0.014 23.7 10.1 132 161-318 203-345 (352)
315 PF04270 Strep_his_triad: Stre 22.4 1.8E+02 0.0039 19.8 3.8 28 195-222 14-41 (53)
316 PRK00276 infA translation init 22.3 3E+02 0.0064 19.6 8.0 59 102-167 8-69 (72)
317 COG0307 RibC Riboflavin syntha 22.3 5.4E+02 0.012 22.6 10.6 131 96-242 32-183 (204)
318 PRK10334 mechanosensitive chan 22.2 2.3E+02 0.005 26.2 5.9 48 94-141 127-179 (286)
319 TIGR00499 lysS_bact lysyl-tRNA 22.1 1.9E+02 0.004 29.1 5.6 52 266-317 56-113 (496)
320 PRK01712 carbon storage regula 21.9 2.5E+02 0.0055 19.9 4.7 32 140-174 8-39 (64)
321 cd01716 Hfq Hfq, an abundant, 21.6 2.5E+02 0.0054 19.7 4.5 36 262-297 18-53 (61)
322 TIGR00084 ruvA Holliday juncti 21.5 2.7E+02 0.0058 24.1 5.9 46 190-240 4-51 (191)
323 KOG3754 Gamma-glutamylcysteine 21.4 1.3E+02 0.0029 29.8 4.2 30 145-174 45-74 (640)
324 PRK05585 yajC preprotein trans 21.4 4E+02 0.0086 20.7 6.8 34 96-129 52-91 (106)
325 PRK14600 ruvA Holliday junctio 21.3 2.4E+02 0.0053 24.3 5.5 45 190-239 4-50 (186)
326 PRK05585 yajC preprotein trans 20.7 3.6E+02 0.0077 21.0 5.8 40 258-297 49-95 (106)
327 PRK04012 translation initiatio 20.6 4.1E+02 0.0088 20.5 6.6 63 189-252 21-85 (100)
328 PRK00143 mnmA tRNA-specific 2- 20.2 5.4E+02 0.012 24.4 8.2 93 57-170 168-265 (346)
329 PF06347 SH3_4: Bacterial SH3 20.0 2E+02 0.0043 19.0 3.8 35 96-133 20-54 (55)
No 1
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.6e-48 Score=361.37 Aligned_cols=245 Identities=47% Similarity=0.855 Sum_probs=229.5
Q ss_pred cCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEE
Q 021034 73 TAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEE 152 (318)
Q Consensus 73 ~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~ 152 (318)
+.++....|++++|+++|++|+..++.|++++|+|+++.++|++|+++++.+||||.+|+++.++.++.++ +++|++++
T Consensus 5 ~~~~~~~~~~~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~-~~~G~~v~ 83 (318)
T PRK07400 5 NTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETRE 83 (318)
T ss_pred cCcccccCCCHHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHc-cCCCCEEE
Confidence 44567789999999999999876799999999999999999999999999999999999999999999888 99999999
Q ss_pred EEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCe
Q 021034 153 FVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKD 232 (318)
Q Consensus 153 v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~ 232 (318)
|+|++++++++++.||+|+......|+.+.++++.|.+|+|+|++++++|++|+++|++||||.||+++....+.++|+.
T Consensus 84 ~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~~~~vG~~ 163 (318)
T PRK07400 84 FFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEE 163 (318)
T ss_pred EEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCccccCCCE
Confidence 99999999999999999998777899999999989999999999999999999999999999999999864434469999
Q ss_pred EeEEEEEEecccCeEeeehhhhhhh-hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034 233 LPLKFVEVDEEQSRLVLSNRKAMAD-SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 233 v~~kVl~vd~~~~~i~lS~K~~l~~-~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
++|+|+++|++++++.||+|+++.+ .+.++++|+++.|+|++|++||+||+++|+.||+|+++++|++..++.+.|++|
T Consensus 164 i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vG 243 (318)
T PRK07400 164 LPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVN 243 (318)
T ss_pred EEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCC
Confidence 9999999999999999999988765 467899999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|.|+|+|
T Consensus 244 d~VkvkV 250 (318)
T PRK07400 244 DEMKVMI 250 (318)
T ss_pred CEEEEEE
Confidence 9999986
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-45 Score=357.79 Aligned_cols=282 Identities=25% Similarity=0.386 Sum_probs=243.8
Q ss_pred ccccccccCCCcc-cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034 6 QQFTGLRCPPISH-TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE 84 (318)
Q Consensus 6 ~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~ 84 (318)
+++.|| .|-.|+ +|-.... ....|......++-.+.. |.++-..=..+++.-..
T Consensus 126 ~gvr~F-lP~S~v~~r~v~d~----------~~~~Gk~~~~kiie~d~~---~n~vv~SrR~~~e~~~~----------- 180 (541)
T COG0539 126 EGVRAF-LPGSLVDVRPVRDL----------DPLIGKELEFKILELDKK---RNNVVLSRRAVLEEERS----------- 180 (541)
T ss_pred CCEEEe-ccHHHhcccccccc----------cccCCceEEEEEEEEccc---cCcEEEEhHHHhhHHHH-----------
Confidence 368899 888888 6555443 456899999999999766 44433222223221111
Q ss_pred HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034 85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
+.-.....++++|++++|+|.+++++||||++++ ++|+||++||||.++.+|++. +++||+|+|+|+++|.+++|
T Consensus 181 ---~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~v-vkvGd~VkvkVi~~D~e~~R 255 (541)
T COG0539 181 ---EQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEV-VKVGDEVKVKVISLDEERGR 255 (541)
T ss_pred ---HHHHHHHhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHh-cccCCEEEEEEEEEccCCCe
Confidence 1122222377899999999999999999999997 999999999999999999999 99999999999999999999
Q ss_pred EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC--Ccchh--cCCeEeEEEEE
Q 021034 165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVE 239 (318)
Q Consensus 165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~--~~~~~--vGq~v~~kVl~ 239 (318)
+.||+|+... .+|+.+.+.+++|+.+.|+|+++.++|+||++. |+.||+|.|+++|.+ .|+++ +||+|.|+|++
T Consensus 256 VsLSlK~l~~-dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~ 334 (541)
T COG0539 256 VSLSLKQLEE-DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLD 334 (541)
T ss_pred EEEEehhccc-CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEe
Confidence 9999999987 599999999999999999999999999999997 999999999999973 36776 69999999999
Q ss_pred EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEE
Q 021034 240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTL 314 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V 314 (318)
+|++++||+||+|++..++| ..+++|+.++|.|.++|++|+||.++ |++||+|.++++|.....+...|++|+.+
T Consensus 335 id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v 414 (541)
T COG0539 335 IDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEV 414 (541)
T ss_pred eCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEE
Confidence 99999999999999987764 45889999999999999999999999 79999999999999988888899999999
Q ss_pred EEEC
Q 021034 315 KVCL 318 (318)
Q Consensus 315 ~v~V 318 (318)
+++|
T Consensus 415 ~~~v 418 (541)
T COG0539 415 EAKV 418 (541)
T ss_pred EEEE
Confidence 9975
No 3
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-44 Score=350.75 Aligned_cols=272 Identities=26% Similarity=0.393 Sum_probs=250.1
Q ss_pred cccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034 7 QFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE 84 (318)
Q Consensus 7 ~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~ 84 (318)
++.|| +|..|| .|+.||++ -|++|++|+++|+.+|.. |+++-..||++..
T Consensus 214 GvdGL-lHiseiS~~rv~~P~~---------vvkvGd~VkvkVi~~D~e---~~RVsLSlK~l~~--------------- 265 (541)
T COG0539 214 GVDGL-LHISEISWKRVDHPSE---------VVKVGDEVKVKVISLDEE---RGRVSLSLKQLEE--------------- 265 (541)
T ss_pred CeeeE-EehhhccccccCCHHH---------hcccCCEEEEEEEEEccC---CCeEEEEehhccc---------------
Confidence 79999 999999 99999999 999999999999999988 8888888887652
Q ss_pred HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034 85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
..|+.....+.+|+.+.|+|+++.++||||+++.+++||+|+|||||.+...|+++ +++||+|+|+|+++|++++|
T Consensus 266 ---dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~ev-v~~Gq~V~V~Vl~id~e~rR 341 (541)
T COG0539 266 ---DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEV-VKVGQEVEVKVLDIDPERRR 341 (541)
T ss_pred ---CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHh-cccCCEEEEEEEeeCchhce
Confidence 36776666778999999999999999999999999999999999999998889999 99999999999999999999
Q ss_pred EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCC---cchh-cCCeEeEEEEE
Q 021034 165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKST---AEEL-LGKDLPLKFVE 239 (318)
Q Consensus 165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~---~~~~-vGq~v~~kVl~ 239 (318)
+.||||++.. ++|+.+.+.++.|..++|+|++++++|+||.++ |++||+|.++++|... ...| .|++++++|+.
T Consensus 342 IsL~iKq~~~-~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~ 420 (541)
T COG0539 342 ISLGLKQLKE-NPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLA 420 (541)
T ss_pred EEeeehhhhc-ChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEE
Confidence 9999999987 599999999999999999999999999999998 6999999999998732 2345 79999999999
Q ss_pred EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEE
Q 021034 240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTL 314 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V 314 (318)
+|++++++.|+.|+...+++ ..++.|++++|+|+++.++|+||+++ ++.||++.++++.+ .|++||.|
T Consensus 421 vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~~i~~~G~~v~l~~~v~G~i~~~~~~~~-------~~~~gd~v 493 (541)
T COG0539 421 VDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRD-------VLKVGDEV 493 (541)
T ss_pred EecccceeeeehhhhccCchhhhHhhccCCCeEEEEEEEEccCceEEEecCceeeeeecchhhhh-------hccCCCEE
Confidence 99999999999999876553 56899999999999999999999999 89999999999976 79999999
Q ss_pred EEEC
Q 021034 315 KVCL 318 (318)
Q Consensus 315 ~v~V 318 (318)
+|+|
T Consensus 494 ~a~v 497 (541)
T COG0539 494 EAVV 497 (541)
T ss_pred EEEE
Confidence 9985
No 4
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=6e-43 Score=341.03 Aligned_cols=235 Identities=31% Similarity=0.543 Sum_probs=217.9
Q ss_pred CHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034 82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA 161 (318)
Q Consensus 82 s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~ 161 (318)
|.++|.++++++...++.|++|+|+|+++.++|++|+++++.+|+||.+|+++....+|++. +++|+.++|+|++++++
T Consensus 18 ~~e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~-~~vGd~Ie~~V~~~~~~ 96 (486)
T PRK07899 18 SAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEV-VEVGDEVEALVLQKEDK 96 (486)
T ss_pred CHHHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhc-CCCCCEEEEEEEEEECC
Confidence 66788888877666799999999999999999999999989999999999999888888887 99999999999999999
Q ss_pred CCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEE
Q 021034 162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE 239 (318)
Q Consensus 162 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~ 239 (318)
++++.||+|++.....|+.++++++.|++++|+|+++.++|++|++ |++||||.|++++. .+++.++||+|+|+|++
T Consensus 97 ~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~~~~~~~vGq~V~vkVle 175 (486)
T PRK07899 97 EGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIE 175 (486)
T ss_pred CCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhcccccCChhhcCCCEEEEEEEE
Confidence 9999999999987789999999998999999999999999999999 79999999999976 45667899999999999
Q ss_pred EecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034 240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
+|++++++.||+|..+.+ ....+++|+++.|+|+++++||+||+++|+.||||.|+++|.++.+|.+.|++|
T Consensus 176 id~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvG 255 (486)
T PRK07899 176 LDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVG 255 (486)
T ss_pred EECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCC
Confidence 999999999999976542 246899999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|.|+|+|
T Consensus 256 d~V~vkV 262 (486)
T PRK07899 256 QEVTVEV 262 (486)
T ss_pred CEEEEEE
Confidence 9999986
No 5
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=1.3e-43 Score=349.35 Aligned_cols=282 Identities=23% Similarity=0.343 Sum_probs=240.9
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
++..|| +|-.|+ -.+.+|+ .+ .|.++.|+|+.+++. ++++-...+.+++.-.
T Consensus 136 ~g~~~f-lP~s~~~~~~~~~~~----------~~-vG~~i~~~V~~id~~---~~~v~lSrk~~~~~~~----------- 189 (491)
T PRK13806 136 LGRRAF-CPVSQIDLRYVEDPE----------SY-VGQTFQFLITRVEEN---GRNIVVSRRALLEREQ----------- 189 (491)
T ss_pred CCEEEE-EEHHHhccccCCChH----------Hc-CCCeEEEEEEEEECC---CCeEEEEeehhhhhhh-----------
Confidence 367888 888876 2244454 33 899999999999866 4444444333332211
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC-
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD- 162 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~- 162 (318)
.+.|+.+..++++|++++|+|+++.++|+||+++++.+||+|.+|+++.+..++.+. |++||.++|+|+++|.++
T Consensus 190 ---~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~-~~vGd~i~vkVl~id~~~~ 265 (491)
T PRK13806 190 ---KEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA-VSVGDTVRVKVLGIERAKK 265 (491)
T ss_pred ---HHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh-cCCCCEEEEEEEEEecccC
Confidence 245555555688999999999999999999999878999999999999999999888 999999999999999876
Q ss_pred ---CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcchh--cCCeE
Q 021034 163 ---DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDL 233 (318)
Q Consensus 163 ---~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~~--vGq~v 233 (318)
+++.||+|++.. .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.+++++. .++.++ +||.|
T Consensus 266 ~~~~ri~lS~K~~~~-~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v 344 (491)
T PRK13806 266 GKGLRISLSIKQAGG-DPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAV 344 (491)
T ss_pred CcceEEEEEehhhhc-ccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEE
Confidence 479999999865 589999888889999999999999999999996 99999999999973 234443 79999
Q ss_pred eEEEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCccccc
Q 021034 234 PLKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVL 308 (318)
Q Consensus 234 ~~kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~ 308 (318)
+++|+++|++++++.||+|++..++| .++++|++|+|+|+++++||+||++. |+.||||+|+++|.+..++.+.|
T Consensus 345 ~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~ 424 (491)
T PRK13806 345 AVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKL 424 (491)
T ss_pred EEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcC
Confidence 99999999999999999999877664 57889999999999999999999998 99999999999999999999999
Q ss_pred CCCCEEEEEC
Q 021034 309 QPGDTLKVCL 318 (318)
Q Consensus 309 ~~Gq~V~v~V 318 (318)
++||+|+|+|
T Consensus 425 ~~Gd~v~~~V 434 (491)
T PRK13806 425 KPGDSVTLVV 434 (491)
T ss_pred CCCCEEEEEE
Confidence 9999999986
No 6
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=4.6e-43 Score=341.83 Aligned_cols=278 Identities=23% Similarity=0.330 Sum_probs=240.7
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
..+.|+ +|-.|+ .+..+|+. .|++|.+|+|.|+..++. ++++....+.+.
T Consensus 57 ~k~eG~-Ip~~Els~~~~~~~~~---------~~~vGd~Ie~~V~~~~~~---~g~liLS~k~~~--------------- 108 (486)
T PRK07899 57 YKTEGV-IPSRELSIKHDVDPNE---------VVEVGDEVEALVLQKEDK---EGRLILSKKRAQ--------------- 108 (486)
T ss_pred CCcEEE-EEHHHhcccccCChhh---------cCCCCCEEEEEEEEEECC---CCeEEEEehhhc---------------
Confidence 467899 999999 56788998 899999999999998766 445555555421
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
+...|+.++...+.|++++|+|+++.++|++|++ +.+||||.+++++.+..++.+ .+|++++|+|+++|.+++
T Consensus 109 --~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~ 181 (486)
T PRK07899 109 --YERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI--GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRN 181 (486)
T ss_pred --ccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE--CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCC
Confidence 1246776654456899999999999999999999 389999999999887777654 489999999999999999
Q ss_pred eEEEEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchh--cCCeEeEE
Q 021034 164 SLVLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK 236 (318)
Q Consensus 164 ~i~lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~--vGq~v~~k 236 (318)
++.||+|.... ...|+.+.+.++.|++++|+|+++.++|+||+++|++||||.++++|. .++.++ +||.|+|+
T Consensus 182 ~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vk 261 (486)
T PRK07899 182 NVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVE 261 (486)
T ss_pred EEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEE
Confidence 99999997543 356777777778999999999999999999999999999999999986 345554 79999999
Q ss_pred EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034 237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
|+++|+++++|.||+|+...+++ ..+++|+++.|+|+++++||+||++. |+.||+|.+++++.++.++.+.|++|
T Consensus 262 Vl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvG 341 (486)
T PRK07899 262 VLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVG 341 (486)
T ss_pred EEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCC
Confidence 99999999999999999877765 35778999999999999999999998 99999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|+|+|+|
T Consensus 342 d~V~VkI 348 (486)
T PRK07899 342 DEVFVKV 348 (486)
T ss_pred CEEEEEE
Confidence 9999986
No 7
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=1.7e-42 Score=356.42 Aligned_cols=280 Identities=21% Similarity=0.342 Sum_probs=244.5
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
.++.|| ||..++ .+..+|+. .|++|.+++|+|+..++. ++++...++... .
T Consensus 514 ~Gv~Gf-vp~SeiS~~~v~~~~~---------~~kvGq~v~vkVi~iD~e---~~rI~LSlK~l~----~---------- 566 (863)
T PRK12269 514 GGFDGL-LHVNDMSWGHVARPRE---------FVKKGQTIELKVIRLDQA---EKRINLSLKHFQ----P---------- 566 (863)
T ss_pred CCEEEE-EEchhccccccCCHHH---------hccCCCEEEEEEEEEecC---CCeEEEEEeccc----c----------
Confidence 478899 998887 56678876 789999999999999876 556666666542 1
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc-ccccCccccCcCCCCEEEEEEEEEeCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEAD 162 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~-~~~~~~~~~~~~~G~~v~v~Vl~vd~~~ 162 (318)
..|..+...+++|++++|+|+++.++|+||+++.+.+|++|++|+++ ....+|.+. |++||+++|+|+++|+++
T Consensus 567 ----~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~-~kvGd~V~vkVl~iD~e~ 641 (863)
T PRK12269 567 ----DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDM-VKIGDEVECMILGYDIQA 641 (863)
T ss_pred ----chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHc-CCCCCEEEEEEEEEeccc
Confidence 35555555688999999999999999999999888999999999998 567888887 999999999999999999
Q ss_pred CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCC---cch-h-cCCeEeEE
Q 021034 163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKST---AEE-L-LGKDLPLK 236 (318)
Q Consensus 163 ~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~---~~~-~-vGq~v~~k 236 (318)
+++.||+|+... .+|+.+.+.+++|++++|+|++++++|+||+++ |++||||.++++|..+ +++ + +||.|+|+
T Consensus 642 ~rIsLS~K~l~~-~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~Vkvk 720 (863)
T PRK12269 642 GRVSLGLKQVTA-NPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECM 720 (863)
T ss_pred CceEEEehhccc-CchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEE
Confidence 999999999876 499999998999999999999999999999996 9999999999998532 332 4 89999999
Q ss_pred EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcc---ccc
Q 021034 237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIA---TVL 308 (318)
Q Consensus 237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~---~~~ 308 (318)
|+++|++++++.||+|+...+++ .++++|+++.|+|.+++++|+||++. |+.||+|.++++|++..++. ..|
T Consensus 721 Vl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f 800 (863)
T PRK12269 721 VIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKY 800 (863)
T ss_pred EEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccchhhcccc
Confidence 99999999999999998876665 34789999999999999999999998 99999999999998765543 469
Q ss_pred CCCCEEEEEC
Q 021034 309 QPGDTLKVCL 318 (318)
Q Consensus 309 ~~Gq~V~v~V 318 (318)
++||.|+|+|
T Consensus 801 ~vGD~V~v~V 810 (863)
T PRK12269 801 AVGDRVKAVI 810 (863)
T ss_pred CCCCEEEEEE
Confidence 9999999986
No 8
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=2.4e-41 Score=325.62 Aligned_cols=279 Identities=24% Similarity=0.353 Sum_probs=242.5
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
.+++|+ +|..|+ .++.+|.. .|++|.+|+|+|+.++.+ ++++....+.+. .
T Consensus 40 ~~~~g~-lp~~e~~~~~~~~~~~---------~~~vGd~v~~~V~~v~~~---~~~i~lS~k~~~----~---------- 92 (390)
T PRK06676 40 YKVEGV-IPISELSNDHIEDIND---------VVKVGDELEVYVLKVEDG---EGNLLLSKRRLE----A---------- 92 (390)
T ss_pred CCcEEE-EEHHHhccccccCccc---------ccCCCCEEEEEEEEEECC---CCCEEEEHHHhh----h----------
Confidence 368899 999998 56788887 899999999999999876 556666666542 1
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
...|+++...++.|++++|+|.++.++|++|+++ +.+||+|.+|+++.+..++.+ + +|+++.|+|+++|.+++
T Consensus 93 ---~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~~~~~~~--~-vG~~v~~~Vl~~d~~~~ 165 (390)
T PRK06676 93 ---EKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSD--F-KGKTLEVKIIELDPEKN 165 (390)
T ss_pred ---hhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCccCCChHH--c-CCCEEEEEEEEEECCCC
Confidence 1456666556789999999999999999999996 479999999999988777764 3 89999999999999999
Q ss_pred eEEEEeeehhhh---HHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchh--cCCeEeEE
Q 021034 164 SLVLSLRMIQYE---LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK 236 (318)
Q Consensus 164 ~i~lS~k~~~~~---~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~--vGq~v~~k 236 (318)
++.||+|..... ..|..+.+.++.|++++|+|+++.++|+||+++|++||+|.+++++. .++.++ +|+.|+|+
T Consensus 166 ~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~ 245 (390)
T PRK06676 166 RVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVK 245 (390)
T ss_pred EEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEE
Confidence 999999987542 46776666678999999999999999999999999999999999986 345443 79999999
Q ss_pred EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034 237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
|+++|++++++.||+|+.+.+++ +++++|++++|+|++++++|+||++. |+.||+|.|+++|.+..++.+.|++|
T Consensus 246 Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~G 325 (390)
T PRK06676 246 VLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEG 325 (390)
T ss_pred EEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCC
Confidence 99999999999999998876554 56899999999999999999999998 99999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|.|+|+|
T Consensus 326 d~v~v~V 332 (390)
T PRK06676 326 QEVKVKV 332 (390)
T ss_pred CEEEEEE
Confidence 9999986
No 9
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.2e-40 Score=331.66 Aligned_cols=283 Identities=23% Similarity=0.377 Sum_probs=241.9
Q ss_pred ccccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHH
Q 021034 6 QQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE 85 (318)
Q Consensus 6 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~ 85 (318)
.++.|| ||-.|+.- ++.+ .+ .+..|.++.|+|+.++.. ++++-...+.++.....
T Consensus 135 ~g~~gf-ip~s~~~~--~~~~-----~~--~~~vG~~i~~~V~~~d~~---~~~i~lS~k~~~~~~~~------------ 189 (565)
T PRK06299 135 NGVEAF-LPGSQVDV--RPVR-----DT--DPLEGKELEFKVIKLDKK---RNNIVVSRRAVLEEERA------------ 189 (565)
T ss_pred CCEEEE-EEHHHccC--cCCC-----Ch--HHhCCCEEEEEEEEEECC---CCEEEEEhHHhhhhhhh------------
Confidence 388999 99888731 1211 11 356999999999999866 55565555655533222
Q ss_pred HHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034 86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (318)
Q Consensus 86 ~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i 165 (318)
..|..+..++++|++++|+|.++.++|+||+++ +.+|++|.+|+++.++.+|.+. +++||++.|+|+++|++++++
T Consensus 190 --~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~-~kvG~~v~v~V~~~d~~~~~i 265 (565)
T PRK06299 190 --EEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEV-VNVGDEVKVKVLKFDKEKKRV 265 (565)
T ss_pred --hHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhc-CCCCCEEEEEEEEEeCCCCeE
Confidence 244444447889999999999999999999998 7999999999999999999888 999999999999999999999
Q ss_pred EEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcch-h-cCCeEeEEEEE
Q 021034 166 VLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE-L-LGKDLPLKFVE 239 (318)
Q Consensus 166 ~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~-~-vGq~v~~kVl~ 239 (318)
.||+|.... .+|+.+.+.++.|+++.|+|+++.++|+||+++ |+.||+|.++++|. .++.+ + +||.|+|+|++
T Consensus 266 ~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~ 344 (565)
T PRK06299 266 SLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLE 344 (565)
T ss_pred EEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEE
Confidence 999999876 599999888889999999999999999999997 99999999999975 23433 3 79999999999
Q ss_pred EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCcccccCCCCE
Q 021034 240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDT 313 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~ 313 (318)
+|++++++.||+|++..+++ ..+++|++|.|+|++++++|+||+++ ++.||+|.++++|.+. .++.+.|++||.
T Consensus 345 id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~ 424 (565)
T PRK06299 345 IDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDE 424 (565)
T ss_pred EcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCE
Confidence 99999999999998866543 46889999999999999999999999 9999999999999876 889999999999
Q ss_pred EEEEC
Q 021034 314 LKVCL 318 (318)
Q Consensus 314 V~v~V 318 (318)
|+|+|
T Consensus 425 v~v~I 429 (565)
T PRK06299 425 VEAVV 429 (565)
T ss_pred EEEEE
Confidence 99986
No 10
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.4e-39 Score=326.95 Aligned_cols=236 Identities=30% Similarity=0.473 Sum_probs=215.1
Q ss_pred CCCCHHHHHHHHhhhc--cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEE
Q 021034 79 VSFTLEEFHSALEKYD--FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156 (318)
Q Consensus 79 ~~~s~~~~~~~~~~~~--~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl 156 (318)
...+.++|+++++++. .+++.|++++|+|+++.++|++|+++++.+||||.+|++... +... +++|++++|+|+
T Consensus 8 ~~~~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~---~~~~-~~vG~~i~~~V~ 83 (565)
T PRK06299 8 QNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ---GELE-VKVGDEVEVYVE 83 (565)
T ss_pred cccchHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc---cccc-CCCCCEEEEEEE
Confidence 3445678999998875 568999999999999999999999998899999999998532 2233 899999999999
Q ss_pred EEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEe
Q 021034 157 GENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLP 234 (318)
Q Consensus 157 ~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~ 234 (318)
++++.++++.||+|++.....|+++.++++.|++++|+|.+++++|++|+++|++||||.+|+++. .++..++||+++
T Consensus 84 ~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~~~~~~~vG~~i~ 163 (565)
T PRK06299 84 RIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELE 163 (565)
T ss_pred EEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCCCChHHhCCCEEE
Confidence 999989999999999988899999999999999999999999999999999999999999999986 345566999999
Q ss_pred EEEEEEecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCccc
Q 021034 235 LKFVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIAT 306 (318)
Q Consensus 235 ~kVl~vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~ 306 (318)
|+|+++|++++++.+|+|+++.+ .+.++++|+++.|+|++++++|+||+++|+.||+|.++++|.++.+|.+
T Consensus 164 ~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~~~~~ 243 (565)
T PRK06299 164 FKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSE 243 (565)
T ss_pred EEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccCCHhh
Confidence 99999999999999999998743 2468999999999999999999999999999999999999999999999
Q ss_pred ccCCCCEEEEEC
Q 021034 307 VLQPGDTLKVCL 318 (318)
Q Consensus 307 ~~~~Gq~V~v~V 318 (318)
.|++||+|+|+|
T Consensus 244 ~~kvG~~v~v~V 255 (565)
T PRK06299 244 VVNVGDEVKVKV 255 (565)
T ss_pred cCCCCCEEEEEE
Confidence 999999999986
No 11
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.8e-39 Score=312.66 Aligned_cols=234 Identities=34% Similarity=0.605 Sum_probs=216.1
Q ss_pred HHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034 83 LEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA 161 (318)
Q Consensus 83 ~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~ 161 (318)
.++|+++++... ++++|++++|+|.+++++|++|++ +++.+|+||.+|+++....+|.+. +++|+.++|+|++++.+
T Consensus 2 ~~~~~~~~~~~~-~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~-~~vGd~v~~~V~~v~~~ 79 (390)
T PRK06676 2 MEEFEESLNSVK-EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDV-VKVGDELEVYVLKVEDG 79 (390)
T ss_pred hHHHHHHhhhhh-cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccc-cCCCCEEEEEEEEEECC
Confidence 467888887554 899999999999999999999999 878999999999999888888877 99999999999999998
Q ss_pred CCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEE
Q 021034 162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE 239 (318)
Q Consensus 162 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~ 239 (318)
++++.||++++.....|+.+.++++.|++++|+|+++.++|++|+++|++||||.+|+++. .+++.++|++++|+|++
T Consensus 80 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~ 159 (390)
T PRK06676 80 EGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIE 159 (390)
T ss_pred CCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccCCChHHcCCCEEEEEEEE
Confidence 8999999999887789999999999999999999999999999999999999999999976 45667799999999999
Q ss_pred EecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034 240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
+|++++++.||+|.++.+ .+.++++|+++.|+|.+++++|+||+++|+.||+|.++++|.++.++.+.|++|
T Consensus 160 ~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vG 239 (390)
T PRK06676 160 LDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVG 239 (390)
T ss_pred EECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCC
Confidence 999999999999987542 246789999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|.|+|+|
T Consensus 240 d~i~~~V 246 (390)
T PRK06676 240 QEVEVKV 246 (390)
T ss_pred CEEEEEE
Confidence 9999986
No 12
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=2e-40 Score=329.95 Aligned_cols=280 Identities=22% Similarity=0.355 Sum_probs=241.3
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
.++.|| +|-.++ .+..+|+. .|++|.++.|+|+.+++. ++++...++.+. .
T Consensus 208 ~g~~g~-lp~~e~s~~~~~~~~~---------~~~vG~~v~v~Vl~~d~~---~~~i~lS~k~~~----~---------- 260 (516)
T TIGR00717 208 GGVDGL-LHITDMSWKRVKHPSE---------YVKVGQEVKVKVIKFDKE---KGRISLSLKQLG----E---------- 260 (516)
T ss_pred CCEEEE-EEHHHcCCCCCCCHHH---------hccCCCEEEEEEEEEECC---CCcEEEEEEecc----h----------
Confidence 478899 988887 45666765 799999999999999876 445544444321 1
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEAD 162 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~ 162 (318)
..|+.+...+++|++++|+|+++.++|+||+++.+.+||+|.+|+++. ...+|.+. +++||.+.|+|+++|+++
T Consensus 261 ----~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~-~~vG~~v~v~V~~id~~~ 335 (516)
T TIGR00717 261 ----DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKV-VKKGDEVEVMILDIDPER 335 (516)
T ss_pred ----hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHh-ccCCCEEEEEEEEEcCCC
Confidence 345555446789999999999999999999998889999999999975 34566666 899999999999999999
Q ss_pred CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC---Ccc-hh-cCCeEeEE
Q 021034 163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAE-EL-LGKDLPLK 236 (318)
Q Consensus 163 ~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~---~~~-~~-vGq~v~~k 236 (318)
+++.||+|.+.. .+|..+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|.. ++. .+ +||.|+|+
T Consensus 336 ~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~ 414 (516)
T TIGR00717 336 RRLSLGLKQCKA-NPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAV 414 (516)
T ss_pred CEEEEEehhccc-CcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEE
Confidence 999999998765 589888877789999999999999999999998 999999999999753 232 34 79999999
Q ss_pred EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034 237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG 311 (318)
Q Consensus 237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G 311 (318)
|+++|++++++.||+|++..+++ +++++|++++|+|++++++|+||++. ++.||+|.++++|++..++.+.|++|
T Consensus 415 Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~G 494 (516)
T TIGR00717 415 VLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVG 494 (516)
T ss_pred EEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCC
Confidence 99999999999999999766554 56889999999999999999999998 89999999999999999999999999
Q ss_pred CEEEEEC
Q 021034 312 DTLKVCL 318 (318)
Q Consensus 312 q~V~v~V 318 (318)
|.++|+|
T Consensus 495 d~v~~~V 501 (516)
T TIGR00717 495 DEVEAKV 501 (516)
T ss_pred CEEEEEE
Confidence 9999986
No 13
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=6e-40 Score=337.53 Aligned_cols=281 Identities=20% Similarity=0.300 Sum_probs=229.5
Q ss_pred cccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccch--hHHHHH----HHHHHHHHHHhhcCCCCCCC
Q 021034 7 QFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAET--REREEL----NQLFEEAYERCRTAPMEGVS 80 (318)
Q Consensus 7 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~----~~~i~e~~~~~~~~~~~~~~ 80 (318)
++.|| ||-.|+. +.+.+. + ..-.|.++++.|+..+... +++.++ +..+++...
T Consensus 423 ~~~gf-iP~se~~-~~~~~~------~--~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~----------- 481 (863)
T PRK12269 423 GMMAF-LPISQSD-CQKVDA------P--ESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERAR----------- 481 (863)
T ss_pred CcEEE-EEHHHhc-cccccc------h--HHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHH-----------
Confidence 67889 9988861 212121 1 2238889999998765420 011111 222222110
Q ss_pred CCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034 81 FTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE 160 (318)
Q Consensus 81 ~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~ 160 (318)
+.++++..++++|++++|+|.++.++|+||+++ +.+||+|.+++++.++.+|.+. +++||+++|+|+++|+
T Consensus 482 -------~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~-~kvGq~v~vkVi~iD~ 552 (863)
T PRK12269 482 -------QAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREF-VKKGQTIELKVIRLDQ 552 (863)
T ss_pred -------HHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHh-ccCCCEEEEEEEEEec
Confidence 122222236789999999999999999999996 6999999999999999999887 8999999999999999
Q ss_pred CCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcchh--cCCeEe
Q 021034 161 ADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDLP 234 (318)
Q Consensus 161 ~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~~--vGq~v~ 234 (318)
+++++.||+|.... .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.|+++|. .++.+. +||+|+
T Consensus 553 e~~rI~LSlK~l~~-~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~ 631 (863)
T PRK12269 553 AEKRINLSLKHFQP-DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVE 631 (863)
T ss_pred CCCeEEEEEecccc-chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEE
Confidence 99999999999765 699999888899999999999999999999997 99999999999983 345553 799999
Q ss_pred EEEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCccccc
Q 021034 235 LKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVL 308 (318)
Q Consensus 235 ~kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~ 308 (318)
|+|+++|++++++.||+|++..++| +++++|++++|+|+++++||+||++. |+.||||.++++|.+. .+++..|
T Consensus 632 vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~ 711 (863)
T PRK12269 632 CMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHEL 711 (863)
T ss_pred EEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhcc
Confidence 9999999999999999999877654 56889999999999999999999998 9999999999999765 4456789
Q ss_pred CCCCEEEEEC
Q 021034 309 QPGDTLKVCL 318 (318)
Q Consensus 309 ~~Gq~V~v~V 318 (318)
++||.|+|+|
T Consensus 712 kvGq~VkvkV 721 (863)
T PRK12269 712 EVGKEIECMV 721 (863)
T ss_pred CCCCEEEEEE
Confidence 9999999986
No 14
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=2.1e-38 Score=315.42 Aligned_cols=281 Identities=23% Similarity=0.372 Sum_probs=234.4
Q ss_pred cccccccCCCccc-ccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHH
Q 021034 7 QFTGLRCPPISHT-RLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE 85 (318)
Q Consensus 7 ~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~ 85 (318)
++.|| +|-.|+. +..+ .. ....|.++.+.|+.++.. ++++-...++++.....
T Consensus 122 g~~~f-lP~s~~~~~~~~-~~---------~~~vG~~i~~~v~~~~~~---~~~iv~Srk~~l~~~~~------------ 175 (516)
T TIGR00717 122 GVEAF-LPGSQVDVKPIK-DL---------DSLIGKTLKFKIIKLDQK---RNNIVVSRRAYLEEERS------------ 175 (516)
T ss_pred CEEEE-EeHHHhcCcccC-ch---------hhhCCCEEEEEEEEEECC---CCcEEEEHHHHHHHHHH------------
Confidence 67899 9988872 2111 11 456999999999999765 33443333333332221
Q ss_pred HHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034 86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (318)
Q Consensus 86 ~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i 165 (318)
..+.....++++|++++|+|.++.++|+||+++ +.+||+|.+|+++....++.+. +++||++.|+|+++|++++++
T Consensus 176 --~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~-~~vG~~v~v~Vl~~d~~~~~i 251 (516)
T TIGR00717 176 --QAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEY-VKVGQEVKVKVIKFDKEKGRI 251 (516)
T ss_pred --HHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHh-ccCCCEEEEEEEEEECCCCcE
Confidence 233333346789999999999999999999997 5999999999999988888887 999999999999999999999
Q ss_pred EEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcch-h-cCCeEeEEEEE
Q 021034 166 VLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE-L-LGKDLPLKFVE 239 (318)
Q Consensus 166 ~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~-~-vGq~v~~kVl~ 239 (318)
.+|+|.... .+|+.+.+.++.|++++|+|+++.++|+||+++ |++||+|.+++++. .++.+ + +||.++|+|++
T Consensus 252 ~lS~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~ 330 (516)
T TIGR00717 252 SLSLKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILD 330 (516)
T ss_pred EEEEEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEE
Confidence 999998865 689998887889999999999999999999996 99999999999974 23443 3 89999999999
Q ss_pred EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCcccccCCCCE
Q 021034 240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDT 313 (318)
Q Consensus 240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~ 313 (318)
+|++++++.||+|++..+++ +++++|+++.|+|++++++|+||+++ |+.||+|.++++|.+. .++...|++||.
T Consensus 331 id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~ 410 (516)
T TIGR00717 331 IDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDE 410 (516)
T ss_pred EcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCE
Confidence 99999999999998766554 46889999999999999999999999 9999999999999764 467789999999
Q ss_pred EEEEC
Q 021034 314 LKVCL 318 (318)
Q Consensus 314 V~v~V 318 (318)
|.|+|
T Consensus 411 V~~~V 415 (516)
T TIGR00717 411 IEAVV 415 (516)
T ss_pred EEEEE
Confidence 99985
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=1.2e-37 Score=316.44 Aligned_cols=256 Identities=30% Similarity=0.485 Sum_probs=228.6
Q ss_pred HHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc
Q 021034 61 NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV 140 (318)
Q Consensus 61 ~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~ 140 (318)
..++++++..+++... -...+.+++.+.|+....++++|++++|+|.++.++|++|+++++.+|+||.+|+++....+|
T Consensus 265 ~~~i~~v~~~l~~~~~-~~~~~~~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~ 343 (647)
T PRK00087 265 DWIIEEVIKKMSELDN-MEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSL 343 (647)
T ss_pred HHHHHHHHHHHHHhcc-ccccCHHHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCCh
Confidence 5677777777765211 112334566666777667899999999999999999999999989999999999999888888
Q ss_pred cccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccC
Q 021034 141 EEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQIS 220 (318)
Q Consensus 141 ~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls 220 (318)
.+. +++|+.++|+|++++++++++.||++.+.....|+.+.++++.|++++|+|+++.++|++|+++|++||||.+|++
T Consensus 344 ~~~-~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gfiP~sel~ 422 (647)
T PRK00087 344 KES-VKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVE 422 (647)
T ss_pred hhc-cCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHhC
Confidence 887 9999999999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred Cc--CCcchhcCCeEeEEEEEEecccCe-Eeeehhhhhh--------hhHhhcccCeEEEEEEEEEEcceEEEEECCeEE
Q 021034 221 SK--STAEELLGKDLPLKFVEVDEEQSR-LVLSNRKAMA--------DSQAQLGIGSVVIGTVQSLKPYGAFIDIGGING 289 (318)
Q Consensus 221 ~~--~~~~~~vGq~v~~kVl~vd~~~~~-i~lS~K~~l~--------~~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~G 289 (318)
+. .++.+++|+.+.|+|+++|+++++ +.+|+|..+. ..++++++|+++.|+|.+++++|+||+++|+.|
T Consensus 423 ~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~G 502 (647)
T PRK00087 423 LGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDG 502 (647)
T ss_pred ccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEE
Confidence 76 456667999999999999999888 9999999864 235789999999999999999999999999999
Q ss_pred EEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 290 LLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 290 lv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+|.++++|.+..++.+.|++||.|+|+|
T Consensus 503 ll~~sels~~~~~~~~~~~~vGd~V~vkV 531 (647)
T PRK00087 503 LLHVSEISWGRVEKPSDVLKVGDEIKVYI 531 (647)
T ss_pred EEEHHHcCccccCCHHHhcCCCCEEEEEE
Confidence 99999999999999999999999999986
No 16
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=100.00 E-value=2.7e-38 Score=321.01 Aligned_cols=279 Identities=28% Similarity=0.391 Sum_probs=238.3
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
..++|+ +|..|+ .++++|+. .|++|.+++++|+.++.. ++++..+.+...
T Consensus 324 ~~~~G~-lp~~els~~~~~~~~~---------~~~vGd~V~v~V~~vd~~---~g~i~LS~k~~~--------------- 375 (647)
T PRK00087 324 YKSEGV-IPLRELTLDEISSLKE---------SVKVGDEIEVKVLKLEDE---DGYVVLSKKEAD--------------- 375 (647)
T ss_pred CCeEEE-EEHHHhcccccCChhh---------ccCCCCEEEEEEEEEECC---CCcEEEEeehhc---------------
Confidence 356799 999988 56788887 899999999999999765 345555554331
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
....|++....+++|+++.|+|.++.++|++|++++ .+||+|.+|+++.+..++++ .+|+++.|+|+++|++++
T Consensus 376 --~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~ 449 (647)
T PRK00087 376 --REKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRR 449 (647)
T ss_pred --chhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCC
Confidence 113555555467899999999999999999999986 99999999999988777764 389999999999999988
Q ss_pred e-EEEEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcch-h-cCCeEeE
Q 021034 164 S-LVLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEE-L-LGKDLPL 235 (318)
Q Consensus 164 ~-i~lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~-~-vGq~v~~ 235 (318)
+ +.+|+|.... ...|....+.++.|++++|+|+++.++|+||+++|++||+|.+++++. .++.+ + +|+.+++
T Consensus 450 ~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~v 529 (647)
T PRK00087 450 KKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKV 529 (647)
T ss_pred cEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEE
Confidence 8 9999998753 234444444467999999999999999999999999999999999976 33443 3 7999999
Q ss_pred EEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCC
Q 021034 236 KFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQP 310 (318)
Q Consensus 236 kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~ 310 (318)
+|+++|++++++.||+|+.+.+++ .++++|+++.|.|++++++|+||++. |+.||+|.++++|++..++.+.|++
T Consensus 530 kV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kv 609 (647)
T PRK00087 530 YILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSE 609 (647)
T ss_pred EEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCC
Confidence 999999999999999999876654 56889999999999999999999998 9999999999999999999999999
Q ss_pred CCEEEEEC
Q 021034 311 GDTLKVCL 318 (318)
Q Consensus 311 Gq~V~v~V 318 (318)
||.|+|+|
T Consensus 610 Gd~V~vkV 617 (647)
T PRK00087 610 GEEVKAKI 617 (647)
T ss_pred CCEEEEEE
Confidence 99999986
No 17
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=1.5e-37 Score=306.38 Aligned_cols=274 Identities=26% Similarity=0.362 Sum_probs=224.6
Q ss_pred cccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHH
Q 021034 7 QFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEF 86 (318)
Q Consensus 7 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~ 86 (318)
.+.|+ +|-.++.. ...+. .+.+|.++.+.|+..+++. + .+...+. .. ..+
T Consensus 57 k~eg~-ip~~e~~~-~~~~~---------~~~~G~~i~~~Vi~~~~~~-----~--~lS~~~~--~~----------~~~ 106 (491)
T PRK13806 57 KVDGV-VDRAELLD-ADGEL---------TVAVGDEVELYVVSVNGQE-----I--RLSKALS--GQ----------GGA 106 (491)
T ss_pred CcEEE-EEHHHhcC-ccccc---------cccCCCEEEEEEEEEcCCE-----E--EEEhHHh--hh----------hhH
Confidence 45777 77666431 11122 6889999999999886541 1 1111111 00 112
Q ss_pred HHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 87 ~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
+.+++ .++.|++++|+|.++.++|++|+++ +.+||||.+++++.+..++++ .+|++++|+|+++|++++++.
T Consensus 107 ~~l~~----~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~---~vG~~i~~~V~~id~~~~~v~ 178 (491)
T PRK13806 107 AMLEE----AYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPES---YVGQTFQFLITRVEENGRNIV 178 (491)
T ss_pred HHHHH----HHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHH---cCCCeEEEEEEEEECCCCeEE
Confidence 23333 4468999999999999999999998 599999999999988888765 389999999999999999999
Q ss_pred EEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcchh--cCCeEeEEEE
Q 021034 167 LSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEEL--LGKDLPLKFV 238 (318)
Q Consensus 167 lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl 238 (318)
||+|.... ...|+.+.+.++.|++++|+|+++.++|+||+++ |++||+|.+|+++. .++.++ +||.|+|+|+
T Consensus 179 lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl 258 (491)
T PRK13806 179 VSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVL 258 (491)
T ss_pred EEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEE
Confidence 99998864 3577777667789999999999999999999996 99999999999986 356664 8999999999
Q ss_pred EEeccc----CeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc-ccccCccccc
Q 021034 239 EVDEEQ----SRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVL 308 (318)
Q Consensus 239 ~vd~~~----~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~-~~~~~~~~~~ 308 (318)
++|.++ +++.||+|++..++| .++++|+++.|+|+++++||+||+++ |+.||+|.|+++| .++.+|.+.|
T Consensus 259 ~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~ 338 (491)
T PRK13806 259 GIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVV 338 (491)
T ss_pred EEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcC
Confidence 999876 479999999977765 47889999999999999999999998 9999999999999 5678899999
Q ss_pred CCCCEEEEEC
Q 021034 309 QPGDTLKVCL 318 (318)
Q Consensus 309 ~~Gq~V~v~V 318 (318)
++||.|+|+|
T Consensus 339 ~~Gd~v~vkV 348 (491)
T PRK13806 339 APGDAVAVKI 348 (491)
T ss_pred CCCCEEEEEE
Confidence 9999999986
No 18
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.95 E-value=1.6e-28 Score=252.26 Aligned_cols=284 Identities=19% Similarity=0.258 Sum_probs=243.8
Q ss_pred ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034 6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL 83 (318)
Q Consensus 6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~ 83 (318)
.+|.|+ +|+.|+ .++|+|++ +|..|+.++||||++|.. |.....+++.++.+...
T Consensus 532 ~ni~g~-lp~~hlsd~~~~~p~~---------~f~v~~~~k~RVl~~~~~---~~~v~l~~K~slv~~~~---------- 588 (1710)
T KOG1070|consen 532 GNIKGV-LPKEHLSDHPLQPPLR---------DFKVGSGVKLRVLSVNRD---RNRVALTLKKSLVNTQL---------- 588 (1710)
T ss_pred Cceeee-cChHhhhhcccccccc---------eeeeccccEEEEEEEEcc---CCeeEEEechhhhcccC----------
Confidence 469999 999999 88999999 999999999999999876 78899999999988843
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
+.-.+|+ ++.+|+++.|+|..+.++||||.|.+++.||+|.++|++.++.+++++ |.+||++.+.|+++|+++.
T Consensus 589 ----plp~d~~-~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~eh-f~vGqTv~~~i~nvd~ek~ 662 (1710)
T KOG1070|consen 589 ----PLPSDFE-QAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEH-FPVGQTVRAKIVNVDDEKR 662 (1710)
T ss_pred ----CCccchh-hcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhh-cccccEEEEEEEecCchhc
Confidence 3445555 677999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred eEEEEeeehhh-hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC---------C----cc-
Q 021034 164 SLVLSLRMIQY-ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---------T----AE- 226 (318)
Q Consensus 164 ~i~lS~k~~~~-~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~---------~----~~- 226 (318)
++.+|||.+.. ........+.+..|.+.++.+...+++.++|++. |+.|.+-..||.|.. + .+
T Consensus 663 rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~~t~~ 742 (1710)
T KOG1070|consen 663 RMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIVEIVDQGITGVGVFGELVDGSVVVNKVLENKLRKNTSL 742 (1710)
T ss_pred eeehhhhhhhhHHHHHHHHHHHhhccccccceeehhccccEEEEccCcceEEEEEEEEEccCceEEccchhhhhhhcchh
Confidence 99999999874 3333444444557788999999999999999995 799999999999751 1 11
Q ss_pred -hh-cCCeEeEEEEEEecccCeEeeehhhhhhhh----------------------------------------------
Q 021034 227 -EL-LGKDLPLKFVEVDEEQSRLVLSNRKAMADS---------------------------------------------- 258 (318)
Q Consensus 227 -~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~---------------------------------------------- 258 (318)
.+ +||...++|++++..+.-+.+|.++-|...
T Consensus 743 ~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~~~~l~k~~~~~~~v~~is~~~~~~a~~~~~i~~v~~s~~v~s~~~d 822 (1710)
T KOG1070|consen 743 LHLVVGQVTVGVILSISLKKSLVLISLCTDLPNNATKLLKGSYALALVRSISKEGKFVAFVSNLIALVKVSHLVDSELDD 822 (1710)
T ss_pred heeeecceeEEEEEEeehhhhhhhccccccccchHHHHhcCchhHHHHHhhhhheeheeecccccceeeccccccccccc
Confidence 12 599999999999987777777765422100
Q ss_pred ---------------------------------------------------------HhhcccCeEEEEEEEEEEcceEE
Q 021034 259 ---------------------------------------------------------QAQLGIGSVVIGTVQSLKPYGAF 281 (318)
Q Consensus 259 ---------------------------------------------------------~~~l~~G~~v~G~V~~i~~~G~f 281 (318)
..++..|++++++|++|.|+++-
T Consensus 823 ~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~~~~~~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~ 902 (1710)
T KOG1070|consen 823 LTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKFIKVSSNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLN 902 (1710)
T ss_pred cceeeeecccceEEEecChhHHHHHHhhcchhhccceeEEEeccccCCCccccccccccceeeeeEEEEEEeeecccceE
Confidence 15788999999999999999999
Q ss_pred EEEC-CeEEEEecCCcCcc--cccCcccccCCCCEEEEEC
Q 021034 282 IDIG-GINGLLHVSQISHD--RVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 282 V~i~-gv~Glv~~s~ls~~--~~~~~~~~~~~Gq~V~v~V 318 (318)
|.++ ++.|-+|+|++-++ -+.+|.+.|++||.|.|||
T Consensus 903 v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrv 942 (1710)
T KOG1070|consen 903 VLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRV 942 (1710)
T ss_pred EeccccccCceehHHhhccccccCChhhhcccCCeEEEEE
Confidence 9999 99999999999886 4678999999999999986
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.95 E-value=1.1e-26 Score=217.10 Aligned_cols=212 Identities=22% Similarity=0.290 Sum_probs=169.5
Q ss_pred cccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034 7 QFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE 84 (318)
Q Consensus 7 ~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~ 84 (318)
...|| +|-.++ .+..+|+. .|++|.+|.|.|+..+++ .+++..-++++. .
T Consensus 54 k~~g~-lp~sEis~~~~~~~~~---------~~~~G~~v~~~Vi~~~~~---~~~i~lS~k~~~----~----------- 105 (318)
T PRK07400 54 KTAAF-MPIQEMSINRVEGPEE---------VLQPNETREFFILSDENE---DGQLTLSIRRIE----Y----------- 105 (318)
T ss_pred CeEEE-EEHHHhccccccCHHH---------ccCCCCEEEEEEEEEeCC---CCeEEEehhhhh----h-----------
Confidence 35788 776666 22345554 799999999999998765 344444444431 1
Q ss_pred HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034 85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
...|++.....+.|++++|+|+++.++|++|+++ +++||+|.+++++.+.. + ..+|+.+.|+|+++|+++++
T Consensus 106 --~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~~---~--~~vG~~i~~kVl~id~~~~~ 177 (318)
T PRK07400 106 --MRAWERVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKPK---E--ELVGEELPLKFLEVDEERNR 177 (318)
T ss_pred --hhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCCc---c--ccCCCEEEEEEEEEEcccCE
Confidence 1356666545567999999999999999999996 69999999999985422 2 35999999999999999999
Q ss_pred EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEE
Q 021034 165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEV 240 (318)
Q Consensus 165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~v 240 (318)
+.||+|++..+.. .+.++.|+++.|+|+++.++|+||+++|+.||+|.+++++.. ++.+ + +||.++|+|+++
T Consensus 178 i~lS~K~~~~~~~----~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~i 253 (318)
T PRK07400 178 LVLSHRRALVERK----MNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDL 253 (318)
T ss_pred EEEEhhHhhhhhh----hccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEE
Confidence 9999997765322 233579999999999999999999999999999999999873 3444 3 799999999999
Q ss_pred ecccCeEeeehhhhhhhh
Q 021034 241 DEEQSRLVLSNRKAMADS 258 (318)
Q Consensus 241 d~~~~~i~lS~K~~l~~~ 258 (318)
|.+++++.||+|+...++
T Consensus 254 D~e~~rI~LS~K~l~~~P 271 (318)
T PRK07400 254 DAERGRISLSTKQLEPEP 271 (318)
T ss_pred eCCCCEEEEEEeccccCh
Confidence 999999999999976554
No 20
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.83 E-value=8.9e-20 Score=188.50 Aligned_cols=259 Identities=21% Similarity=0.264 Sum_probs=213.1
Q ss_pred ccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCC
Q 021034 20 RLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSEL 99 (318)
Q Consensus 20 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~ 99 (318)
-|-+||+ +|+.|..+.|-|+.-+.. ..+.++ -..+.++...+
T Consensus 1026 ~le~~e~---------~F~~g~al~~~V~~~~~~------------~tv~~i-----------------G~~~~~k~~s~ 1067 (1710)
T KOG1070|consen 1026 VLELPES---------LFPLGKALDEYVVRNDKS------------KTVRAI-----------------GFSKSDKNPSP 1067 (1710)
T ss_pred hhhCchh---------hcccccceeeEEecccce------------eEEEec-----------------ccccCCCCCCc
Confidence 3778999 999999999999977422 010000 01222335569
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEe-CcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh----
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY---- 174 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp-~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~---- 174 (318)
|+++-|+|.++.+++++++++.+..|-.. +.+|++.+..+|.++ |..++.+-+.++.++..++.+.||++.+..
T Consensus 1068 G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~-f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~ 1146 (1710)
T KOG1070|consen 1068 GDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEH-FTKIQIVYVCVLSVSALNKGLELSLRESRTKITP 1146 (1710)
T ss_pred chhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHh-cccccEEEEEEEEEecccccceeecccccccCcc
Confidence 99999999999999999999888888444 558888888899888 999999999999999887779999994332
Q ss_pred ----hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccC
Q 021034 175 ----ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQS 245 (318)
Q Consensus 175 ----~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~ 245 (318)
+.....+++ ++.|+++.|.|.++.+.|+|+.++ ++.||+|.+++++. +.+++ + +||.+.++|+.+++..+
T Consensus 1147 ~~~kd~~iks~eD-lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~ 1225 (1710)
T KOG1070|consen 1147 VDSKDGSIKSIED-LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSK 1225 (1710)
T ss_pred ccccCCcccchhh-cccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCc
Confidence 112233444 469999999999999999999998 99999999999976 33443 4 79999999999999999
Q ss_pred eEeeehhhhhhh-------hHhhcccCeEEEEEEEEEEcceEEEEEC-C--eEEEEecCCcCcccccCcccccCCCCEEE
Q 021034 246 RLVLSNRKAMAD-------SQAQLGIGSVVIGTVQSLKPYGAFIDIG-G--INGLLHVSQISHDRVADIATVLQPGDTLK 315 (318)
Q Consensus 246 ~i~lS~K~~l~~-------~~~~l~~G~~v~G~V~~i~~~G~fV~i~-g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~ 315 (318)
|+.||+|++-.. .+.++++|+...|+|.+..++|+||++. + +.|++|.++.++.+..+....|+.|+.|.
T Consensus 1226 riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~ 1305 (1710)
T KOG1070|consen 1226 RIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVK 1305 (1710)
T ss_pred eEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhcccceeccceee
Confidence 999999986332 2478999999999999999999999998 3 69999999999999999999999999999
Q ss_pred EEC
Q 021034 316 VCL 318 (318)
Q Consensus 316 v~V 318 (318)
|.+
T Consensus 1306 a~~ 1308 (1710)
T KOG1070|consen 1306 ACV 1308 (1710)
T ss_pred eEe
Confidence 864
No 21
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.70 E-value=2.7e-15 Score=133.23 Aligned_cols=192 Identities=19% Similarity=0.166 Sum_probs=155.0
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCe-EEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKS-SAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~-~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
+..+|++..+.|.+..++|+|++-+... .-+||.++..+. ...+||+|++.|. -+.++++++|.+.+..
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~--------e~evGdev~vFiY--~D~~~rl~aTt~~p~~ 71 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED--------ELEVGDEVTVFIY--VDSEDRLIATTREPKA 71 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC--------ccccCcEEEEEEE--ECCCCceeheeecceE
Confidence 4679999999999999999999986543 678888876332 1679999999994 3567899999998876
Q ss_pred hHHHHHHhhhcCCCcEEEEEEEEEE-cCeEEEEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehh
Q 021034 175 ELAWERCRQLQSEDVVVKGKVVGAN-KGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 175 ~~~~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
..|..-.++|++++ +-|+|+++| .-+.++|.+++...+.++.-+|+.+-|.+ .+|.+ +|+.-.++
T Consensus 72 -----------tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~l-~~Dkk-~Ri~g~~a 138 (287)
T COG2996 72 -----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVYL-YVDKK-GRIWGTLA 138 (287)
T ss_pred -----------eecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccCCCCCCEEEEEE-EEccC-CcEEEEec
Confidence 48999999999998 889999998 78999999999976665556899998884 57754 57776654
Q ss_pred hh--hhhhHhhcc---cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 253 KA--MADSQAQLG---IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 253 ~~--l~~~~~~l~---~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.- +.+...... .|+.|+|+|++....|.||-.. +.-||||.||.... ++.||.+++||
T Consensus 139 ~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~--------prlG~~l~~rV 202 (287)
T COG2996 139 IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE--------PRLGERLTARV 202 (287)
T ss_pred chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc--------ccCCceEEEEE
Confidence 32 222222222 2999999999999999999998 99999999997644 78999999986
No 22
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.70 E-value=3.1e-17 Score=151.35 Aligned_cols=121 Identities=18% Similarity=0.168 Sum_probs=110.9
Q ss_pred CCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034 98 ELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE 175 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~ 175 (318)
++|++|.|+|.++.++|+||++. ++.+||||.||+|+.++.+++++ +++||++.|+|+++|++++++.||+|+...+
T Consensus 16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~-vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~ 94 (319)
T PTZ00248 16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKL-IRVGRHEVVVVLRVDKEKGYIDLSKKRVSPE 94 (319)
T ss_pred CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHh-cCCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence 37999999999999999999994 57999999999999999999998 9999999999999999999999999999886
Q ss_pred HHHHHHhhhcCCCcEEEEEEEEEE-cCeEEEE-------ECCEEEEEeCcccC
Q 021034 176 LAWERCRQLQSEDVVVKGKVVGAN-KGGVVAE-------VEGLRGFVPFSQIS 220 (318)
Q Consensus 176 ~~~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~-------i~gl~gfip~s~ls 220 (318)
+|..+.+.++.|++++|+|..+. +.|++++ +.+.++|.|..+..
T Consensus 95 -pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af 146 (319)
T PTZ00248 95 -DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDAL 146 (319)
T ss_pred -hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHH
Confidence 99999999999999999999994 5899987 34788888877654
No 23
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.65 E-value=2.9e-17 Score=151.59 Aligned_cols=128 Identities=17% Similarity=0.282 Sum_probs=112.7
Q ss_pred CCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhhH
Q 021034 187 EDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADSQ 259 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~ 259 (318)
.|++|.|+|+++.++|+||+| +|+.||||.|+++++ .+++++ +||++.|+|+++|+++++|.||.|+...++|
T Consensus 17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw 96 (319)
T PTZ00248 17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDI 96 (319)
T ss_pred CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchH
Confidence 799999999999999999999 489999999999987 566665 7999999999999999999999999877665
Q ss_pred ----hhcccCeEEEEEEEEEEc-ceEEEE------EC-CeEEEEecCCcCcccccCcccccC---CCCEE
Q 021034 260 ----AQLGIGSVVIGTVQSLKP-YGAFID------IG-GINGLLHVSQISHDRVADIATVLQ---PGDTL 314 (318)
Q Consensus 260 ----~~l~~G~~v~G~V~~i~~-~G~fV~------i~-gv~Glv~~s~ls~~~~~~~~~~~~---~Gq~V 314 (318)
..++.|++++|.|+++.+ +|+|++ .. .+.++.|..++....+.+|.+.|. +++.+
T Consensus 97 ~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev 166 (319)
T PTZ00248 97 EACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDIPEEV 166 (319)
T ss_pred HHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCCCHHH
Confidence 678899999999999965 999998 33 789999999998888888887776 55543
No 24
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=7.1e-15 Score=115.66 Aligned_cols=77 Identities=18% Similarity=0.349 Sum_probs=73.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
.+++|++++|+|+.++++||||++.++..|++|+||+++.++++..++ +++||.|.|+|+++|. +|++.||+|.+..
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~-L~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDH-LKVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHH-hcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence 578999999999999999999999988999999999999999999999 9999999999999997 9999999999876
No 25
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.54 E-value=8.5e-14 Score=102.48 Aligned_cols=73 Identities=22% Similarity=0.338 Sum_probs=69.2
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
++.|+++.|+|.++.++|+||+++++.+||||.+|+++.+..++.+. +++||++.|+|+++|.+++++.+|+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~-~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEV-YKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGT-CETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccc-cCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 57899999999999999999999988999999999999888888887 99999999999999999999999986
No 26
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.53 E-value=5.6e-14 Score=103.74 Aligned_cols=71 Identities=13% Similarity=0.138 Sum_probs=65.1
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc---cccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV---EEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~---~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
+++|+++.|+|.++.++|+||+++.+.+||+|++|+++.++.++ .+. |++||.++|+|+++|++++++.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~-~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKY-LPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcc-cCCCCEEEEEEEEEECCCCEEecC
Confidence 47899999999999999999999989999999999999886665 356 999999999999999999999886
No 27
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.49 E-value=1.2e-13 Score=104.17 Aligned_cols=79 Identities=15% Similarity=0.165 Sum_probs=72.3
Q ss_pred HHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 89 ~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
++..+. ++++|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. |++||+++|+|+++|.+++++.||
T Consensus 5 l~~~~~-~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~-~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 5 LPTNFS-DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFG-FKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred chhhHH-hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHh-cCCCCEEEEEEEEEcCCCCEEEEe
Confidence 444554 789999999999999999999999888999999999999988888887 999999999999999999999998
Q ss_pred e
Q 021034 169 L 169 (318)
Q Consensus 169 ~ 169 (318)
+
T Consensus 83 l 83 (83)
T cd04461 83 L 83 (83)
T ss_pred C
Confidence 5
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=99.46 E-value=6.1e-13 Score=98.13 Aligned_cols=71 Identities=18% Similarity=0.250 Sum_probs=64.4
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~ 173 (318)
+++.|+++.|+|.++.++|+||+++ ++..||+|.+|+++. +. +++||.+.|+|+++|++++++.||+|+..
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~-~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SK-LKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cc-cCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 4689999999999999999999997 579999999999875 23 89999999999999999999999999764
No 29
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.46 E-value=3.9e-13 Score=97.85 Aligned_cols=70 Identities=24% Similarity=0.356 Sum_probs=65.9
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~-~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEH-FRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHc-ccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 78999999999999999999888999999999998888888877 99999999999999999999999985
No 30
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.44 E-value=6.7e-13 Score=97.73 Aligned_cols=70 Identities=20% Similarity=0.254 Sum_probs=65.2
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
|++++|+|.++.++|++|.++.+++|++|.+++++.. ..++.+. |++||.++|+|+++|++++++.||.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~-~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKK-FPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHh-CCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999988899999999999763 6778777 99999999999999999999999986
No 31
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.44 E-value=7.4e-14 Score=109.96 Aligned_cols=58 Identities=36% Similarity=0.714 Sum_probs=56.0
Q ss_pred hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.+++|++++|+|++|++||+||+|. |-+||||+|++++.++.++.+.+++||.|+|+|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKV 60 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKV 60 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEE
Confidence 4789999999999999999999998 899999999999999999999999999999986
No 32
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.42 E-value=3e-13 Score=99.83 Aligned_cols=57 Identities=23% Similarity=0.346 Sum_probs=53.1
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCc---ccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADI---ATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~---~~~~~~Gq~V~v~V 318 (318)
+++|++|.|+|++++++|+||+++ ++.|++|.+++||.++.+| .+.|++||.|+|+|
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kV 61 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKV 61 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEE
Confidence 578999999999999999999998 9999999999999987765 58999999999986
No 33
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.40 E-value=2.2e-12 Score=93.96 Aligned_cols=70 Identities=33% Similarity=0.444 Sum_probs=66.1
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
|+++.|+|.++.++|++|+++++.+|+||.+|+++.+..++.+. +++||.++|+|++++++++++.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~-~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDE-VKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHc-CCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 78999999999999999999888999999999999888888887 99999999999999988899999985
No 34
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.39 E-value=2.3e-12 Score=93.15 Aligned_cols=65 Identities=40% Similarity=0.775 Sum_probs=59.4
Q ss_pred CcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEEEecccCeEeeehh
Q 021034 188 DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
|++++|+|+++.++|++|+++|++||+|.+|+++. .++..++||.++|+|+++|.+++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 68999999999999999999999999999999965 345556999999999999999999999986
No 35
>PRK07252 hypothetical protein; Provisional
Probab=99.39 E-value=2.5e-12 Score=103.59 Aligned_cols=81 Identities=21% Similarity=0.263 Sum_probs=74.8
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHH
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA 177 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~ 177 (318)
++|+++.|+|+++.++|+||+++++..|++|.+++++.+..++.+. +++||.+.|+|+++|.+.+++.+|++....+..
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~-~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~ 80 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQL-LKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQ 80 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhc-cCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc
Confidence 5799999999999999999999888999999999999888888777 999999999999999999999999999988656
Q ss_pred HH
Q 021034 178 WE 179 (318)
Q Consensus 178 ~~ 179 (318)
|.
T Consensus 81 ~~ 82 (120)
T PRK07252 81 HF 82 (120)
T ss_pred cc
Confidence 64
No 36
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.38 E-value=2.7e-12 Score=93.22 Aligned_cols=69 Identities=28% Similarity=0.430 Sum_probs=64.5
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
|+++.|+|.++.++|++|+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|.+++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~-~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKK-FKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHc-CCCCCEEEEEEEEEECCCCEEEEEC
Confidence 78999999999999999999888999999999999887777776 9999999999999999999999985
No 37
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.38 E-value=5.5e-12 Score=92.58 Aligned_cols=73 Identities=16% Similarity=0.142 Sum_probs=67.3
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
+++|+++.|+|.++.++|++|++..+.+|++|.+++++.+..++.+. |++||.++++|+++|.+++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~-~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYK-FKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccc-cCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 46899999999999999999999988999999999998877777776 99999999999999999999999975
No 38
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.37 E-value=3.4e-12 Score=93.72 Aligned_cols=71 Identities=20% Similarity=0.179 Sum_probs=65.5
Q ss_pred CCCCCEEEEEEEEEEC-CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 97 SELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~-~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
+++|+++.|+|.++.+ .|++++++.+.+|++|++++++.+..++.+. +++||.++|+|++++. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~-~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEG-FKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHh-CCCCCEEEEEEEEecC--CEEEEEeC
Confidence 4689999999999986 7999999989999999999999999998887 9999999999999974 89999985
No 39
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.36 E-value=7.6e-12 Score=91.99 Aligned_cols=68 Identities=31% Similarity=0.600 Sum_probs=61.4
Q ss_pred cCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcc-hh-cCCeEeEEEEEEecccCeEeeehh
Q 021034 185 QSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAE-EL-LGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 185 ~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
++.|++++|+|.+++++|+||+++ +++||||.+++++. .++. .+ +||++.|+|+++|++++++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 368999999999999999999998 99999999999986 3333 34 799999999999999999999987
No 40
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=4.7e-12 Score=92.65 Aligned_cols=69 Identities=22% Similarity=0.233 Sum_probs=63.7
Q ss_pred CCEEE-EEEEEE-ECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 100 GTKVK-GTVFCT-DNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 100 G~iv~-G~V~~i-~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
|++++ |+|+++ .++|+||++.++.+||+|.+++++....++.+. +++||.++++|+++|+.++++.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~-~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGP-FKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccc-cCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78899 999999 699999999878999999999998887877776 9999999999999999999999985
No 41
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=4.3e-12 Score=93.61 Aligned_cols=67 Identities=22% Similarity=0.362 Sum_probs=60.9
Q ss_pred CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAM 255 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l 255 (318)
+.|+++.|+|+++.++|+||+++ |+.||+|.+++++. ..+ +||.+.|+|+++|++++++.||+|+..
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~---~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~ 72 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF---SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK 72 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc---cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 58999999999999999999996 89999999999986 333 799999999999999999999998753
No 42
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.35 E-value=4e-12 Score=92.09 Aligned_cols=68 Identities=18% Similarity=0.191 Sum_probs=64.1
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|++++++.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~-~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKR-FKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhc-cCCCCEEEEEEEEEeCCCCEEecC
Confidence 78999999999999999999888999999999999888888887 999999999999999999999876
No 43
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.35 E-value=9e-12 Score=92.03 Aligned_cols=73 Identities=22% Similarity=0.236 Sum_probs=67.6
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCC--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
+.|+++.|+|.++.++|+||++.+ +.+|++|.+++++.+..++.+. |++||.+.++|+++|.+++++.||+|+
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~-~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKL-VKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHe-eCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 579999999999999999999963 4899999999999988888887 999999999999999989999999874
No 44
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.33 E-value=1.1e-11 Score=90.78 Aligned_cols=72 Identities=22% Similarity=0.318 Sum_probs=67.6
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
|+++.|+|.++.++|++|+++++.+|++|.+++++.+..++.+. |++||.++|+|+++|.+++++.||+|..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~-~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATER-FKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHc-cCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 78999999999999999999888999999999999888888887 9999999999999999889999999874
No 45
>PRK08582 hypothetical protein; Provisional
Probab=99.32 E-value=1.3e-11 Score=101.98 Aligned_cols=82 Identities=20% Similarity=0.332 Sum_probs=74.0
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE 175 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~ 175 (318)
.+++|+++.|+|+++.++|+||+++++..|++|++++++.++.++.+. +++||.|+|+|++++. ++++.||++++...
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~-l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~ 79 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDH-LKVGDEVEVKVLNVED-DGKIGLSIKKAKDR 79 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccc-cCCCCEEEEEEEEECC-CCcEEEEEEecccC
Confidence 467999999999999999999999988999999999999888888777 9999999999999986 58999999998653
Q ss_pred HHHHH
Q 021034 176 LAWER 180 (318)
Q Consensus 176 ~~~~~ 180 (318)
+|..
T Consensus 80 -~~~~ 83 (139)
T PRK08582 80 -PKRQ 83 (139)
T ss_pred -chhh
Confidence 6653
No 46
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.31 E-value=3.8e-12 Score=95.94 Aligned_cols=64 Identities=30% Similarity=0.501 Sum_probs=59.4
Q ss_pred hhhhHhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 255 MADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 255 l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+...+.++++|+++.|+|.+++++|+||+++ ++.||+|.+++++++..++.+.|++||+|+|+|
T Consensus 5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV 69 (83)
T cd04461 5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV 69 (83)
T ss_pred chhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEE
Confidence 3445678999999999999999999999998 999999999999999999999999999999986
No 47
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.30 E-value=1.8e-11 Score=88.35 Aligned_cols=67 Identities=30% Similarity=0.470 Sum_probs=60.7
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
|++++|+|.++.++|++|++ ++.+||+|.++++..+..++.+ .+||.++|+|+++|.+++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~---~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE---YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH---hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 5799999999999877666654 4899999999999998999999985
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=99.30 E-value=2.4e-11 Score=89.81 Aligned_cols=74 Identities=19% Similarity=0.304 Sum_probs=68.0
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
++|+++.|+|.++.++|+||++.+ +.+|++|.+++++.+..++.+. |++||.++|+|+++|.+++++.+|+|.+
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~-~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKL-FRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHe-ecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 369999999999999999999974 7999999999998887777777 9999999999999999999999999875
No 49
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.30 E-value=1.4e-11 Score=90.73 Aligned_cols=65 Identities=31% Similarity=0.421 Sum_probs=58.0
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc----CCcc-hh-cCCeEeEEEEEEecccCeEeeehh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK----STAE-EL-LGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~----~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
|++++|+|+++.++|+||+++ +++||+|.+++++. .++. .+ +||.++|+|+++|++++++.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 689999999999999999996 99999999999864 2333 34 899999999999999999999986
No 50
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.30 E-value=3.8e-12 Score=93.42 Aligned_cols=57 Identities=25% Similarity=0.538 Sum_probs=54.1
Q ss_pred cccCeEEEEEEEEEEc-ceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKP-YGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~-~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+++|++|.|+|.++.+ +|+||+++ |.+|++|+|+++|++..+|.+.|++||.|+|+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV 59 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEE
Confidence 4689999999999996 89999998 999999999999999999999999999999986
No 51
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.27 E-value=3.6e-11 Score=88.44 Aligned_cols=70 Identities=24% Similarity=0.305 Sum_probs=63.5
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
+.|++++|+|.++.++|+||++.+ +.+|++|++|+++.+..++.+. +++||++.|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~-~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEV-VDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhE-ECCCCEEEEEEEEECCCC-cEEEEe
Confidence 579999999999999999999954 3799999999999888888887 999999999999999865 888886
No 52
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.27 E-value=2.5e-11 Score=87.48 Aligned_cols=66 Identities=17% Similarity=0.092 Sum_probs=58.6
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
|++++|+|.++.++|++|++.++.+||+|.+|++..... .+. |++|+.++|+|+++|++++++.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~-~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KST-YKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccC-cCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999997779999999999765433 344 999999999999999999998886
No 53
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.27 E-value=3e-11 Score=86.94 Aligned_cols=69 Identities=22% Similarity=0.355 Sum_probs=64.3
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
|+++.|+|.++.++|+||+++.+.+||+|.+++++.+..++.+. +++||.+.++|++++. ++++.+|+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~-~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDV-LKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHc-cCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 78999999999999999999988999999999998888888777 9999999999999998 899999985
No 54
>PHA02945 interferon resistance protein; Provisional
Probab=99.26 E-value=4.1e-11 Score=89.12 Aligned_cols=74 Identities=15% Similarity=0.222 Sum_probs=67.5
Q ss_pred CCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCccc--ccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEA--CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEl--s~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
.++|+++.|+|.. .++|+||++ +++.+||+|.||. +..++++ .++ + .||++.|+|+.+|+.+|.+-||+|+.
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~-l-~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDK-L-VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeE-e-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 4789999999999 999999999 5589999999965 9999999 887 7 99999999999999999999999986
Q ss_pred hh
Q 021034 173 QY 174 (318)
Q Consensus 173 ~~ 174 (318)
..
T Consensus 85 ~~ 86 (88)
T PHA02945 85 CR 86 (88)
T ss_pred cc
Confidence 53
No 55
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.26 E-value=1.5e-11 Score=90.41 Aligned_cols=56 Identities=36% Similarity=0.570 Sum_probs=52.9
Q ss_pred ccCeEEEEEEEEEEcceEEEEECC--eEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
..|+++.|.|.++++||+||++.| .+||+|.++++|.+..++.+.|++||+|+|+|
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv 59 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKV 59 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEE
Confidence 479999999999999999999975 79999999999999999999999999999985
No 56
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.24 E-value=2.6e-11 Score=94.70 Aligned_cols=76 Identities=14% Similarity=0.156 Sum_probs=67.4
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-------------------cCccccCcCCCCEEEEEEEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-------------------KHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-------------------~~~~~~~~~~G~~v~v~Vl~ 157 (318)
+++|+++.|+|.++.+.|++|++.++..||+|.+++++.+. .++.+. |++||.+.|+|++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-f~vGd~V~~kVi~ 79 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDL-FSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHh-ccCCCEEEEEEEE
Confidence 46899999999999999999999888999999999998653 235566 9999999999999
Q ss_pred EeCC---CCeEEEEeeehh
Q 021034 158 ENEA---DDSLVLSLRMIQ 173 (318)
Q Consensus 158 vd~~---~~~i~lS~k~~~ 173 (318)
+|++ ++++.||+|+..
T Consensus 80 ~d~~~~~~~~i~LSlr~~~ 98 (100)
T cd05693 80 LDKSKSGKKRIELSLEPEL 98 (100)
T ss_pred ccCCcCCCcEEEEEecHHH
Confidence 9987 789999999864
No 57
>PRK08059 general stress protein 13; Validated
Probab=99.21 E-value=1.1e-10 Score=94.69 Aligned_cols=78 Identities=19% Similarity=0.300 Sum_probs=72.3
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
++++|+++.|+|.++.++|++|+++.+.+|++|.++++..+..++.+. +++||.+.|+|+++|.+++++.+|++....
T Consensus 4 ~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~-~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDF-LSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred cCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHc-CCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 467999999999999999999999988999999999998888777776 899999999999999999999999999865
No 58
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.21 E-value=2.8e-11 Score=107.30 Aligned_cols=77 Identities=21% Similarity=0.271 Sum_probs=73.4
Q ss_pred CCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
.+.|++|-|||.++.++|+||.+ +++.+||+|+||++..++++..++ +++||.+-|+|+++|+++|.+-||+|+...
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~-vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDY-VKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHH-hhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 57899999999999999999998 678999999999999999999999 999999999999999999999999999876
No 59
>PRK05807 hypothetical protein; Provisional
Probab=99.21 E-value=1.2e-10 Score=95.86 Aligned_cols=75 Identities=20% Similarity=0.312 Sum_probs=69.1
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~ 173 (318)
.+++|++++|+|..+.++|+||++. +..|++|++|+++.++.++.+. +++||.++|+|++++. ++++.||+|...
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~-~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREH-LKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCcccc-CCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 4578999999999999999999994 6899999999999999888877 9999999999999987 799999999975
No 60
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.21 E-value=7.5e-11 Score=89.40 Aligned_cols=76 Identities=21% Similarity=0.170 Sum_probs=66.0
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc----ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~----~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
.+++|+++.|+|+++.++|++|+++++.+|+||.+|+++ .+..+..+. +++||.+.|+|++++++ +++.||++.
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~-l~vGd~i~~~V~~~~~~-~~i~LS~~~ 80 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSY-LDEGDLIVAEVQSVDSD-GSVSLHTRS 80 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhh-CCCCCEEEEEEEEECCC-CCEEEEeCc
Confidence 457999999999999999999999989999999999985 333455555 89999999999999865 899999988
Q ss_pred hh
Q 021034 172 IQ 173 (318)
Q Consensus 172 ~~ 173 (318)
..
T Consensus 81 ~~ 82 (86)
T cd05789 81 LK 82 (86)
T ss_pred cc
Confidence 64
No 61
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.21 E-value=9.2e-11 Score=88.16 Aligned_cols=75 Identities=21% Similarity=0.198 Sum_probs=68.2
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
..++|+++.|+|+++.+++++|+++++.+|++|.++++..+..+..+. +++||.+.|+|++++++ +++.||++..
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKS-LQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhc-CCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 357999999999999999999999999999999999998777777776 99999999999999876 8999999874
No 62
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.21 E-value=2.6e-11 Score=87.76 Aligned_cols=54 Identities=28% Similarity=0.517 Sum_probs=52.1
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|+|+++.++|+||++. ++.||+|.+++++++..++.+.|++||.++|+|
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v 55 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKI 55 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEE
Confidence 789999999999999999998 899999999999999999999999999999986
No 63
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.21 E-value=1.2e-10 Score=83.89 Aligned_cols=72 Identities=28% Similarity=0.422 Sum_probs=65.7
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
++|+++.|+|.++.++|++|+++++..|++|.+++...+..++.+. +++||.+.|+|++++.+++++.+|++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 3699999999999999999999988999999999998876666666 99999999999999988899999975
No 64
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.20 E-value=7.9e-11 Score=85.27 Aligned_cols=68 Identities=18% Similarity=0.317 Sum_probs=61.5
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc-ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~-~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
|+++.|+|.++.++|+||++.++.+|++|.+++++ ....++.+. |++||.+.|+|+++|.+++++.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~-~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEI-YKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhE-ECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999888999999999985 456677776 999999999999999999998775
No 65
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.20 E-value=4.8e-11 Score=87.55 Aligned_cols=57 Identities=16% Similarity=0.416 Sum_probs=53.9
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+++|+++.|+|++++++|+||+++ +++|++|.++++|++..++.+.|++||.++|+|
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V 58 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACV 58 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEE
Confidence 468999999999999999999999 999999999999998888899999999999986
No 66
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.20 E-value=7.5e-11 Score=85.74 Aligned_cols=65 Identities=29% Similarity=0.552 Sum_probs=58.1
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
|+++.|+|+++.++|+||+++ ++.||+|.+++++. .++.+ + +||.++|+|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 689999999999999999996 89999999999865 34444 3 799999999999999999999975
No 67
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.20 E-value=9.1e-11 Score=84.58 Aligned_cols=63 Identities=19% Similarity=0.330 Sum_probs=55.6
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc-CCcchh-cCCeEeEEEEEEecccCeEeee
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK-STAEEL-LGKDLPLKFVEVDEEQSRLVLS 250 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~-~~~~~~-vGq~v~~kVl~vd~~~~~i~lS 250 (318)
|++++|+|+++.++|++|++. +++||+|.+|++.. ...+.+ +|++++|+|+++|++++++.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 689999999999999999995 89999999999854 224455 8999999999999999999887
No 68
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.19 E-value=1.1e-10 Score=84.83 Aligned_cols=64 Identities=25% Similarity=0.466 Sum_probs=56.8
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcc-hh-cCCeEeEEEEEEecccCeEeeeh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAE-EL-LGKDLPLKFVEVDEEQSRLVLSN 251 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~ 251 (318)
|++++|+|+++.++|++|+++ +++||+|.+++++. .++. .+ +||.++|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 689999999999999999996 89999999999976 2333 34 79999999999999999999984
No 69
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.19 E-value=6.1e-11 Score=122.41 Aligned_cols=125 Identities=17% Similarity=0.164 Sum_probs=100.0
Q ss_pred HHHHHHHHHHHHH-hhcCCCCCCC---CCHHHHHHH---HhhhccCCCCCCEEE-EEEEEEECCeEEEEeCCCeEEEEeC
Q 021034 58 EELNQLFEEAYER-CRTAPMEGVS---FTLEEFHSA---LEKYDFNSELGTKVK-GTVFCTDNRGALVDITAKSSAYLPT 129 (318)
Q Consensus 58 ~~~~~~i~e~~~~-~~~~~~~~~~---~s~~~~~~~---~~~~~~~~~~G~iv~-G~V~~i~~~G~~V~i~~~~~g~lp~ 129 (318)
+.|++|+++.-.. ++-.+.+.+. .+.+.++.+ ++.+..+.++|+++. |+|+++.++|+||++..+.+||||+
T Consensus 705 ktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHI 784 (891)
T PLN00207 705 KKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHI 784 (891)
T ss_pred hhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEh
Confidence 5889999997666 4444444443 233333333 455545788999996 6999999999999998889999999
Q ss_pred cccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhc
Q 021034 130 QEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQ 185 (318)
Q Consensus 130 sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~ 185 (318)
+|+++.++.++++. +++||.|+|+|+++|. ++++.||+|.... .+|+...+..
T Consensus 785 SeLs~~rv~~~~dv-~kvGD~V~VkVi~ID~-~grI~LSlK~l~~-~Pw~~~~~~~ 837 (891)
T PLN00207 785 SELSSNWLAKPEDA-FKVGDRIDVKLIEVND-KGQLRLSRRALLP-EANSEKSSQK 837 (891)
T ss_pred hhcCCccccCHHHh-cCCCCEEEEEEEEECC-CCcEEEEEecccc-Cchhhhhhhh
Confidence 99999999999888 9999999999999997 7899999999765 5999886643
No 70
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.19 E-value=3.7e-11 Score=87.00 Aligned_cols=54 Identities=33% Similarity=0.735 Sum_probs=50.6
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc-ccccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~-~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|+|.++++||+||++. +++||+|.++++| .+..++.+.|++||+|+|+|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v 56 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVV 56 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEE
Confidence 789999999999999999998 9999999999997 57788999999999999985
No 71
>PRK08582 hypothetical protein; Provisional
Probab=99.19 E-value=5e-11 Score=98.54 Aligned_cols=57 Identities=33% Similarity=0.689 Sum_probs=54.9
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+++|++|.|+|++|+++|+||+|+ +++||||.++++|+++.++.+.|++||.|+|+|
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV 60 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKV 60 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEE
Confidence 678999999999999999999998 999999999999999999999999999999986
No 72
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.18 E-value=4.1e-11 Score=91.39 Aligned_cols=58 Identities=36% Similarity=0.649 Sum_probs=54.3
Q ss_pred hcccCeEEEEEEEEEEcc--eEEEEEC-CeEEEEecCCcCc---ccccCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~--G~fV~i~-gv~Glv~~s~ls~---~~~~~~~~~~~~Gq~V~v~V 318 (318)
.+++|+++.|.|++|.++ |+||+++ |..||+|.|+++| .++.++.+.+++||.|.|+|
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV 67 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQV 67 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEE
Confidence 467899999999999997 9999999 9999999999999 77889999999999999986
No 73
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.17 E-value=1.3e-10 Score=84.99 Aligned_cols=64 Identities=28% Similarity=0.349 Sum_probs=55.9
Q ss_pred CcEEE-EEEEEE-EcCeEEEEEC-CEEEEEeCcccCCc--CC-cchh-cCCeEeEEEEEEecccCeEeeeh
Q 021034 188 DVVVK-GKVVGA-NKGGVVAEVE-GLRGFVPFSQISSK--ST-AEEL-LGKDLPLKFVEVDEEQSRLVLSN 251 (318)
Q Consensus 188 G~iv~-g~V~~v-~~~G~~V~i~-gl~gfip~s~ls~~--~~-~~~~-vGq~v~~kVl~vd~~~~~i~lS~ 251 (318)
|++++ |+|+++ .++|+||++. |++||+|.|++++. .+ .+.+ +||.++++|+++|+.++++.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 67888 999998 6999999996 89999999999865 22 3345 89999999999999999999985
No 74
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.16 E-value=1.5e-10 Score=83.06 Aligned_cols=68 Identities=24% Similarity=0.316 Sum_probs=62.8
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
|+++.|+|.++.++|+||+++.+..|++|.+++++.+..++.+. +++||.+.|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~-~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDV-VSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHh-cCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999888999999999998877777776 899999999999999988998876
No 75
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.16 E-value=1.9e-10 Score=82.68 Aligned_cols=68 Identities=24% Similarity=0.331 Sum_probs=62.6
Q ss_pred CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
+|+++.|+|.++.++|++|+++ +.+|++|.+|+++.+..++.+. |++||.+.|+|+++|.+++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~-~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHE-ECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999997 5999999999998878788777 999999999999999988998876
No 76
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=99.16 E-value=4.4e-10 Score=109.96 Aligned_cols=122 Identities=14% Similarity=0.121 Sum_probs=91.4
Q ss_pred eEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHH-----HHHHhhhcC--CCcEEEEEE
Q 021034 123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA-----WERCRQLQS--EDVVVKGKV 195 (318)
Q Consensus 123 ~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~-----~~~~~~~~~--~G~iv~g~V 195 (318)
..+.+|++++... +|. +.+|+.+.+.|...+ -+|+.++..+....+. ++.+.+.|+ .|++|+|+|
T Consensus 71 ~~~eI~L~eAk~~---~~~---~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V 142 (470)
T PRK09202 71 PTKEISLEEARKI---DPD---AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVV 142 (470)
T ss_pred CcceeeHHHHhhh---Ccc---ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEE
Confidence 4477777766432 232 789999999997765 4454444333322223 345666665 899999999
Q ss_pred EEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccC--eEeeehhhh
Q 021034 196 VGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS--RLVLSNRKA 254 (318)
Q Consensus 196 ~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~--~i~lS~K~~ 254 (318)
.++.++|++|+++|+.||||.++++.+..+ .+|+.++++|++++++++ .|.||++..
T Consensus 143 ~ri~~~giiVDLggvea~LP~sE~ip~E~~--~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 143 KRVERGNIIVDLGRAEAILPRKEQIPRENF--RPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred EEEecCCEEEEECCeEEEecHHHcCCCccC--CCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 999999999999999999999999744221 289999999999998877 899999875
No 77
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.15 E-value=1e-10 Score=85.59 Aligned_cols=57 Identities=30% Similarity=0.629 Sum_probs=51.9
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcc-cccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~-~~~~~~~~~~~Gq~V~v~V 318 (318)
+++|+++.|.|.+++++|+||++. +++||+|.++++|. +..++.+.|++||+|+|+|
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v 59 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMV 59 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEE
Confidence 468999999999999999999998 89999999999985 5557888999999999985
No 78
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.14 E-value=2.6e-10 Score=82.05 Aligned_cols=68 Identities=21% Similarity=0.312 Sum_probs=62.8
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
|+++.|+|.++.++|+||+++.+..||+|.+++++.+..++.+. +++||.+.|+|.++|+ ++++.+|+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~-~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDV-LKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHc-cCCCCEEEEEEEEECC-CCcEEeeC
Confidence 78999999999999999999888999999999998887777776 9999999999999998 88999885
No 79
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.14 E-value=3.9e-10 Score=84.10 Aligned_cols=72 Identities=15% Similarity=0.271 Sum_probs=64.9
Q ss_pred CCEEEEEEEEEECCeEEEEeC---CCeEEEEeCcccccccc-cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 100 GTKVKGTVFCTDNRGALVDIT---AKSSAYLPTQEACIHKI-KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~---~~~~g~lp~sEls~~~~-~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
|+++.|+|.++.++|+||+++ .+..||+|.+++++.+. .++.+. |++||.+.|+|+++| ++++.+|+|....
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~-~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDV-VKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhe-eCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 789999999999999999997 35899999999998875 788777 999999999999998 7899999998653
No 80
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.13 E-value=3.5e-10 Score=102.96 Aligned_cols=84 Identities=21% Similarity=0.276 Sum_probs=74.7
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCC--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
+++|+++.|+|.++.++|+||++.. +.+||||.+|++..+..++.+. +++||.+.|+|+++|.+++++.||+|....
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~-~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~ 84 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDH-VKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHh-CCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 5789999999999999999999953 6999999999999888888887 999999999999999999999999998776
Q ss_pred hHHHHHH
Q 021034 175 ELAWERC 181 (318)
Q Consensus 175 ~~~~~~~ 181 (318)
.+.|+.+
T Consensus 85 ~e~~~~~ 91 (262)
T PRK03987 85 HQRREKI 91 (262)
T ss_pred chHHHHH
Confidence 5444433
No 81
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.12 E-value=3.8e-09 Score=94.36 Aligned_cols=146 Identities=20% Similarity=0.178 Sum_probs=114.3
Q ss_pred CCCCCCEEEEEEEEEE-CCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 96 NSELGTKVKGTVFCTD-NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~-~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
.+.+|+.-.++|+.+. +.|+|||.|-.-+.++|.+|+.... +.=+++|+.+-|.+. +| .++|+..+++...
T Consensus 70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~-----~~wpq~Gd~l~v~l~-~D-kk~Ri~g~~a~~~- 141 (287)
T COG2996 70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK-----SLWPQKGDKLLVYLY-VD-KKGRIWGTLAIEK- 141 (287)
T ss_pred eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc-----ccCCCCCCEEEEEEE-Ec-cCCcEEEEecchh-
Confidence 5678999999999999 7899999998899999999986421 111578999998873 44 4668887776543
Q ss_pred hHHHHHHhh-hcC--CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeee
Q 021034 175 ELAWERCRQ-LQS--EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLS 250 (318)
Q Consensus 175 ~~~~~~~~~-~~~--~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS 250 (318)
..+.+.. .+. .++.++|+|.+....|.||-.+ +..||||.|+..-.. .+|+.++++|+.+.+ .+++.||
T Consensus 142 --~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p----rlG~~l~~rVi~~re-Dg~lnLS 214 (287)
T COG2996 142 --ILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAEP----RLGERLTARVIGVRE-DGKLNLS 214 (287)
T ss_pred --HHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcccc----cCCceEEEEEEEEcc-CCeeecc
Confidence 2222222 221 3789999999999999999986 999999999865432 389999999999987 8999999
Q ss_pred hhhhhh
Q 021034 251 NRKAMA 256 (318)
Q Consensus 251 ~K~~l~ 256 (318)
.++...
T Consensus 215 l~p~~~ 220 (287)
T COG2996 215 LRPRAH 220 (287)
T ss_pred cccccH
Confidence 998643
No 82
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.10 E-value=2.1e-10 Score=84.69 Aligned_cols=56 Identities=27% Similarity=0.482 Sum_probs=53.0
Q ss_pred ccCeEEEEEEEEEEcceEEEEEC---CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~---gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
++|+++.|+|.++.++|+||++. |+.||+|.++++|++..++.+.|++||.|+|+|
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv 60 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEE
Confidence 57999999999999999999995 599999999999999999999999999999985
No 83
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.10 E-value=5.6e-10 Score=85.10 Aligned_cols=75 Identities=17% Similarity=0.170 Sum_probs=64.7
Q ss_pred CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCccccc---ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACI---HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~---~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
.++.|+++.|+|+++.++ ||||+++.+.+||||.+|+++ .++.++.+. +++||.+.|.|++....+....||.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~-~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKL-LKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHc-CCCCCEEEEEEEEecCCCCCceEEEE
Confidence 567999999999999996 999999988999999999998 556677776 99999999999998766666777765
Q ss_pred e
Q 021034 171 M 171 (318)
Q Consensus 171 ~ 171 (318)
-
T Consensus 83 ~ 83 (88)
T cd04453 83 I 83 (88)
T ss_pred E
Confidence 4
No 84
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.10 E-value=6.3e-10 Score=81.31 Aligned_cols=70 Identities=19% Similarity=0.253 Sum_probs=61.2
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
.+|+++.|+|.++.++|+||++..+.+|++|.+++++. ...++.+. +++||.+.|+|+++|.+++++.+|
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence 58999999999999999999998789999999999864 33355555 899999999999999988888764
No 85
>PRK07252 hypothetical protein; Provisional
Probab=99.08 E-value=2.8e-10 Score=91.72 Aligned_cols=56 Identities=36% Similarity=0.725 Sum_probs=53.7
Q ss_pred ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
++|+++.|+|.+|+++|+||++. ++.||+|.+++++++..++.+.|++||.|+|+|
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI 58 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQV 58 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEE
Confidence 57999999999999999999998 899999999999999999999999999999986
No 86
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.07 E-value=4.1e-10 Score=113.55 Aligned_cols=112 Identities=22% Similarity=0.224 Sum_probs=89.3
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc
Q 021034 59 ELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK 138 (318)
Q Consensus 59 ~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~ 138 (318)
.+++|+.+.....++...++-.++- .+-..+.. ++++|++++|+|.++.++|+||++|-+.+|++|+|++++.+++
T Consensus 622 Tl~dIi~eL~kp~rdpR~~f~~~~~---~~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~ 697 (780)
T COG2183 622 TLEDIILELEKPGRDPRDEFHTPTL---DEGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVK 697 (780)
T ss_pred hHHHHHHHhhcCCCCCcccccccch---hhhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcC
Confidence 3455555555555554333222222 22223333 8999999999999999999999999999999999999999999
Q ss_pred CccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034 139 HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE 175 (318)
Q Consensus 139 ~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~ 175 (318)
+|.+. +++||.|+|+|+++|..++++.||++.....
T Consensus 698 ~P~~v-v~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~ 733 (780)
T COG2183 698 DPNEV-VKVGDIVKVKVIEVDTARKRIALSMRLDEEE 733 (780)
T ss_pred ChHHh-cccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence 99988 9999999999999999999999999988753
No 87
>PRK05807 hypothetical protein; Provisional
Probab=99.07 E-value=3.9e-10 Score=92.92 Aligned_cols=57 Identities=37% Similarity=0.670 Sum_probs=54.7
Q ss_pred cccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+++|++|.|+|+.|+++|+||++.+..||+|++++++.++.++.+.|++||.|+|+|
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV 59 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKV 59 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEE
Confidence 678999999999999999999999899999999999999999999999999999986
No 88
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.06 E-value=3.7e-10 Score=81.17 Aligned_cols=54 Identities=59% Similarity=1.037 Sum_probs=51.8
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|+|.+++++|+||+++ +..||+|.+++++++..++.+.|++||.++|+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v 55 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKV 55 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEE
Confidence 789999999999999999999 999999999999999999999999999999985
No 89
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.06 E-value=2.3e-10 Score=115.84 Aligned_cols=120 Identities=19% Similarity=0.183 Sum_probs=93.6
Q ss_pred eEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCC---CHHHHHHH---Hhhhcc--CCCCCCEEEEEEEEEECCe
Q 021034 43 IVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFHSA---LEKYDF--NSELGTKVKGTVFCTDNRG 114 (318)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~---s~~~~~~~---~~~~~~--~~~~G~iv~G~V~~i~~~G 114 (318)
-|-+-++...+ +.|+.++++.=..++-.+.+.+.+ +.+....+ ++.+.. .+++|++++|+|+++.++|
T Consensus 587 ~ki~~vIG~gG----k~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfG 662 (719)
T TIGR02696 587 DKIGEVIGPKG----KMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFG 662 (719)
T ss_pred HHhhheeCCCc----HhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECce
Confidence 34455666555 699999999877777766666543 33333332 333333 4789999999999999999
Q ss_pred EEEEeCCCeEEEEeCcccc----cccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 115 ALVDITAKSSAYLPTQEAC----IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 115 ~~V~i~~~~~g~lp~sEls----~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
+||++..+.+||||+||++ +.++.++.+. +++||.|+|+|+++|. ++++.|+
T Consensus 663 aFVel~~G~eGLvHISeisdls~~~rv~~~~dv-~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 663 AFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred EEEEecCCceEEEEhhhccccccccCcCCHHHc-CCCCCEEEEEEEEECC-CCCeeec
Confidence 9999988899999999996 4678899988 9999999999999995 7788775
No 90
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.06 E-value=8.7e-10 Score=113.32 Aligned_cols=113 Identities=17% Similarity=0.235 Sum_probs=91.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCC---HHHHH---HHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034 58 EELNQLFEEAYERCRTAPMEGVSFT---LEEFH---SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE 131 (318)
Q Consensus 58 ~~~~~~i~e~~~~~~~~~~~~~~~s---~~~~~---~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE 131 (318)
..|++|+++.-..++-.+.+.+..+ .+..+ ++++.+..++++|+++.|+|+++.++|+||++.++.+|++|+++
T Consensus 574 ~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSe 653 (693)
T PRK11824 574 KTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISE 653 (693)
T ss_pred hhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeee
Confidence 5789999987665555444444332 23332 23344445788999999999999999999999888999999999
Q ss_pred cccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 132 ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
+++.++.++.+. +++||.++|+|+++|++ +++.||+|..
T Consensus 654 ls~~~v~~~~~v-~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 654 IADERVEKVEDV-LKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred ccCccccCccce-eCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 999999999888 99999999999999976 9999999874
No 91
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.05 E-value=1.1e-09 Score=79.49 Aligned_cols=65 Identities=28% Similarity=0.584 Sum_probs=57.9
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
|++++|+|.++.++|++|+++ +..|++|.+++++. .++.+ + +||.++++|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 689999999999999999997 89999999999975 34544 3 799999999999988899999975
No 92
>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=99.05 E-value=1.4e-09 Score=78.54 Aligned_cols=64 Identities=25% Similarity=0.336 Sum_probs=55.5
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC--CeEEEEe
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSL 169 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~--~~i~lS~ 169 (318)
..|++++|+|.++.++|+||++++ .+||||.+|++. .+. +++|+.+++.|.++++++ +++.||+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~------~~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP------GES-YRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC------CCc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 469999999999999999999976 999999999963 334 899999999999998654 4788885
No 93
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.04 E-value=5.9e-10 Score=87.02 Aligned_cols=71 Identities=31% Similarity=0.494 Sum_probs=61.9
Q ss_pred CCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC---------------------Ccch-h-cCCeEeEEEEEEe
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---------------------TAEE-L-LGKDLPLKFVEVD 241 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~---------------------~~~~-~-vGq~v~~kVl~vd 241 (318)
..|++|.|+|+++.+.|++|.+. |+.||+|.+++++.+ ++.+ + +||.++|+|+++|
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence 58999999999999999999996 999999999999731 1333 3 7999999999999
Q ss_pred cc---cCeEeeehhhhhh
Q 021034 242 EE---QSRLVLSNRKAMA 256 (318)
Q Consensus 242 ~~---~~~i~lS~K~~l~ 256 (318)
++ ++++.||+|+++.
T Consensus 82 ~~~~~~~~i~LSlr~~~v 99 (100)
T cd05693 82 KSKSGKKRIELSLEPELV 99 (100)
T ss_pred CCcCCCcEEEEEecHHHC
Confidence 87 7899999998764
No 94
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=99.02 E-value=7e-09 Score=101.60 Aligned_cols=117 Identities=18% Similarity=0.262 Sum_probs=91.1
Q ss_pred hccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeE
Q 021034 36 NSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGA 115 (318)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~ 115 (318)
.+..|..+...+...+.+ |..+...-...++.+++. +.+.++++| .-+.|++++|+|.++.++|+
T Consensus 86 ~~~vGD~ie~~I~~~~fg---Ria~q~aKq~i~Qkire~----------ere~i~~ey--k~~~GeIV~G~V~ri~~~gi 150 (470)
T PRK09202 86 DAEVGDYIEEEIESVDFG---RIAAQTAKQVIVQKIREA----------ERERVYEEY--KDRVGEIITGVVKRVERGNI 150 (470)
T ss_pred cccCCCeEEEEEccccCC---hHHHHHHHHHHHHHHHHH----------HHHHHHHHH--HhhcCCEEEEEEEEEecCCE
Confidence 567999999999887755 533333323344555552 344566666 23489999999999999999
Q ss_pred EEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEEeeehhhh
Q 021034 116 LVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSLRMIQYE 175 (318)
Q Consensus 116 ~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS~k~~~~~ 175 (318)
+|+++ +.+||||.+|++ |.+. |++|++++|+|++++.+.+ +++||++.+...
T Consensus 151 iVDLg-gvea~LP~sE~i------p~E~-~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l 204 (470)
T PRK09202 151 IVDLG-RAEAILPRKEQI------PREN-FRPGDRVRAYVYEVRKEARGPQIILSRTHPEFL 204 (470)
T ss_pred EEEEC-CeEEEecHHHcC------CCcc-CCCCCEEEEEEEEEecCCCCCeEEEEeCcHHHH
Confidence 99996 599999999985 5566 9999999999999998766 899999998763
No 95
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.02 E-value=1.6e-09 Score=79.17 Aligned_cols=67 Identities=25% Similarity=0.508 Sum_probs=59.1
Q ss_pred CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehhhh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRKA 254 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~~ 254 (318)
|+++.|+|+++.++|++|+++ +++||+|.+++++. .++.+ + +||.++|+|+++|.+++++.||+|..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 689999999999999999996 99999999999976 33433 3 79999999999999999999998753
No 96
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.01 E-value=2.1e-09 Score=79.32 Aligned_cols=68 Identities=22% Similarity=0.412 Sum_probs=60.2
Q ss_pred CCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEEecccCeEeeehhhh
Q 021034 187 EDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRKA 254 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~~ 254 (318)
.|+++.|+|+++.++|+||++. +..|++|.+++++.. ++.+ + +||.++|+|+++|++++++.+|+|++
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 6899999999999999999996 699999999999763 3333 3 79999999999999999999999875
No 97
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.01 E-value=7.8e-10 Score=82.44 Aligned_cols=54 Identities=31% Similarity=0.602 Sum_probs=50.7
Q ss_pred CeEEEEEEEEEEcceEEEEEC----CeEEEEecCCcCcccc-cCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQISHDRV-ADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~----gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|.|.++++||+||+++ +..||+|.++++|.+. .++.+.|++||.|+|+|
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v 59 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKV 59 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEE
Confidence 789999999999999999998 6899999999999986 89999999999999975
No 98
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.01 E-value=5.8e-10 Score=80.00 Aligned_cols=54 Identities=35% Similarity=0.669 Sum_probs=51.5
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|+|.+++++|+||+++ +..||+|.+++++.+..++.+.|++||.++|+|
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i 55 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKV 55 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEE
Confidence 689999999999999999999 999999999999998889999999999999985
No 99
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.98 E-value=1.2e-09 Score=78.53 Aligned_cols=55 Identities=45% Similarity=0.819 Sum_probs=52.3
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+|+++.|+|.+++++|+||+++++.|++|.++++|.+..++.+.|++||.|+|+|
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i 55 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKV 55 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEE
Confidence 4899999999999999999999999999999999999989999999999999985
No 100
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.98 E-value=2.9e-09 Score=77.53 Aligned_cols=63 Identities=19% Similarity=0.127 Sum_probs=56.7
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
|+++.|+|+++.++|++|+++.+.+|++|.+++++.+ ..++.+. |++||.+.|+|++++.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~-~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSK-FKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHh-CCCCCEEEEEEEEEeCccc
Confidence 7899999999999999999998999999999999874 6677676 9999999999999987653
No 101
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.98 E-value=2e-09 Score=76.00 Aligned_cols=65 Identities=18% Similarity=0.240 Sum_probs=58.8
Q ss_pred EEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 103 VKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 103 v~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
+.|+|.++.++|++|+++.+.+|++|.+++++.+..++.+. +++||.+.|+|+++|.+++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~-~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV-FKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhE-eCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999988999999999998877777776 999999999999999988888775
No 102
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.97 E-value=1.3e-09 Score=79.37 Aligned_cols=54 Identities=22% Similarity=0.410 Sum_probs=51.1
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc--ccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~--~~~~~~~~~~Gq~V~v~V 318 (318)
|++|.|+|.++.++|+||+++ |++|++|.+++++++ ..++.+.|++||.|+|+|
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kV 57 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARV 57 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEE
Confidence 789999999999999999998 999999999999884 788999999999999986
No 103
>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=98.96 E-value=1.8e-09 Score=77.63 Aligned_cols=54 Identities=41% Similarity=0.766 Sum_probs=51.3
Q ss_pred CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
|+++.|+|.++.++|+||+++ +..||+|.+++++.+..++.+.|++||.++|+|
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v 55 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKV 55 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEE
Confidence 689999999999999999998 899999999999999889999999999999985
No 104
>PHA02945 interferon resistance protein; Provisional
Probab=98.95 E-value=3.3e-09 Score=78.97 Aligned_cols=69 Identities=17% Similarity=0.214 Sum_probs=60.6
Q ss_pred cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCccc--CCc--CCcchh-cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034 185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQI--SSK--STAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAM 255 (318)
Q Consensus 185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~l--s~~--~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l 255 (318)
-+.|+++-|+|.. .++|+||.+. |++||+|.|+. +.+ ++ +++ .||++.|+|+.+|+.++.|-||+|..-
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l~GqkvV~KVirVd~~kg~IDlSlK~V~ 85 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKLVGKTVKVKVIRVDYTKGYIDVNYKRMC 85 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEecCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence 3689999999999 9999999983 99999999966 755 56 555 799999999999999999999999753
No 105
>PRK08059 general stress protein 13; Validated
Probab=98.92 E-value=2e-09 Score=87.29 Aligned_cols=59 Identities=44% Similarity=0.780 Sum_probs=55.8
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+++++|+++.|.|.+++++|+||+++ ++.|++|.+++++++..++.+.|++||.|+|+|
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI 62 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKV 62 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEE
Confidence 45889999999999999999999999 999999999999999999999999999999986
No 106
>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=98.90 E-value=4.4e-09 Score=106.72 Aligned_cols=58 Identities=36% Similarity=0.647 Sum_probs=54.3
Q ss_pred hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcC----cccccCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----HDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls----~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.+++|+++.|+|++|++||+||++. |++||+|+|+++ |.++.++.+.|++||.|+|+|
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKV 706 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEI 706 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEE
Confidence 4789999999999999999999998 999999999996 468999999999999999986
No 107
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.89 E-value=7.4e-09 Score=74.93 Aligned_cols=63 Identities=19% Similarity=0.383 Sum_probs=54.9
Q ss_pred CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc--CC---cchh-cCCeE-eEEEEEEecccCeEeeehh
Q 021034 188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK--ST---AEEL-LGKDL-PLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~--~~---~~~~-vGq~v-~~kVl~vd~~~~~i~lS~K 252 (318)
|++|+|+|.++++++++|+++ |++||+|..||+|. ++ ++++ +||++ ++.|+ +..++.+.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 679999999999999999995 89999999999995 22 4455 89999 88888 888899999976
No 108
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.87 E-value=1.4e-08 Score=72.93 Aligned_cols=66 Identities=35% Similarity=0.625 Sum_probs=58.4
Q ss_pred CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034 187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
.|+++.|+|.++++.|++++++ ++.||+|.+++.+.. ++.+ + +||.++|+|++++++++++.+|++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 6899999999999999999998 999999999999762 2222 4 799999999999998899999875
No 109
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.86 E-value=8.1e-08 Score=90.60 Aligned_cols=116 Identities=19% Similarity=0.267 Sum_probs=86.6
Q ss_pred hccCCceeEEEEEEeccchhHHHHHHHHHHHHH-HHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCe
Q 021034 36 NSRKNKTIVSAVAISNAETREREELNQLFEEAY-ERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRG 114 (318)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~-~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G 114 (318)
.+..|..+...+-.-+.+ | ..-.+.+..+ +.+++. +.+.++++|. -+.|++++|+|.++.++|
T Consensus 83 ~~~vGD~I~~~I~~~~fg---R-~aaq~aKqvi~Qkire~----------ere~i~~ey~--~k~GeiV~G~V~~v~~~g 146 (341)
T TIGR01953 83 DVQIGDEVKKEIPPENFG---R-IAAQTAKQVILQKIREA----------ERERVYDEFS--SKEGEIISGTVKRVNRRG 146 (341)
T ss_pred ccccCCEEEEEecccCCC---H-HHHHHHHHHHHHHHHHH----------HHHHHHHHHH--hhcCCEEEEEEEEEecCC
Confidence 567899998887555444 4 3333333322 444442 3456777773 368999999999999987
Q ss_pred -EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC--CCeEEEEeeehhhh
Q 021034 115 -ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA--DDSLVLSLRMIQYE 175 (318)
Q Consensus 115 -~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~--~~~i~lS~k~~~~~ 175 (318)
++|+++ +.+||||.+|+. |.+. |++|++++|.|++++.. ..++.||++.+...
T Consensus 147 ~v~VdiG-~~ea~LP~~E~i------p~E~-~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~v 202 (341)
T TIGR01953 147 NLYVELG-KTEGILPKKEQI------PGEK-FRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFV 202 (341)
T ss_pred cEEEEEC-CeEEEecHHHcC------CCcC-CCCCCEEEEEEEEEEcCCCCCeEEEEeCcHHHH
Confidence 699996 799999999986 3445 89999999999999854 35899999998763
No 110
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.84 E-value=2.6e-08 Score=74.49 Aligned_cols=70 Identities=10% Similarity=0.145 Sum_probs=59.2
Q ss_pred CCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 99 LGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
.|+++.|+|+++.++|+||+++. +.+|++|.+++++.+.. ..... +++||.++|+|.++|.+++++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEE
Confidence 38999999999999999999986 79999999999864321 22234 8999999999999998889998
Q ss_pred EEe
Q 021034 167 LSL 169 (318)
Q Consensus 167 lS~ 169 (318)
+++
T Consensus 80 ~~l 82 (83)
T cd04471 80 FEL 82 (83)
T ss_pred EEE
Confidence 875
No 111
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.84 E-value=1.2e-08 Score=96.18 Aligned_cols=105 Identities=18% Similarity=0.211 Sum_probs=79.2
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEeeeh-h----hhHHHHHHhhhc--CCCcEEEEEEEEEEcCe-EEEEECCEEEEEeC
Q 021034 145 IVPGLKEEFVIIGENEADDSLVLSLRMI-Q----YELAWERCRQLQ--SEDVVVKGKVVGANKGG-VVAEVEGLRGFVPF 216 (318)
Q Consensus 145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~-~----~~~~~~~~~~~~--~~G~iv~g~V~~v~~~G-~~V~i~gl~gfip~ 216 (318)
+.+|+.+.+.+... +-++..++..+. . .+..++.+.+.| +.|++|+|+|.++.++| ++|++++..||||.
T Consensus 84 ~~vGD~I~~~I~~~--~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~ 161 (341)
T TIGR01953 84 VQIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPK 161 (341)
T ss_pred cccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecH
Confidence 78999999888432 234544433333 1 134555555555 48999999999999977 69999999999999
Q ss_pred cccCCcCCcchh-cCCeEeEEEEEEeccc--CeEeeehhhh
Q 021034 217 SQISSKSTAEEL-LGKDLPLKFVEVDEEQ--SRLVLSNRKA 254 (318)
Q Consensus 217 s~ls~~~~~~~~-vGq~v~~kVl~vd~~~--~~i~lS~K~~ 254 (318)
+++..+.. + +|+++++.|++++.+. ..+.||++..
T Consensus 162 ~E~ip~E~---~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 162 KEQIPGEK---FRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred HHcCCCcC---CCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 99886533 4 7999999999999553 5799999875
No 112
>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=98.84 E-value=5.5e-09 Score=79.11 Aligned_cols=57 Identities=23% Similarity=0.341 Sum_probs=51.7
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc----ccccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH----DRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~----~~~~~~~~~~~~Gq~V~v~V 318 (318)
.++|++|.|+|.+++++|+||+++ ++.|++|.+++++ .+..++.+.|++||.++|+|
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEV 65 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEE
Confidence 468999999999999999999999 9999999999997 44567778899999999986
No 113
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.82 E-value=4.8e-08 Score=72.49 Aligned_cols=64 Identities=16% Similarity=0.166 Sum_probs=57.5
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
+++.|+.+.|+|.++.++|+||++.++..|++|.+++. +. ++.||.++++|.++ .+++++.+|.
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~-~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RD-YEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------Cc-CCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 57799999999999999999999988899999999973 22 89999999999999 7889998874
No 114
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.78 E-value=1.8e-07 Score=88.88 Aligned_cols=117 Identities=19% Similarity=0.163 Sum_probs=90.5
Q ss_pred hccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeE
Q 021034 36 NSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGA 115 (318)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~ 115 (318)
....|..+...+-..+.+ |..+...-....+.+++. +.+.++++| .-+.|++++|+|.++.++|+
T Consensus 86 ~~~vGD~i~~~I~~~~fg---R~aaq~akqvI~Qkire~----------ere~v~~ef--~~k~GeiV~G~V~~~~~~~~ 150 (362)
T PRK12327 86 AYELGDVIEIEVTPKDFG---RIAAQTAKQVIMQRLREA----------EREIIYNEF--SEREGDIVTGVVQRRDNRFV 150 (362)
T ss_pred cccCCCEEEEecCcCCCC---hHHHHHHHHHHHHHHHHH----------HHHHHHHHH--HHhcCCEEEEEEEEEeCCcE
Confidence 456899998888766666 655555555556666653 344677777 34689999999999999999
Q ss_pred EEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEEeeehhhh
Q 021034 116 LVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSLRMIQYE 175 (318)
Q Consensus 116 ~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS~k~~~~~ 175 (318)
+|++++ .+||||.+|+. |.+. |++|++++|+|++++.+.+ ++.||+..+...
T Consensus 151 ~Vdlg~-vEa~LP~~E~i------p~e~-~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p~~v 204 (362)
T PRK12327 151 YVNLGK-IEAVLPPAEQI------PGET-YKHGDRIKVYVVKVEKTTKGPQIFVSRTHPGLV 204 (362)
T ss_pred EEEeCC-eEEEecHHHcC------CCCC-CCCCCEEEEEEEEEecCCCCCeEEEEeCCHHHH
Confidence 999975 99999998874 3455 8999999999999986543 699999887653
No 115
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.77 E-value=2.5e-08 Score=103.43 Aligned_cols=100 Identities=19% Similarity=0.372 Sum_probs=75.9
Q ss_pred CCeEEEEeeehhh-hHHHHHHhhh---cCCCcEEE-EEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCC
Q 021034 162 DDSLVLSLRMIQY-ELAWERCRQL---QSEDVVVK-GKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGK 231 (318)
Q Consensus 162 ~~~i~lS~k~~~~-~~~~~~~~~~---~~~G~iv~-g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq 231 (318)
++.+.+....... +...+.++++ .+.|+++. |+|+++.++|+||++. |++||+|.|++++. .++.+ + +||
T Consensus 724 dg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD 803 (891)
T PLN00207 724 DGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGD 803 (891)
T ss_pred CeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCC
Confidence 4555555444333 3333334333 46899995 6999999999999996 99999999999986 34444 3 799
Q ss_pred eEeEEEEEEecccCeEeeehhhhhhhhHhhc
Q 021034 232 DLPLKFVEVDEEQSRLVLSNRKAMADSQAQL 262 (318)
Q Consensus 232 ~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~l 262 (318)
.|+|+|+++|+ ++++.||+|+.+.++|+..
T Consensus 804 ~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~~ 833 (891)
T PLN00207 804 RIDVKLIEVND-KGQLRLSRRALLPEANSEK 833 (891)
T ss_pred EEEEEEEEECC-CCcEEEEEeccccCchhhh
Confidence 99999999997 7899999999887776433
No 116
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.77 E-value=2.2e-08 Score=74.95 Aligned_cols=55 Identities=27% Similarity=0.601 Sum_probs=48.3
Q ss_pred cCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCccccc-----------CcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~~-----------~~~~~~~~Gq~V~v~V 318 (318)
+|+++.|+|++++++|+||++. |+.|++|.+++++++.. ++...|++||.|+|+|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v 68 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRV 68 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEE
Confidence 3899999999999999999998 79999999999986422 4567899999999986
No 117
>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=98.77 E-value=5.1e-08 Score=70.37 Aligned_cols=63 Identities=19% Similarity=0.355 Sum_probs=54.0
Q ss_pred CCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEeccc--CeEeeeh
Q 021034 187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQ--SRLVLSN 251 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~--~~i~lS~ 251 (318)
.|++++|+|.+++++|++|++++..||||.+++++...+ .+|+++++.|++++.++ ..+.||+
T Consensus 3 ~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~~~~--~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESY--RPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCCCcC--CCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 689999999999999999999999999999999864221 28999999999998654 4688885
No 118
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.76 E-value=1.9e-08 Score=87.61 Aligned_cols=79 Identities=22% Similarity=0.324 Sum_probs=66.2
Q ss_pred EEEEecccCeEeeehhhhhhhhHhhcccCeEEEEEEEEEEcceEEEEEC-----------CeEEEEecCCcCcccccCcc
Q 021034 237 FVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIA 305 (318)
Q Consensus 237 Vl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-----------gv~Glv~~s~ls~~~~~~~~ 305 (318)
++++|.+++++.+... ......+++|++|.|+|++++++|+||+++ ++.|++|.+++++.+..++.
T Consensus 40 ~~~id~~~~~Isv~P~---~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~ 116 (189)
T PRK09521 40 KVFIDDINRKISVIPF---KKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT 116 (189)
T ss_pred EEEEcCCCCEEEEecC---cCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence 4567877778877532 222346679999999999999999999994 58899999999999888999
Q ss_pred cccCCCCEEEEEC
Q 021034 306 TVLQPGDTLKVCL 318 (318)
Q Consensus 306 ~~~~~Gq~V~v~V 318 (318)
+.|++||.|.|+|
T Consensus 117 ~~~~~GD~V~akV 129 (189)
T PRK09521 117 DAFKIGDIVRAKV 129 (189)
T ss_pred hccCCCCEEEEEE
Confidence 9999999999986
No 119
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.73 E-value=2.4e-08 Score=102.57 Aligned_cols=107 Identities=16% Similarity=0.224 Sum_probs=84.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCC---CHHHHHH---HHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034 58 EELNQLFEEAYERCRTAPMEGVSF---TLEEFHS---ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE 131 (318)
Q Consensus 58 ~~~~~~i~e~~~~~~~~~~~~~~~---s~~~~~~---~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE 131 (318)
+.|+.+++++=..++-.+.+.+.. ..+.... .++.....+++|+++.|+|+++.++|+||++.++.+||||+++
T Consensus 571 k~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSe 650 (684)
T TIGR03591 571 KVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISE 650 (684)
T ss_pred HHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHH
Confidence 577888888766666555444422 3333333 3344445678999999999999999999999888999999999
Q ss_pred cccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 132 ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
+++.++.++.+. +++||.+.|+|+++|. ++++.
T Consensus 651 i~~~~v~~~~~~-~kvGD~V~VkVi~id~-~gki~ 683 (684)
T TIGR03591 651 IANERVEKVEDV-LKEGDEVKVKVLEIDK-QGRIK 683 (684)
T ss_pred cCCCcccChhhc-cCCCCEEEEEEEEECC-CCCcc
Confidence 999999999888 9999999999999997 56654
No 120
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.72 E-value=2.2e-08 Score=89.09 Aligned_cols=71 Identities=24% Similarity=0.410 Sum_probs=64.2
Q ss_pred cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034 185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAM 255 (318)
Q Consensus 185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l 255 (318)
-+.|++|-|+|.++.++|+||.+. |++||+|.|+++.+ ++..++ .||.+-|+||.+|++++.|-||+|..-
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~ 86 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT 86 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence 368999999999999999999984 89999999999966 677776 599999999999999999999999753
No 121
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.71 E-value=4.7e-08 Score=72.56 Aligned_cols=51 Identities=29% Similarity=0.592 Sum_probs=46.6
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.++++|+.+.|.|.+++++|+||++. +..||+|.+++. +.|++||+++++|
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I 63 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQV 63 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEE
Confidence 56889999999999999999999998 899999999863 4599999999985
No 122
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.71 E-value=4.3e-08 Score=85.38 Aligned_cols=80 Identities=23% Similarity=0.187 Sum_probs=68.1
Q ss_pred HHhhhccCCCCCCEEEEEEEEEECCeEEEEeC----------CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034 89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDIT----------AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (318)
Q Consensus 89 ~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~----------~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v 158 (318)
.|..+...+++|++|.|+|+++.++|++|+++ .+.+|++|.+++++.+..++.+. |++||.+.|+|+++
T Consensus 54 P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~-~~~GD~V~akV~~i 132 (189)
T PRK09521 54 PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA-FKIGDIVRAKVISY 132 (189)
T ss_pred cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc-cCCCCEEEEEEEec
Confidence 35444457789999999999999999999995 24789999999998777777776 99999999999998
Q ss_pred eCCCCeEEEEeeeh
Q 021034 159 NEADDSLVLSLRMI 172 (318)
Q Consensus 159 d~~~~~i~lS~k~~ 172 (318)
+ +++.||++..
T Consensus 133 ~---~~i~LS~k~~ 143 (189)
T PRK09521 133 T---DPLQLSTKGK 143 (189)
T ss_pred C---CcEEEEEecC
Confidence 7 6899999853
No 123
>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=98.70 E-value=7.7e-08 Score=72.18 Aligned_cols=67 Identities=15% Similarity=0.132 Sum_probs=58.5
Q ss_pred CCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehhh
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRK 253 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~ 253 (318)
+.|++|.|+|+++.+.+++|+++ +..|++|.++++.. .++.+ + +|+.+.|+|+++|.+ +++.||++.
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 58999999999999999999997 89999999999864 23333 3 799999999999986 899999875
No 124
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.68 E-value=1.4e-08 Score=102.59 Aligned_cols=59 Identities=41% Similarity=0.671 Sum_probs=57.7
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.+|++|+++.|+|+|+++||+||+++ ..+||+|+|++++.++.+|.+++++||.|+|+|
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V 713 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKV 713 (780)
T ss_pred hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEE
Confidence 69999999999999999999999999 999999999999999999999999999999986
No 125
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.67 E-value=1.3e-07 Score=85.08 Aligned_cols=75 Identities=23% Similarity=0.209 Sum_probs=66.3
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc----cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~----~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
..++|++|.|+|+++.+++++|+++....|+||.+++++.+. .++.+. |++||.|.|+|++++++ +.+.||++.
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~-~~~GDlV~akV~~i~~~-~~~~LS~k~ 137 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKY-LDIGDYIIAKVKDVDRT-RDVVLTLKG 137 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhh-CCCCCEEEEEEEEECCC-CcEEEEEcC
Confidence 568999999999999999999999988999999999998765 666666 99999999999999864 459999975
Q ss_pred h
Q 021034 172 I 172 (318)
Q Consensus 172 ~ 172 (318)
.
T Consensus 138 ~ 138 (235)
T PRK04163 138 K 138 (235)
T ss_pred C
Confidence 3
No 126
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.67 E-value=4.7e-08 Score=92.73 Aligned_cols=106 Identities=13% Similarity=0.122 Sum_probs=74.5
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEeeehhh----hHHHHHHhhhc--CCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcc
Q 021034 145 IVPGLKEEFVIIGENEADDSLVLSLRMIQY----ELAWERCRQLQ--SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQ 218 (318)
Q Consensus 145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~----~~~~~~~~~~~--~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ 218 (318)
..+|+.+.+.+...+-. +....+.|+... +...+.+.+.| +.|++++|+|.++.++|++|+++++.||||.++
T Consensus 87 ~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E 165 (362)
T PRK12327 87 YELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAE 165 (362)
T ss_pred ccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHH
Confidence 78999999887543321 212222222221 11223333333 689999999999999999999999999999888
Q ss_pred cCCcCCcchh-cCCeEeEEEEEEecccC--eEeeehhhh
Q 021034 219 ISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSNRKA 254 (318)
Q Consensus 219 ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~K~~ 254 (318)
+..+. .+ +|+++++.|++++.+++ .+.||+...
T Consensus 166 ~ip~e---~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p 201 (362)
T PRK12327 166 QIPGE---TYKHGDRIKVYVVKVEKTTKGPQIFVSRTHP 201 (362)
T ss_pred cCCCC---CCCCCCEEEEEEEEEecCCCCCeEEEEeCCH
Confidence 76532 23 79999999999996554 599998654
No 127
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.66 E-value=4.5e-08 Score=100.78 Aligned_cols=59 Identities=37% Similarity=0.704 Sum_probs=56.6
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.++++|+++.|+|+++.+||+||++. |.+||+|+|+++|+++.++.+.|++||.|+|+|
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV 676 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKV 676 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEE
Confidence 56889999999999999999999998 999999999999999999999999999999986
No 128
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.65 E-value=2.4e-08 Score=99.57 Aligned_cols=123 Identities=15% Similarity=0.216 Sum_probs=98.8
Q ss_pred EEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHH------HHHhhhccCCCCCCEEEEEEEEEECCeEEE
Q 021034 44 VSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFH------SALEKYDFNSELGTKVKGTVFCTDNRGALV 117 (318)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~------~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V 117 (318)
|-+-.+.+++ +.+++++++.=..++..+.+.+..+..+-+ +.++.+...+++|+++.|+|+++.++|+||
T Consensus 562 KI~dvIG~gG----k~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv 637 (692)
T COG1185 562 KIRDVIGPGG----KTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFV 637 (692)
T ss_pred HHhhccCCcc----cchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEE
Confidence 4455566555 688999999777777766666533332211 234555568899999999999999999999
Q ss_pred EeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 118 DITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 118 ~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
.+.++-+|++|++++++.++.+.++. ++.||.+.|+++.+|+ .+++.+|++..
T Consensus 638 ~l~~gkdgl~hiS~~~~~rv~kv~dv-lk~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 638 ELLPGKDGLVHISQLAKERVEKVEDV-LKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred EecCCcceeEEehhhhhhhhhcccce-eecCceEEEEEeeecc-cCCccceehhc
Confidence 99989999999999999988888888 9999999999999984 68999998864
No 129
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.64 E-value=1e-07 Score=86.85 Aligned_cols=70 Identities=23% Similarity=0.393 Sum_probs=61.8
Q ss_pred cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhh
Q 021034 185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKA 254 (318)
Q Consensus 185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~ 254 (318)
.+.|++|.|+|+++.++|+||++. |+.||+|.|++++. .++.+. +||.+.|+|+++|++++++.||+|..
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v 82 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 468999999999999999999994 79999999999965 344443 79999999999999999999999854
No 130
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.63 E-value=5.7e-08 Score=68.37 Aligned_cols=51 Identities=35% Similarity=0.713 Sum_probs=47.9
Q ss_pred EEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 268 v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+.|+|.++.++|+||+++ +..|++|.+++++.+..++.+.|++||.|+|+|
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v 52 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKV 52 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEE
Confidence 479999999999999999 999999999999988888889999999999986
No 131
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.61 E-value=1.2e-07 Score=97.54 Aligned_cols=59 Identities=37% Similarity=0.709 Sum_probs=56.3
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
...++|+++.|+|+++.+||+||++. |.+||+|+|+++|.++.++.+.|++||.|+|+|
T Consensus 614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkV 673 (684)
T TIGR03591 614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKV 673 (684)
T ss_pred cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEE
Confidence 46788999999999999999999998 999999999999999999999999999999986
No 132
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.54 E-value=1.8e-07 Score=93.47 Aligned_cols=80 Identities=28% Similarity=0.596 Sum_probs=66.8
Q ss_pred EEEecccCeEeeehhhhh---------hhhHhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccc
Q 021034 238 VEVDEEQSRLVLSNRKAM---------ADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV 307 (318)
Q Consensus 238 l~vd~~~~~i~lS~K~~l---------~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~ 307 (318)
++++ +.+.+.++-...- ...-.++++|+++.|+|+++.+||+||.|. |-.||||+|++++.++.+.++.
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dv 663 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDV 663 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccce
Confidence 4555 5677666544321 112368899999999999999999999998 9999999999999999999999
Q ss_pred cCCCCEEEEEC
Q 021034 308 LQPGDTLKVCL 318 (318)
Q Consensus 308 ~~~Gq~V~v~V 318 (318)
+++||.+.|+|
T Consensus 664 lk~Gd~v~Vkv 674 (692)
T COG1185 664 LKEGDEVKVKV 674 (692)
T ss_pred eecCceEEEEE
Confidence 99999999985
No 133
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.53 E-value=5.5e-07 Score=70.04 Aligned_cols=78 Identities=18% Similarity=0.110 Sum_probs=63.2
Q ss_pred CEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc-----------cccCcCCCCEEEEEEEEEeCCC-----Ce
Q 021034 101 TKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV-----------EEAGIVPGLKEEFVIIGENEAD-----DS 164 (318)
Q Consensus 101 ~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~-----------~~~~~~~G~~v~v~Vl~vd~~~-----~~ 164 (318)
+++.|+|+++.++|+||++.+ .+|++|.++++..+.... .+. |++||.+.++|.++|.+. ++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRV-LKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCE-ECCCCEEEEEEEEEeHHHCcCCCce
Confidence 478999999999999999984 999999999987654432 244 899999999999999764 57
Q ss_pred EEEEeeehhhhHHHHHH
Q 021034 165 LVLSLRMIQYELAWERC 181 (318)
Q Consensus 165 i~lS~k~~~~~~~~~~~ 181 (318)
+.||.+.... -+|.-+
T Consensus 79 i~ls~k~~~~-g~~~~~ 94 (99)
T cd04460 79 IGLTMRQPGL-GKLEWI 94 (99)
T ss_pred EEEEEecCCC-CcHHHh
Confidence 9999998876 344444
No 134
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.42 E-value=4.1e-07 Score=88.48 Aligned_cols=78 Identities=17% Similarity=0.209 Sum_probs=69.4
Q ss_pred cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
.+++.|-+++|+|.++.+.|++|.++++..|+||++|++..++.+|++. +.+||.++++.++.|+..+ +.+|.|..+.
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~-levGq~I~vk~ie~d~~g~-~~ls~ralLp 741 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDL-LEVGQEIQVKYIERDPRGG-IMLSSRALLP 741 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHH-HhhcceeEEEEEeecCccc-eeehhhhhcC
Confidence 4788999999999999999999999999999999999999999999999 9999999999999997555 5555555544
No 135
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.38 E-value=1.4e-06 Score=63.10 Aligned_cols=69 Identities=19% Similarity=0.212 Sum_probs=56.4
Q ss_pred CCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccc-cCcCCCCEE-EEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEE-AGIVPGLKE-EFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~-~~~~~G~~v-~v~Vl~vd~~~~~i~lS~k 170 (318)
|++|+|+|....+++++|++.+ ++.|+||..++++..-++... ..+++||++ ++.|+ +...+.+.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 7899999999999999999955 899999999999943333222 137899999 99998 677788888875
No 136
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.36 E-value=1e-06 Score=68.49 Aligned_cols=53 Identities=40% Similarity=0.684 Sum_probs=46.9
Q ss_pred eEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccC-----------cccccCCCCEEEEEC
Q 021034 266 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD-----------IATVLQPGDTLKVCL 318 (318)
Q Consensus 266 ~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~-----------~~~~~~~Gq~V~v~V 318 (318)
+++.|+|.++.++|+||++.++.|++|.+++++++... +...|++||.|+|+|
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI 64 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARI 64 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEE
Confidence 47899999999999999999999999999999876543 357899999999986
No 137
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.34 E-value=7e-07 Score=86.86 Aligned_cols=58 Identities=26% Similarity=0.499 Sum_probs=55.8
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.++..|-+++|+|+.+.+||+||+|. +..||+|.|+++..++.+|++.|.+||.+.++
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk 722 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVK 722 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEE
Confidence 47888999999999999999999999 99999999999999999999999999999986
No 138
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=98.32 E-value=3.4e-06 Score=59.69 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=37.6
Q ss_pred CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
+|++.+.+|.++.+.|+|++.+...+-+||.+|+... +++|+.++|+|. .+.++++.+|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~---------~~~Gd~v~VFvY--~D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP---------LKVGDEVEVFVY--LDKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG---------------TTSEEEEEEE--E-TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC---------CCCCCEEEEEEE--ECCCCCEEEecC
Confidence 4889999999999999999998879999999987422 789999999994 456789999875
No 139
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=98.32 E-value=1.7e-05 Score=75.16 Aligned_cols=116 Identities=19% Similarity=0.200 Sum_probs=82.6
Q ss_pred hccCCceeEEEEEEeccchhHHHHHHHHHHHH-HHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEEC-C
Q 021034 36 NSRKNKTIVSAVAISNAETREREELNQLFEEA-YERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDN-R 113 (318)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~-~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~-~ 113 (318)
....|..+.--+-..+-+ | .--.+.+.. .+++++. +.+..+++| .-+.|+++.|+|.++.. +
T Consensus 90 ~~~vGd~i~~~i~~~~fg---R-iaaq~akq~i~Qkir~~----------er~~i~~ey--~~~~Geiv~g~V~r~~~~~ 153 (374)
T PRK12328 90 SVEIGDELTYELSLENMG---R-TAANTLFKELEYHIQRL----------LEESIFEKY--KKKVGKIVFGTVVRVDNEE 153 (374)
T ss_pred CCCCCCEEEEecChhhCC---H-HHHHHHHHHHHHHHHHH----------HHHHHHHHH--HHhcCcEEEEEEEEEecCC
Confidence 456788887766555444 3 222333332 2333332 123566666 45689999999999997 5
Q ss_pred eEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC---eEEEEeeehhhh
Q 021034 114 GALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD---SLVLSLRMIQYE 175 (318)
Q Consensus 114 G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~---~i~lS~k~~~~~ 175 (318)
+++|+++ +.+|+||.+|.. |.+. |++|+.+.|.|.+++...+ ++.||+..+...
T Consensus 154 ~i~vdlg-~~ea~LP~~eqi------p~E~-~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v 210 (374)
T PRK12328 154 NTFIEID-EIRAVLPMKNRI------KGEK-FKVGDVVKAVLKRVKIDKNNGILIELSRTSPKFL 210 (374)
T ss_pred CEEEEcC-CeEEEeCHHHcC------CCCc-CCCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH
Confidence 6999997 699999998864 4555 9999999999999987654 799999888653
No 140
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.30 E-value=1e-06 Score=79.29 Aligned_cols=58 Identities=28% Similarity=0.353 Sum_probs=54.1
Q ss_pred hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc----cCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~----~~~~~~~~~Gq~V~v~V 318 (318)
..++|++|.|.|.+++++|+||+++ ++.|++|.++++|.++ .++.+.|++||.|.|+|
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV 122 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKV 122 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEE
Confidence 3468999999999999999999999 8999999999999887 78899999999999986
No 141
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.29 E-value=3.7e-06 Score=64.57 Aligned_cols=74 Identities=19% Similarity=0.148 Sum_probs=62.4
Q ss_pred CCCCCEEEEEEEEEECCeEEEEe--------CCCeEEEEeCccccccccc--CccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDI--------TAKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i--------~~~~~g~lp~sEls~~~~~--~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
.++|++|.|+|+++....+.|++ .....|+||.+++...+.. ++.+. |++||.+.++|+++++ ...+.
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~-f~~GDiV~AkVis~~~-~~~~~ 81 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKC-FRPGDIVRAKVISLGD-ASSYY 81 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhh-cCCCCEEEEEEEEcCC-CCCcE
Confidence 57999999999999999999999 6678999999998766554 45555 9999999999999875 35688
Q ss_pred EEeeeh
Q 021034 167 LSLRMI 172 (318)
Q Consensus 167 lS~k~~ 172 (318)
||.+..
T Consensus 82 Lst~~~ 87 (92)
T cd05791 82 LSTAEN 87 (92)
T ss_pred EEecCC
Confidence 998764
No 142
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.28 E-value=5.6e-06 Score=71.49 Aligned_cols=77 Identities=18% Similarity=0.182 Sum_probs=63.4
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-Cc----------cccCcCCCCEEEEEEEEEe-----
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-HV----------EEAGIVPGLKEEFVIIGEN----- 159 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-~~----------~~~~~~~G~~v~v~Vl~vd----- 159 (318)
....|+++.|+|++++++|++|+++ ..+|+++.+++..++.. ++ ... ++.|+.|+++|.+++
T Consensus 78 ~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~Gd~VrvrV~~v~~~~~~ 155 (179)
T TIGR00448 78 KPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKV-LDEGDKVRARIVALSLKDRR 155 (179)
T ss_pred eccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEccCCC
Confidence 4568999999999999999999996 59999999998754432 11 233 889999999999998
Q ss_pred CCCCeEEEEeeehhh
Q 021034 160 EADDSLVLSLRMIQY 174 (318)
Q Consensus 160 ~~~~~i~lS~k~~~~ 174 (318)
++..++.+|+|++-.
T Consensus 156 ~~~~~I~lt~k~~~L 170 (179)
T TIGR00448 156 PEGSKIGLTMRQPLL 170 (179)
T ss_pred CCcceEEEEeccCcC
Confidence 556789999998754
No 143
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.22 E-value=5.1e-06 Score=61.40 Aligned_cols=70 Identities=7% Similarity=0.098 Sum_probs=63.0
Q ss_pred CCCCCEEEEEEEEEECCeEEEEe-CCCeEEEEe-CcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 97 SELGTKVKGTVFCTDNRGALVDI-TAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp-~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
.++|+.+. .|+.+.+.|++|.+ +++.+|++. .+|++-.+++..++. + +|.++.+.|+.+|.++|.+-||.
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kl-l-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKK-L-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhh-h-cCCeeEEEEEEECCCCCEEEeEc
Confidence 47899999 89999999999998 456999888 999999888888876 6 99999999999999999999984
No 144
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.16 E-value=9.1e-06 Score=70.16 Aligned_cols=68 Identities=21% Similarity=0.336 Sum_probs=58.0
Q ss_pred CCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcC---C----------c-chh-cCCeEeEEEEEEe-----cccCe
Q 021034 187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS---T----------A-EEL-LGKDLPLKFVEVD-----EEQSR 246 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~---~----------~-~~~-vGq~v~~kVl~vd-----~~~~~ 246 (318)
.|+++.|+|+++++.|+||+++.++|+++.+++.+.. + . ..+ +|+.|+++|.++| ++..+
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~ 160 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSK 160 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcce
Confidence 7899999999999999999999999999999988541 1 1 123 6999999999998 56778
Q ss_pred Eeeehhhh
Q 021034 247 LVLSNRKA 254 (318)
Q Consensus 247 i~lS~K~~ 254 (318)
+.+|+|+.
T Consensus 161 I~lt~k~~ 168 (179)
T TIGR00448 161 IGLTMRQP 168 (179)
T ss_pred EEEEeccC
Confidence 99999986
No 145
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.16 E-value=1.4e-05 Score=83.06 Aligned_cols=73 Identities=8% Similarity=0.156 Sum_probs=61.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCCCC
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
.-.+|++++|+|+++.++|+||++.+ +.+|++|.+++++.+. .+.... +++||.|+|+|.++|..++
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~-~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-FRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcE-ECCCCEEEEEEEEEecccC
Confidence 44689999999999999999999975 6999999999986432 222233 8999999999999999999
Q ss_pred eEEEEe
Q 021034 164 SLVLSL 169 (318)
Q Consensus 164 ~i~lS~ 169 (318)
++.+++
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 999875
No 146
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.11 E-value=1.2e-05 Score=68.56 Aligned_cols=85 Identities=20% Similarity=0.192 Sum_probs=66.0
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc----------cCccccCcCCCCEEEEEEEEEeCCC---
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----------KHVEEAGIVPGLKEEFVIIGENEAD--- 162 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~----------~~~~~~~~~~G~~v~v~Vl~vd~~~--- 162 (318)
....|+++.|+|+++.+.|+||.++. .+||+|.+++.+.++ ..-++..+..|+.|.++|++.+...
T Consensus 78 kP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~ 156 (183)
T COG1095 78 KPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP 156 (183)
T ss_pred EeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence 45679999999999999999999994 999999999988633 1111212778999999999887544
Q ss_pred --CeEEEEeeehhh-hHHHHHH
Q 021034 163 --DSLVLSLRMIQY-ELAWERC 181 (318)
Q Consensus 163 --~~i~lS~k~~~~-~~~~~~~ 181 (318)
.++.+|+|++-. ...|-..
T Consensus 157 ~~~~I~lTmrq~~LGklew~~~ 178 (183)
T COG1095 157 RESKIGLTMRQPGLGKLEWIEE 178 (183)
T ss_pred ccceEEEEeccccCCcchhhhh
Confidence 578999998876 3356443
No 147
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.09 E-value=4.5e-06 Score=71.06 Aligned_cols=55 Identities=40% Similarity=0.703 Sum_probs=47.8
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc----------cC-cccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------AD-IATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~----------~~-~~~~~~~Gq~V~v~V 318 (318)
.|++|.|.|.++.++|+||.++-++||+|.+++.++.. .+ -...+++||.|++||
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RI 146 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARI 146 (183)
T ss_pred cccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEE
Confidence 48999999999999999999999999999999999832 22 233789999999986
No 148
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.05 E-value=8.2e-06 Score=62.64 Aligned_cols=56 Identities=25% Similarity=0.487 Sum_probs=51.3
Q ss_pred ccCeEEEEEEEEEEcceEEEEE--------C-CeEEEEecCCcCccccc--CcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDI--------G-GINGLLHVSQISHDRVA--DIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i--------~-gv~Glv~~s~ls~~~~~--~~~~~~~~Gq~V~v~V 318 (318)
++|++|.|.|.+++...+.|++ . .+.|++|.+++...... ++.+.|++||-|+|+|
T Consensus 5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkV 71 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKV 71 (92)
T ss_pred CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEE
Confidence 6899999999999999999999 6 68999999999877666 6889999999999986
No 149
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=98.00 E-value=0.00019 Score=69.31 Aligned_cols=79 Identities=13% Similarity=0.149 Sum_probs=64.4
Q ss_pred HHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeC---C--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034 87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT---A--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA 161 (318)
Q Consensus 87 ~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~---~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~ 161 (318)
..++++| .-..|+++.|+|.++..++++|+++ + +.+|+||.+|.. |.+. |++|+.+.|.|.++...
T Consensus 142 ~~i~~ef--~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~-y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 142 KMIQEEF--QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDN-YRANATFKVFLKEVSEG 212 (449)
T ss_pred HHHHHHH--HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCc-CCCCCEEEEEEEEeecC
Confidence 3566666 4568999999999999999999983 3 389999998863 4555 99999999999999765
Q ss_pred C---CeEEEEeeehhh
Q 021034 162 D---DSLVLSLRMIQY 174 (318)
Q Consensus 162 ~---~~i~lS~k~~~~ 174 (318)
. -++.||+..+..
T Consensus 213 ~~kGpqIilSRt~p~l 228 (449)
T PRK12329 213 PRRGPQLFVSRANAGL 228 (449)
T ss_pred CCCCCEEEEEcCCHHH
Confidence 2 379999988765
No 150
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.97 E-value=9.1e-05 Score=64.33 Aligned_cols=77 Identities=19% Similarity=0.176 Sum_probs=62.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCC-
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD- 163 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~- 163 (318)
....|+++.|+|+++.++|++|+++. .+|+++.+++...+.. +.... ++.|+.++++|.+++..++
T Consensus 78 ~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-i~~Gd~VrvrV~~v~~~~~~ 155 (187)
T PRK08563 78 KPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRV-LKVGDVVRARIVAVSLKERR 155 (187)
T ss_pred eccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEcccCC
Confidence 45689999999999999999999984 9999999999765322 12233 7899999999999986543
Q ss_pred ----eEEEEeeehhh
Q 021034 164 ----SLVLSLRMIQY 174 (318)
Q Consensus 164 ----~i~lS~k~~~~ 174 (318)
.+.+|++..-.
T Consensus 156 ~~~~~I~ls~~~~~L 170 (187)
T PRK08563 156 PRGSKIGLTMRQPGL 170 (187)
T ss_pred CCCCEEEEEecCCCC
Confidence 78889998765
No 151
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.93 E-value=9.8e-05 Score=70.08 Aligned_cols=103 Identities=17% Similarity=0.213 Sum_probs=71.4
Q ss_pred cCCCCEEEEEEEEEeCCCCeEE-EEeeehhh--------hHHHHHHhhhcCCCcEEEEEEEEEEc-CeEEEEECCEEEEE
Q 021034 145 IVPGLKEEFVIIGENEADDSLV-LSLRMIQY--------ELAWERCRQLQSEDVVVKGKVVGANK-GGVVAEVEGLRGFV 214 (318)
Q Consensus 145 ~~~G~~v~v~Vl~vd~~~~~i~-lS~k~~~~--------~~~~~~~~~~~~~G~iv~g~V~~v~~-~G~~V~i~gl~gfi 214 (318)
+.+|+.+...+--.+ =+|+. -+.|+... +..++.+.+ ..|++++|+|.++.. ++++|++++..|+|
T Consensus 91 ~~vGd~i~~~i~~~~--fgRiaaq~akq~i~Qkir~~er~~i~~ey~~--~~Geiv~g~V~r~~~~~~i~vdlg~~ea~L 166 (374)
T PRK12328 91 VEIGDELTYELSLEN--MGRTAANTLFKELEYHIQRLLEESIFEKYKK--KVGKIVFGTVVRVDNEENTFIEIDEIRAVL 166 (374)
T ss_pred CCCCCEEEEecChhh--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hcCcEEEEEEEEEecCCCEEEEcCCeEEEe
Confidence 789999987663211 12221 12222221 111223333 489999999999986 56999999999999
Q ss_pred eCcccCCcCCcchh-cCCeEeEEEEEEecccC---eEeeehhhh
Q 021034 215 PFSQISSKSTAEEL-LGKDLPLKFVEVDEEQS---RLVLSNRKA 254 (318)
Q Consensus 215 p~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~---~i~lS~K~~ 254 (318)
|.++...+. .| .|+.++|.|.+++...+ .+.||+...
T Consensus 167 P~~eqip~E---~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p 207 (374)
T PRK12328 167 PMKNRIKGE---KFKVGDVVKAVLKRVKIDKNNGILIELSRTSP 207 (374)
T ss_pred CHHHcCCCC---cCCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence 999877542 24 79999999999998765 799998754
No 152
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=97.93 E-value=1.9e-05 Score=82.10 Aligned_cols=58 Identities=28% Similarity=0.555 Sum_probs=49.8
Q ss_pred hcccCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCcccc-----------cCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~-----------~~~~~~~~~Gq~V~v~V 318 (318)
.-+.|+++.|.|++|++||+||++. |+.||+|.+++++++. .+....|++||.|+|+|
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv 694 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRV 694 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEE
Confidence 3457999999999999999999997 6999999999996543 33456799999999986
No 153
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.92 E-value=9.4e-05 Score=55.87 Aligned_cols=74 Identities=19% Similarity=-0.003 Sum_probs=61.3
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI 172 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~ 172 (318)
..++||.|-|+|+.+..+++.|||+....|+||..++... .++.... +++|+.|-++|..++.. ....|||..+
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~-L~~GDlV~ArV~~~~~~-~~~eLtc~~~ 76 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPN-LNVGDLVYARVVKANRD-MEPELSCVDS 76 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-ccccccc-CCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence 4678999999999999999999999889999999887543 2333334 89999999999998864 5689999875
No 154
>PRK11642 exoribonuclease R; Provisional
Probab=97.87 E-value=9.1e-05 Score=77.70 Aligned_cols=73 Identities=14% Similarity=0.121 Sum_probs=61.7
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSL 165 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~~i 165 (318)
.+|+.++|+|+++.++|+||++.. +++|++|.+++.+++.. +.... |++||.|+|+|.++|.+++++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~-~~lGD~V~VkV~~vD~~~rkI 720 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQT-YRLGDRVEVRVEAVNMDERKI 720 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcE-ECCCCEEEEEEEEeecCCCeE
Confidence 689999999999999999999965 49999999999865321 11233 899999999999999999999
Q ss_pred EEEeee
Q 021034 166 VLSLRM 171 (318)
Q Consensus 166 ~lS~k~ 171 (318)
.+++-.
T Consensus 721 ~f~l~~ 726 (813)
T PRK11642 721 DFSLIS 726 (813)
T ss_pred EEEEec
Confidence 999853
No 155
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.86 E-value=5.3e-05 Score=57.67 Aligned_cols=55 Identities=22% Similarity=0.318 Sum_probs=45.8
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCc-----------ccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI-----------ATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~-----------~~~~~~Gq~V~v~V 318 (318)
.|+++.|.|++++++|+||.++.+.+|+|.+.++.+..-+| ...+.+|+.|++||
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV 66 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKI 66 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEE
Confidence 48999999999999999999999999999998876543333 34478899999886
No 156
>PRK11642 exoribonuclease R; Provisional
Probab=97.86 E-value=7e-05 Score=78.56 Aligned_cols=67 Identities=16% Similarity=0.276 Sum_probs=57.9
Q ss_pred CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc---CC-----------cchh-cCCeEeEEEEEEecccCeEe
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---ST-----------AEEL-LGKDLPLKFVEVDEEQSRLV 248 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~---~~-----------~~~~-vGq~v~~kVl~vd~~~~~i~ 248 (318)
..|++++|+|++++++|+||+++ +++|++|.+++.+. .+ .+.+ +||.|+++|.++|.++++|.
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~ 721 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID 721 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence 48999999999999999999996 59999999999854 11 1235 79999999999999999999
Q ss_pred eehh
Q 021034 249 LSNR 252 (318)
Q Consensus 249 lS~K 252 (318)
+++-
T Consensus 722 f~l~ 725 (813)
T PRK11642 722 FSLI 725 (813)
T ss_pred EEEe
Confidence 9873
No 157
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.86 E-value=1.6e-05 Score=70.77 Aligned_cols=79 Identities=20% Similarity=0.230 Sum_probs=73.4
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~ 173 (318)
-.+++++|-+.|.+|.+-|+||.+ +++.+|++-.+|+|-.+++..+.+ .++|..--|.|+.+|.++|.+-||.++..
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kl-irVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKL-IRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHH-HhcCCcceEEEEEEcCCCCceechhccCC
Confidence 357899999999999999999998 678999999999999999999988 99999999999999999999999999987
Q ss_pred hh
Q 021034 174 YE 175 (318)
Q Consensus 174 ~~ 175 (318)
.+
T Consensus 92 ~e 93 (304)
T KOG2916|consen 92 PE 93 (304)
T ss_pred HH
Confidence 63
No 158
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.86 E-value=3.7e-05 Score=66.80 Aligned_cols=55 Identities=38% Similarity=0.698 Sum_probs=48.5
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCccccc-----------CcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~-----------~~~~~~~~Gq~V~v~V 318 (318)
.|+++.|.|.+++++|+||+++.+.|++|.+++.+++.. +....|++||.|+++|
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV 146 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARI 146 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence 599999999999999999999999999999999876432 3456799999999986
No 159
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=97.81 E-value=0.00014 Score=74.92 Aligned_cols=72 Identities=14% Similarity=0.174 Sum_probs=60.7
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034 97 SELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
-.+|+.++|+|+++.++|+||++. .+.+|++|.+++.+.+. ++.... |++||+|+|+|.++|.++++
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~-~~lGD~V~Vki~~vd~~~~~ 648 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKV-YRIGDRVTVKLTEVNMETRS 648 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcE-ECCCCEEEEEEEEEecccCe
Confidence 357999999999999999999996 67999999999986531 112233 88999999999999999999
Q ss_pred EEEEe
Q 021034 165 LVLSL 169 (318)
Q Consensus 165 i~lS~ 169 (318)
+.+++
T Consensus 649 I~f~l 653 (654)
T TIGR00358 649 IIFEL 653 (654)
T ss_pred EEEEE
Confidence 98874
No 160
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.73 E-value=4.7e-05 Score=73.93 Aligned_cols=59 Identities=34% Similarity=0.581 Sum_probs=50.2
Q ss_pred hhcccCeEEEEEEEEEEcc--eEEEEEC-CeEEEEecCCcCcc------------cccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~--G~fV~i~-gv~Glv~~s~ls~~------------~~~~~~~~~~~Gq~V~v~V 318 (318)
....+|+++.|.|.++.|+ |+||+++ +-.||+|.+++.+. +..++.+.+++||.|.|.|
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV 94 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV 94 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence 3456899999999999998 9999999 89999999999763 2335567899999999976
No 161
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.66 E-value=0.00014 Score=70.58 Aligned_cols=61 Identities=20% Similarity=0.218 Sum_probs=50.6
Q ss_pred CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccc------------cccCccccCcCCCCEEEEEEEE
Q 021034 96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~------------~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
...+|+++.|+|.++.++ ||||++|.+..||||.+|+... ..++..+. +++||.+-|.|.+
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~G~~IlVQV~K 96 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISEL-LRPGQSVLVQVVK 96 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHh-CcCCCEEEEEEee
Confidence 345899999999999998 9999999989999999998642 12234445 8899999999977
No 162
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=97.63 E-value=0.0002 Score=73.76 Aligned_cols=66 Identities=15% Similarity=0.391 Sum_probs=56.8
Q ss_pred CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC---C-----------cchh-cCCeEeEEEEEEecccCeEe
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---T-----------AEEL-LGKDLPLKFVEVDEEQSRLV 248 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~---~-----------~~~~-vGq~v~~kVl~vd~~~~~i~ 248 (318)
..|+.++|+|++++++|+||+++ ++.|++|.+++.+.. + ...+ +||+|+++|.++|.++++|.
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~ 650 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII 650 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 47999999999999999999996 799999999998641 0 1234 79999999999999999998
Q ss_pred eeh
Q 021034 249 LSN 251 (318)
Q Consensus 249 lS~ 251 (318)
+++
T Consensus 651 f~l 653 (654)
T TIGR00358 651 FEL 653 (654)
T ss_pred EEE
Confidence 874
No 163
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=97.63 E-value=0.00018 Score=75.51 Aligned_cols=95 Identities=18% Similarity=0.114 Sum_probs=76.6
Q ss_pred CCCCHHHHHHHHhhhc-cCCCCCCEEEEEEEEEECCe---EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEE
Q 021034 79 VSFTLEEFHSALEKYD-FNSELGTKVKGTVFCTDNRG---ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFV 154 (318)
Q Consensus 79 ~~~s~~~~~~~~~~~~-~~~~~G~iv~G~V~~i~~~G---~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~ 154 (318)
-.++.++.=.++..-. ..+..|.+|.++|.+++.+- +-|.+..+..||||..++|+..+.+|.+. +++||++.|+
T Consensus 964 ~~l~~eeiF~mLTget~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~-v~vgq~v~~k 1042 (1299)
T KOG1856|consen 964 HELTGEEIFDMLTGETPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENR-VKVGQTVYCK 1042 (1299)
T ss_pred CCCCHHHHHHHHhCCChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHh-hccCceEEEE
Confidence 3455555444554332 35889999999999998754 34577788999999999999999999887 9999999999
Q ss_pred EEEEeCCCCeEEEEeeehhh
Q 021034 155 IIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 155 Vl~vd~~~~~i~lS~k~~~~ 174 (318)
|+++|.++=.+.|||+.+..
T Consensus 1043 vi~id~e~f~v~Ls~r~sdl 1062 (1299)
T KOG1856|consen 1043 VIKIDKERFSVELSCRTSDL 1062 (1299)
T ss_pred eeeeeHhhhhhhhhhhhHHh
Confidence 99999877778899998765
No 164
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.60 E-value=0.00022 Score=52.79 Aligned_cols=65 Identities=12% Similarity=0.300 Sum_probs=55.4
Q ss_pred CCCcEEEEEEEEEEcCeEEEEE-C-CEEEEEe-CcccCCc--CCcchh-cCCeEeEEEEEEecccCeEeeeh
Q 021034 186 SEDVVVKGKVVGANKGGVVAEV-E-GLRGFVP-FSQISSK--STAEEL-LGKDLPLKFVEVDEEQSRLVLSN 251 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i-~-gl~gfip-~s~ls~~--~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~ 251 (318)
+.|+++. .|+.+.+.|++|.+ + |++|+|. .++++.+ ...++. +|....+.|+.+|++++-|-||.
T Consensus 15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kllVGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKLVGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhhcCCeeEEEEEEECCCCCEEEeEc
Confidence 5788888 88899999999998 4 7999998 9999965 344444 89999999999999999998884
No 165
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.57 E-value=0.00065 Score=51.65 Aligned_cols=64 Identities=14% Similarity=0.137 Sum_probs=47.6
Q ss_pred CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCcc----------ccCcCCCCEEEEEEEEEeCCCC
Q 021034 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~----------~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
.|+++.|+|.++++.|+++++|. +++|++...+..+...++. +..+..|+.|+++|+++..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 48999999999999999999985 8888888777544333321 1226678889988877765433
No 166
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.54 E-value=0.00064 Score=60.44 Aligned_cols=75 Identities=21% Similarity=0.190 Sum_probs=62.9
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc----ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK----IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~----~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
..++||+|-|.|+.+...++.||+++...|+||.+++-... ..+.... +.+||.+.++|..+|. ++.+.|++|.
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~-l~vGD~v~AkV~~vd~-~~~~~L~~k~ 138 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPF-LNVGDLVYAKVVDVDR-DGEVELTLKD 138 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccc-cccCCEEEEEEEEccC-CCceEEEeec
Confidence 67899999999999999999999999999999999993322 2344455 8999999999999985 6778888855
Q ss_pred h
Q 021034 172 I 172 (318)
Q Consensus 172 ~ 172 (318)
.
T Consensus 139 ~ 139 (239)
T COG1097 139 E 139 (239)
T ss_pred C
Confidence 3
No 167
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.35 E-value=0.00078 Score=65.15 Aligned_cols=66 Identities=20% Similarity=0.273 Sum_probs=54.7
Q ss_pred CCCcEEEEEEEEEEcCeEEEEE----C--CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEeccc---CeEeeehhhh
Q 021034 186 SEDVVVKGKVVGANKGGVVAEV----E--GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQ---SRLVLSNRKA 254 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i----~--gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~---~~i~lS~K~~ 254 (318)
..|++++|+|.++.+++++|++ + ++.|+||.++...+.. | .|+.++|.|.+++... -.|.||+-..
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~---y~~Gdrika~i~~V~~~~~kGpqIilSRt~p 226 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDN---YRANATFKVFLKEVSEGPRRGPQLFVSRANA 226 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCc---CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence 3899999999999999999998 4 2899999998775433 3 7999999999998653 3699998654
No 168
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.30 E-value=0.0015 Score=56.26 Aligned_cols=77 Identities=8% Similarity=0.006 Sum_probs=57.1
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCC--C
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEA--D 162 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~--~ 162 (318)
..-.|+++.|.|+++++.|+++++|. .++|+|.+.|.+...- +.++..+..|+.|+++|+++..+ +
T Consensus 78 rPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 156 (176)
T PTZ00162 78 KPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN 156 (176)
T ss_pred ecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence 45689999999999999999999985 7799999999743111 11112277899999999776543 3
Q ss_pred CeEEEEeeehh
Q 021034 163 DSLVLSLRMIQ 173 (318)
Q Consensus 163 ~~i~lS~k~~~ 173 (318)
.....|+|.+-
T Consensus 157 ~~~i~T~~~~~ 167 (176)
T PTZ00162 157 LFAIATINSDY 167 (176)
T ss_pred cEEEEEecCCC
Confidence 45777887753
No 169
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.22 E-value=0.00075 Score=58.04 Aligned_cols=55 Identities=22% Similarity=0.342 Sum_probs=45.5
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc------------cCcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV------------ADIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~------------~~~~~~~~~Gq~V~v~V 318 (318)
.|+++.|.|++++++|+||++|-+++++|.++|.++.. .+-...+..|+.|++||
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV 147 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRL 147 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence 59999999999999999999997889999999975321 11235689999999986
No 170
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.13 E-value=0.0012 Score=46.65 Aligned_cols=47 Identities=32% Similarity=0.504 Sum_probs=29.1
Q ss_pred cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.|++.+..|..++++|+|++-+ +-+-|+|.+++... +++||+|.|.|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFv 48 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFV 48 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEE
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEE
Confidence 4889999999999999999998 69999999987633 89999999875
No 171
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=97.05 E-value=0.00084 Score=50.23 Aligned_cols=56 Identities=20% Similarity=0.445 Sum_probs=38.6
Q ss_pred ccCeEEEEEEEEEEcceEEEEEC-------------------CeEEEEecCCcCccccc--CcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIG-------------------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~-------------------gv~Glv~~s~ls~~~~~--~~~~~~~~Gq~V~v~V 318 (318)
++|++|.|.|+++++.-++++|- .+.|+++++++...... ++.+.|++||-|.|+|
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV 79 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence 47999999999999888877763 36899999998776544 4689999999999986
No 172
>PRK05054 exoribonuclease II; Provisional
Probab=96.94 E-value=0.0045 Score=63.73 Aligned_cols=63 Identities=19% Similarity=0.366 Sum_probs=52.9
Q ss_pred CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc---C----C--------cchh-cCCeEeEEEEEEecccCeEee
Q 021034 188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---S----T--------AEEL-LGKDLPLKFVEVDEEQSRLVL 249 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~---~----~--------~~~~-vGq~v~~kVl~vd~~~~~i~l 249 (318)
|+.++|.|++++++|+||++. |+.||+|.+.|.+. + + -+.| +||.|+++|.++|..+++|.+
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~ 641 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA 641 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence 459999999999999999995 89999999998642 1 1 1234 799999999999999999877
Q ss_pred e
Q 021034 250 S 250 (318)
Q Consensus 250 S 250 (318)
+
T Consensus 642 ~ 642 (644)
T PRK05054 642 R 642 (644)
T ss_pred E
Confidence 5
No 173
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.91 E-value=0.0028 Score=54.28 Aligned_cols=73 Identities=22% Similarity=0.323 Sum_probs=59.8
Q ss_pred CeEeeehhhhhhhhHhhcccCeEEEEEEEEEEcceEEEEECC-----------eEEEEecCCcCcccccCcccccCCCCE
Q 021034 245 SRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-----------INGLLHVSQISHDRVADIATVLQPGDT 313 (318)
Q Consensus 245 ~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~g-----------v~Glv~~s~ls~~~~~~~~~~~~~Gq~ 313 (318)
++...|.++... .+.-++.|++|-|.|+.+....+.|++.+ ..|-+|.|+++.....+.++.|++||.
T Consensus 46 ~n~~~~V~p~~~-~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDi 124 (188)
T COG1096 46 KNRVISVKPGKK-TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI 124 (188)
T ss_pred cceEEEeccCCC-CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccE
Confidence 444555554332 34568889999999999999999999853 456789999999999999999999999
Q ss_pred EEEEC
Q 021034 314 LKVCL 318 (318)
Q Consensus 314 V~v~V 318 (318)
|+|+|
T Consensus 125 vrA~V 129 (188)
T COG1096 125 VRARV 129 (188)
T ss_pred EEEEE
Confidence 99986
No 174
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.86 E-value=0.0057 Score=52.36 Aligned_cols=74 Identities=20% Similarity=0.157 Sum_probs=62.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCC----------CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~----------~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i 165 (318)
-++.|++|-|.|+++....+.|.+.+ ...|-+|+++.++.+.++.++. |++||.+.++|++.- ..+
T Consensus 61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~-f~~GDivrA~Vis~~---~~~ 136 (188)
T COG1096 61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDA-FRIGDIVRARVISTG---DPI 136 (188)
T ss_pred CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccc-cccccEEEEEEEecC---CCe
Confidence 56789999999999999999988732 1468999999999999998887 999999999998864 568
Q ss_pred EEEeeehh
Q 021034 166 VLSLRMIQ 173 (318)
Q Consensus 166 ~lS~k~~~ 173 (318)
.||.+...
T Consensus 137 ~Lst~~~d 144 (188)
T COG1096 137 QLSTKGND 144 (188)
T ss_pred EEEecCCc
Confidence 88887653
No 175
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.74 E-value=0.0057 Score=45.75 Aligned_cols=61 Identities=18% Similarity=0.175 Sum_probs=38.7
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeC------------------CCeEEEEeCcccccccccC--ccccCcCCCCEEEEEEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDIT------------------AKSSAYLPTQEACIHKIKH--VEEAGIVPGLKEEFVII 156 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~------------------~~~~g~lp~sEls~~~~~~--~~~~~~~~G~~v~v~Vl 156 (318)
.++|++|.|+|+++.+.-++++|- ....|.|+.+++......+ +.+- |++||.|.++|+
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~-FrpGDIVrA~Vi 80 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC-FRPGDIVRARVI 80 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT---SSSEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc-cCCCCEEEEEEe
Confidence 368999999999999999988771 1356888888876543332 3444 999999999998
Q ss_pred EE
Q 021034 157 GE 158 (318)
Q Consensus 157 ~v 158 (318)
+.
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 73
No 176
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.65 E-value=0.0053 Score=64.37 Aligned_cols=59 Identities=19% Similarity=0.253 Sum_probs=47.7
Q ss_pred CCCCEEEEEEEEEEC--CeEEEEeCCCeEEEEeCcccccccccC---------ccccCcCCCCEEEEEEEE
Q 021034 98 ELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIKH---------VEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~--~G~~V~i~~~~~g~lp~sEls~~~~~~---------~~~~~~~~G~~v~v~Vl~ 157 (318)
.+|.|+.|+|.++.+ +++||+||.+..||||+++.......+ ..+. +++||.|-|-|.+
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~-Lk~GqeILVQV~K 106 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDK 106 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccc-cCCCCEEEEEEee
Confidence 489999999999998 699999999999999999996432211 1233 7889999999966
No 177
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.50 E-value=0.021 Score=56.77 Aligned_cols=145 Identities=14% Similarity=0.160 Sum_probs=98.2
Q ss_pred cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
++++.|....|+|.++.+.|+||+++..+.|+++.++++.. + .+.+|+.+-+.+..+.+.++.+.+.-..+..
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~----~---~~~vgdeiiV~v~~vr~~~geidf~~~~~~~ 190 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD----P---DYAVGDEIIVQVSDVRPEKGEIDFEPVGLDR 190 (715)
T ss_pred hhcccceeeeccccchhhhcceeecChhhhccccccccCCC----C---CCCCCCeEEEEeeccCCCCCccceeecCCcc
Confidence 38899999999999999999999999999999999998752 1 2789999999999998877776655544431
Q ss_pred -----------hHHHHHHhhhcCCC--cEEEEEEEEEE-cCe-EEEEECCEEEEEeCcccCCc--CCcchh-cCCeEeEE
Q 021034 175 -----------ELAWERCRQLQSED--VVVKGKVVGAN-KGG-VVAEVEGLRGFVPFSQISSK--STAEEL-LGKDLPLK 236 (318)
Q Consensus 175 -----------~~~~~~~~~~~~~G--~iv~g~V~~v~-~~G-~~V~i~gl~gfip~s~ls~~--~~~~~~-vGq~v~~k 236 (318)
......+.+. .| ..++|.|+.+. ..| -+..+..=.|+++..-.... ...-++ +|+.|.+.
T Consensus 191 Y~~~~~~ke~~r~~i~~id~~--ig~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGvRAyP~IevGdiV~Vi 268 (715)
T COG1107 191 YREVQVEKELPRTLIDDLDEM--IGKTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVI 268 (715)
T ss_pred chhhhhhhhcccccHHHHHhh--cCceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCcccCCCCCCCceEEEE
Confidence 0112334442 45 35789999983 333 34455444677776655532 221223 78887754
Q ss_pred EEEEecccCeEee
Q 021034 237 FVEVDEEQSRLVL 249 (318)
Q Consensus 237 Vl~vd~~~~~i~l 249 (318)
=+++...+++.+
T Consensus 269 -G~V~~r~g~lQi 280 (715)
T COG1107 269 -GEVTRRDGRLQI 280 (715)
T ss_pred -EEEeecCCcEEE
Confidence 234445566544
No 178
>PRK11712 ribonuclease G; Provisional
Probab=96.44 E-value=0.0088 Score=59.34 Aligned_cols=61 Identities=21% Similarity=0.312 Sum_probs=47.6
Q ss_pred CCCCCCEEEEEEEEEEC--CeEEEEeCCCeEEEEeCcccccc------------cccCccccCcCCCCEEEEEEEE
Q 021034 96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~--~G~~V~i~~~~~g~lp~sEls~~------------~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
...+|.++.|+|.++.+ ++|||++|.+-.||||.+++... ......+. +++||.+-|.|.+
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~Gq~iLVQV~K 109 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISEL-VRQGQDIMVQVVK 109 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHh-ccCCCEEEEEEEe
Confidence 34589999999999998 69999999999999999987310 01112334 7889999998866
No 179
>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=96.41 E-value=0.027 Score=43.52 Aligned_cols=67 Identities=19% Similarity=0.202 Sum_probs=51.0
Q ss_pred HHHHHHHhhhc---cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034 84 EEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (318)
Q Consensus 84 ~~~~~~~~~~~---~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v 158 (318)
+.|++++..+- ..-..|.+|.|+|..+.++-+|+|+|++..++++..+... +. +..|..|.+++.+.
T Consensus 5 ~sFaslLR~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~-y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 5 ESFASLLRNSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EK-YVRGSRVRLRLKDL 74 (104)
T ss_pred ccHHHHhcCChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cc-cccCCEEEEEECCH
Confidence 46777774432 1124799999999999999999999999999999765432 22 77899999888543
No 180
>PRK05054 exoribonuclease II; Provisional
Probab=96.38 E-value=0.022 Score=58.67 Aligned_cols=72 Identities=13% Similarity=0.117 Sum_probs=55.9
Q ss_pred CCC--CEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccc---ccc--C------ccccCcCCCCEEEEEEEEEeCCCC
Q 021034 98 ELG--TKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIH---KIK--H------VEEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 98 ~~G--~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~---~~~--~------~~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
.+| +...|.|+.++++|+||.+ ..+++|++|.+.+.+. +.- + .....|++||.|+|+|.++|..++
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 365 4999999999999999999 4569999999998652 110 1 011128899999999999999998
Q ss_pred eEEEEe
Q 021034 164 SLVLSL 169 (318)
Q Consensus 164 ~i~lS~ 169 (318)
++.++.
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 887653
No 181
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.28 E-value=0.0026 Score=62.98 Aligned_cols=54 Identities=24% Similarity=0.503 Sum_probs=47.2
Q ss_pred HhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 259 ~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+.++..|..++|+|.++..||+||+++ .+.||+|.++++.. ..|.+|+.+-|.+
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v 171 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQV 171 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEe
Confidence 467899999999999999999999999 89999999999863 2378899887764
No 182
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.19 E-value=0.01 Score=52.82 Aligned_cols=57 Identities=30% Similarity=0.462 Sum_probs=50.6
Q ss_pred cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc----ccCcccccCCCCEEEEEC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR----VADIATVLQPGDTLKVCL 318 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~----~~~~~~~~~~Gq~V~v~V 318 (318)
-+.||.|-|.|..+.+.+..|+++ -..+++|.|++.+.. ..+....|++||.|.|+|
T Consensus 62 P~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV 123 (239)
T COG1097 62 PEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKV 123 (239)
T ss_pred CCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEE
Confidence 446999999999999999999999 699999999996655 356788899999999986
No 183
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.18 E-value=0.0079 Score=63.65 Aligned_cols=59 Identities=17% Similarity=0.251 Sum_probs=53.4
Q ss_pred hhcccCeEEEEEEEEEEcce---EEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYG---AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G---~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
+.+.+|.+|.++|++++..- +-|.+. |++|+|+.+++|+..+.+|...+++||+|.|+|
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kv 1043 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKV 1043 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEe
Confidence 56889999999999999644 567777 999999999999999999999999999999986
No 184
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.12 E-value=0.027 Score=58.04 Aligned_cols=63 Identities=17% Similarity=0.364 Sum_probs=51.5
Q ss_pred CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCC--c-C--C-------c--c-hh-cCCeEeEEEEEEecccCeEee
Q 021034 188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISS--K-S--T-------A--E-EL-LGKDLPLKFVEVDEEQSRLVL 249 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~--~-~--~-------~--~-~~-vGq~v~~kVl~vd~~~~~i~l 249 (318)
|....|.|++++++|+||++. |+.||+|.+.+.+ . . + + . .| +||.|+++|.++|.++++|.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 458999999999999999994 8999999999865 1 1 1 1 1 24 799999999999999888875
Q ss_pred e
Q 021034 250 S 250 (318)
Q Consensus 250 S 250 (318)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 185
>PRK11712 ribonuclease G; Provisional
Probab=96.09 E-value=0.0087 Score=59.38 Aligned_cols=58 Identities=31% Similarity=0.516 Sum_probs=46.1
Q ss_pred hcccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCcc------------cccCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~------------~~~~~~~~~~~Gq~V~v~V 318 (318)
...+|.++.|.|.+|.| .++||++| +-.||+|.+++... ...+..+.+++||.|-|.|
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV 107 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQV 107 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEE
Confidence 44579999999999998 78999999 99999999987321 0112355699999998875
No 186
>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=96.09 E-value=0.02 Score=43.30 Aligned_cols=55 Identities=22% Similarity=0.134 Sum_probs=45.9
Q ss_pred ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
++||.|-|.|..++..+.+|+++ -..|++|.+.+.-. ..+....|++||-|-|||
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV 60 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARV 60 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEE
Confidence 57999999999999999999998 78999999776432 333456699999999986
No 187
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.09 E-value=0.0097 Score=62.47 Aligned_cols=56 Identities=25% Similarity=0.509 Sum_probs=46.1
Q ss_pred ccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCccccc---------CcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVA---------DIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~~~~---------~~~~~~~~Gq~V~v~V 318 (318)
.+|.++.|+|.+|.+ .++||+|| |-.||+|.+++...... +....+++||.|-|.|
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV 104 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI 104 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEE
Confidence 479999999999987 78999999 99999999998643221 2345689999999875
No 188
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.08 E-value=0.0067 Score=54.46 Aligned_cols=71 Identities=21% Similarity=0.423 Sum_probs=61.2
Q ss_pred CCCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhh
Q 021034 186 SEDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMA 256 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~ 256 (318)
+.+++|-+.|.++..-|++|.+ +++.|++-.|+||.+ ....++ ||..=.|.|+.+|++++-|-||.+..-.
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 4789999999999999999987 599999999999976 344444 7988889999999999999999887543
No 189
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=95.87 E-value=0.015 Score=60.71 Aligned_cols=58 Identities=28% Similarity=0.569 Sum_probs=48.3
Q ss_pred hcccCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCcccc-----------cCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~-----------~~~~~~~~~Gq~V~v~V 318 (318)
.-.+|+...|+|.+++.+|+||.+. +++|++|.+.+..++. ......|+.||.|++++
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v 689 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKV 689 (706)
T ss_pred HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEE
Confidence 4557999999999999999999997 6999999999996322 23344699999999985
No 190
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=95.78 E-value=0.027 Score=58.74 Aligned_cols=74 Identities=11% Similarity=0.086 Sum_probs=58.9
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCC-eEEEEeCcccccccccCcc----------ccCcCCCCEEEEEEEEEeCCCCe
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~-~~g~lp~sEls~~~~~~~~----------~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
.-.+|+...|+|.++..+|++|.+... .+|++|.+.+...+..... ...++.|+.|++++.+++...+.
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~ 698 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK 698 (706)
T ss_pred HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence 446899999999999999999999654 8999999999853321111 11278999999999999988888
Q ss_pred EEEEe
Q 021034 165 LVLSL 169 (318)
Q Consensus 165 i~lS~ 169 (318)
+.++.
T Consensus 699 i~~~~ 703 (706)
T COG0557 699 IDFEL 703 (706)
T ss_pred eEEEe
Confidence 87764
No 191
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=95.71 E-value=0.1 Score=53.73 Aligned_cols=69 Identities=13% Similarity=0.138 Sum_probs=53.5
Q ss_pred CCEEEEEEEEEECCeEEEEe-CCCeEEEEeCccccc--c-cc--cCc------cccCcCCCCEEEEEEEEEeCCCCeEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--H-KI--KHV------EEAGIVPGLKEEFVIIGENEADDSLVL 167 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~--~-~~--~~~------~~~~~~~G~~v~v~Vl~vd~~~~~i~l 167 (318)
|+...|.|+.+.++|+||.+ ..+.+|++|.+.+.+ + +. .+. .+..|++||.|+|+|.++|.+++++.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 45899999999999999999 567999999999864 2 11 100 111288999999999999988888765
Q ss_pred E
Q 021034 168 S 168 (318)
Q Consensus 168 S 168 (318)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 3
No 192
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=94.74 E-value=0.25 Score=39.84 Aligned_cols=62 Identities=15% Similarity=0.109 Sum_probs=44.4
Q ss_pred CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc---------ccc---CccccCcCCCCEEEEEEEEEeC
Q 021034 99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH---------KIK---HVEEAGIVPGLKEEFVIIGENE 160 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~---------~~~---~~~~~~~~~G~~v~v~Vl~vd~ 160 (318)
+|+++.|+|.+-++.|+.|.++---+-|+|.+.|-.. ++- .-.++-+..|+.|+++|.++.-
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 6999999999999999999998777899999888631 111 1122225789999999987654
No 193
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=94.11 E-value=0.19 Score=42.10 Aligned_cols=55 Identities=22% Similarity=0.315 Sum_probs=38.5
Q ss_pred cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCc----ccccC-c------ccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISH----DRVAD-I------ATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~----~~~~~-~------~~~~~~Gq~V~v~V 318 (318)
.|++|+|+|+.+...|+|++.|-++-++..-.+.. .+-++ | ....++|..|+++|
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~ki 146 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKI 146 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEE
Confidence 49999999999999999999997777665544432 22222 2 12467777777664
No 194
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=93.90 E-value=0.29 Score=37.91 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=42.0
Q ss_pred ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.+|.+|.|.|..+.+.-+||+|| .+.+.|+...... +.|+.|..|.+++
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrL 71 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRL 71 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEE
Confidence 36999999999999999999999 7999999765432 4589999999874
No 195
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.61 E-value=0.53 Score=39.47 Aligned_cols=66 Identities=17% Similarity=0.196 Sum_probs=42.0
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc----ccccCc------cccCcCCCCEEEEEEEEEeCCCC
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHV------EEAGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~----~~~~~~------~~~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
.-.|+++.|+|.++.+.|+|++.|. .+.|+...-+-. ..-.++ .+.....|.+|+++|++...+..
T Consensus 79 pfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~ 154 (170)
T KOG3298|consen 79 PFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET 154 (170)
T ss_pred ecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence 3479999999999999999999986 555544322211 111110 11125678888888887654333
No 196
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=93.47 E-value=0.44 Score=40.38 Aligned_cols=72 Identities=19% Similarity=0.142 Sum_probs=51.8
Q ss_pred CCCCCEEEEEEEEEECCeEEEEe---CC-----CeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDI---TA-----KSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i---~~-----~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
...|++|+++|..+...-+-|+| +. ..+|+||..++-... .-++-+. |++||.|.++|++... +....
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ks-FrPgDiVlAkVis~~~-~~~y~ 143 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKS-FRPGDIVLAKVISLGD-GSNYL 143 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhc-cCCCcEEEEEEeecCC-CCcEE
Confidence 35799999999999998887766 32 358999998885321 1123333 8999999999999654 44566
Q ss_pred EEee
Q 021034 167 LSLR 170 (318)
Q Consensus 167 lS~k 170 (318)
||.-
T Consensus 144 LTtA 147 (193)
T KOG3409|consen 144 LTTA 147 (193)
T ss_pred EEEe
Confidence 6653
No 197
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=93.01 E-value=0.55 Score=37.88 Aligned_cols=56 Identities=18% Similarity=0.251 Sum_probs=42.1
Q ss_pred CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc------CC-----c---chh---cCCeEeEEEEEEec
Q 021034 187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK------ST-----A---EEL---LGKDLPLKFVEVDE 242 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~------~~-----~---~~~---vGq~v~~kVl~vd~ 242 (318)
.|+++.|+|.+.++.|+.|.++ --+-|||.+.|... .. . .++ .|+.|++||.++.-
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 6899999999999999999998 46789999998843 10 1 122 59999999988754
No 198
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=91.98 E-value=0.26 Score=49.13 Aligned_cols=63 Identities=22% Similarity=0.230 Sum_probs=49.6
Q ss_pred CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccccccCccc----cCcCCCCEEEEEEEEEe
Q 021034 96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKIKHVEE----AGIVPGLKEEFVIIGEN 159 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~~~~~~~~----~~~~~G~~v~v~Vl~vd 159 (318)
...+|.++.|.|.++.++ .+|||+|..-.||||.+|+.. +.+.+.+ ..++.||.+-+.|+...
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 345899999999999995 799999999999999999988 3333322 12788998888886643
No 199
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=91.64 E-value=0.38 Score=40.72 Aligned_cols=55 Identities=20% Similarity=0.353 Sum_probs=42.2
Q ss_pred cCeEEEEEEEEEEcceEEEEEC---------CeEEEEecCCcCccc--ccCcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHDR--VADIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~---------gv~Glv~~s~ls~~~--~~~~~~~~~~Gq~V~v~V 318 (318)
+|++|.+.|.+++.-=+-|+|- .+.|++|+.++.... -.++-+.|++||.|.|+|
T Consensus 68 ~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkV 133 (193)
T KOG3409|consen 68 VGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKV 133 (193)
T ss_pred cCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEE
Confidence 5888888888887766666653 289999998886642 345777899999999986
No 200
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=91.51 E-value=2 Score=35.10 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=53.1
Q ss_pred HHHHHHHHhhhc---cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEe
Q 021034 83 LEEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159 (318)
Q Consensus 83 ~~~~~~~~~~~~---~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd 159 (318)
.+.|++++.... ..-..|..|.|+|..+..+-+|+|||++..+.+..-++.. + . +..|..|..++++.+
T Consensus 63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~------e-~-Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNG------E-A-YQKGARVRLRLIDLE 134 (173)
T ss_pred hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCH------H-H-hhcCceEEEEEcChh
Confidence 568999885432 2335799999999999999999999999999888766532 2 2 678988888886543
No 201
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=90.94 E-value=0.21 Score=49.75 Aligned_cols=58 Identities=33% Similarity=0.492 Sum_probs=47.6
Q ss_pred hhcccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCcccccC-----cccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVAD-----IATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~~~~~-----~~~~~~~Gq~V~v~V 318 (318)
....+|.++.|.|++|.| -.+||+++ +-.||+|.+++.+ +... .+..++.||.+-|.|
T Consensus 33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv 98 (487)
T COG1530 33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQV 98 (487)
T ss_pred cEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEE
Confidence 455679999999999998 56999999 8999999999998 3333 245789999987754
No 202
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=86.92 E-value=3.4 Score=36.31 Aligned_cols=63 Identities=17% Similarity=0.037 Sum_probs=50.0
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE 160 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~ 160 (318)
-..+|+.|-|.|+....+..-||+++...|.||.--+....-++-.+ +.+|+-+-++|...++
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPn--l~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPN--LQVGDLIYAKVVDANK 124 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCc--cccccEEEEEEEecCC
Confidence 56789999999999999999999998788988876665443232222 8899999999977553
No 203
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=86.84 E-value=3.2 Score=31.21 Aligned_cols=65 Identities=17% Similarity=0.163 Sum_probs=44.7
Q ss_pred cEEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhh
Q 021034 189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRK 253 (318)
Q Consensus 189 ~iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~ 253 (318)
-.++|+|++...++.| |.++ |..-+.+.+-=......+-+.||.|.+.+...|..+++|+.-.|+
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 3689999999888877 6886 654444322211111223336999999999999999999877663
No 204
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=86.60 E-value=4.8 Score=28.96 Aligned_cols=60 Identities=15% Similarity=0.166 Sum_probs=40.9
Q ss_pred EEEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034 102 KVKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV 166 (318)
Q Consensus 102 iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~ 166 (318)
.+.|+|++..+++.| |.+.++..-..+++- .++.- .....+||.|.+.+-.+|.++++++
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~-rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMH-YIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhc-cEEECCCCEEEEEECcccCCcEeEE
Confidence 568999999999877 687665544444321 11110 1126789999999998988888875
No 205
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=86.33 E-value=5.7 Score=29.94 Aligned_cols=64 Identities=9% Similarity=0.036 Sum_probs=45.2
Q ss_pred EEEEEEEEEECCeEE-EEeCCCeEEEEeCcc-cccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 102 KVKGTVFCTDNRGAL-VDITAKSSAYLPTQE-ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 102 iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sE-ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
.++|+|+...+++.| |.+.++..-+.+++- |.-.+ ....+||.|.|.+-.+|..+++|+.-.+.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r------IrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR------IRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee------EEecCCCEEEEEECcccCCceeEEEEecC
Confidence 568999999998877 688665544444321 11111 12678999999999999999999877664
No 206
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=85.32 E-value=5.1 Score=28.81 Aligned_cols=59 Identities=19% Similarity=0.233 Sum_probs=39.8
Q ss_pred EEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEe
Q 021034 190 VVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLV 248 (318)
Q Consensus 190 iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~ 248 (318)
.+.|+|++...++.| |.++ |..-..+.+-=......+-..|+.|.+.+-..|.++++|+
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 589999999888876 6875 6554444322111111222369999999999998888876
No 207
>PRK15464 cold shock-like protein CspH; Provisional
Probab=84.96 E-value=8.6 Score=27.73 Aligned_cols=50 Identities=18% Similarity=0.319 Sum_probs=35.8
Q ss_pred EEEEEEEEEC-CeE-EEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 103 VKGTVFCTDN-RGA-LVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 103 v~G~V~~i~~-~G~-~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.+|+|...++ .|. |+.- .++-+.|+|++.+.....+. +.+||.|++.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~-----l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEV-----LIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCC-----CCCCCEEEEEEEE
Confidence 4799999976 333 4544 45679999999996442222 6789999998854
No 208
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=84.06 E-value=12 Score=26.13 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=35.3
Q ss_pred EEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 103 VKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 103 v~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.+|+|....+ +|.+..-++..+-|+|.+++...... .+..|+.|++.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~-----~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFR-----SLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSST-----S--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccc-----cCCCCCEEEEEEEE
Confidence 3699999986 35544445556999999999765411 17889999999966
No 209
>PRK10943 cold shock-like protein CspC; Provisional
Probab=83.36 E-value=13 Score=26.55 Aligned_cols=51 Identities=20% Similarity=0.244 Sum_probs=36.6
Q ss_pred EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.++|+|...++ +|.+-.-.++-+-|+|++.+.....+. +..|+.|++.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKT-----LAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCC-----CCCCCEEEEEEEE
Confidence 56899999876 344444455679999999986542222 6789999998854
No 210
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=82.89 E-value=12 Score=27.37 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=40.0
Q ss_pred EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
+|+|...+. +|.+..-.++-+.|+|++.+.....+. +..||.|++.+.. ..++.-.....
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~-----l~~G~~V~f~~~~--~~~G~~A~~V~ 65 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT-----LKAGQSVQFDVHQ--GPKGNHASVIV 65 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCC-----CCCCCEEEEEEEE--CCCCceeeEEE
Confidence 488988875 344444456689999999986442222 6789999999854 44555444333
No 211
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=81.25 E-value=9.3 Score=27.38 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=36.1
Q ss_pred EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.++|+|...++ +|.+-.-.++-+-|+|.+.+.....+. +.+|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKT-----LAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCC-----CCCCCEEEEEEEE
Confidence 46799999875 344443355679999999986432222 6789999998854
No 212
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=80.70 E-value=5.5 Score=34.95 Aligned_cols=73 Identities=22% Similarity=0.151 Sum_probs=51.9
Q ss_pred cCCCCCCEEEEEEEEEECC--eEEEEeCC----CeEEEEeCcccccccccCc-cc----cCcCCCCEEEEEEEEEeCCCC
Q 021034 95 FNSELGTKVKGTVFCTDNR--GALVDITA----KSSAYLPTQEACIHKIKHV-EE----AGIVPGLKEEFVIIGENEADD 163 (318)
Q Consensus 95 ~~~~~G~iv~G~V~~i~~~--G~~V~i~~----~~~g~lp~sEls~~~~~~~-~~----~~~~~G~~v~v~Vl~vd~~~~ 163 (318)
.+++.|+++-|+.....+. |++|+++- -.++++|..++...+-.+| .+ .++-....++|.|..+|...+
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~ 150 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQ 150 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhh
Confidence 4788999999999999775 56677643 2579999999876554444 22 234456789999988887555
Q ss_pred eEEE
Q 021034 164 SLVL 167 (318)
Q Consensus 164 ~i~l 167 (318)
.+-+
T Consensus 151 EIea 154 (247)
T COG4044 151 EIEA 154 (247)
T ss_pred hhhh
Confidence 5443
No 213
>PRK15463 cold shock-like protein CspF; Provisional
Probab=79.79 E-value=18 Score=25.98 Aligned_cols=50 Identities=18% Similarity=0.333 Sum_probs=35.6
Q ss_pred EEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 103 VKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 103 v~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
..|+|...++ +|.+-.-.++-+.|+|++.+....... +.+|+.|++.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~-----l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEE-----LTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCC-----CCCCCEEEEEEEE
Confidence 3799999876 344433355679999999996542222 6789999998744
No 214
>PRK14998 cold shock-like protein CspD; Provisional
Probab=79.51 E-value=17 Score=26.36 Aligned_cols=58 Identities=12% Similarity=0.101 Sum_probs=38.9
Q ss_pred EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
+|+|...+. +|.+-.-.++-+.|+|.+.+.....+. +..|+.|++.+.. ..+|.....
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~-----l~~G~~V~f~~~~--~~~G~~A~~ 63 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT-----LKAGQSVRFDVHQ--GPKGNHASV 63 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCC-----CCCCCEEEEEEEE--CCCCceeEE
Confidence 489988875 344444455689999999986442222 6789999999854 445543333
No 215
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=76.51 E-value=9.4 Score=26.31 Aligned_cols=47 Identities=30% Similarity=0.406 Sum_probs=32.1
Q ss_pred CEEEEEEEEEECCe----EEEEeCCC--eEEEEeCcccccccccCccccCcCCCCEEEEEE
Q 021034 101 TKVKGTVFCTDNRG----ALVDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (318)
Q Consensus 101 ~iv~G~V~~i~~~G----~~V~i~~~--~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~V 155 (318)
..+.|+|..+.+.| ++++++++ ..+.++.... .+..+++|+++.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~--------~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA--------EELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH--------HHCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH--------HHcCCCCCCEEEEEE
Confidence 46899999999988 66677654 4666665433 233488999998876
No 216
>PRK09890 cold shock protein CspG; Provisional
Probab=75.88 E-value=26 Score=25.08 Aligned_cols=50 Identities=14% Similarity=0.142 Sum_probs=35.2
Q ss_pred EEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 103 VKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 103 v~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.+|+|...++ +|.+-.-+++.+-|+|.+.+.....+. +.+|+.|++.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~-----l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRT-----LNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCC-----CCCCCEEEEEEEE
Confidence 4799999875 344443355589999999986543222 6789999997743
No 217
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=75.42 E-value=21 Score=25.42 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=34.2
Q ss_pred EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
+|+|...+. +|.+-.-.++-+.|+|.+.+.....+. +..|+.|++.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~-----l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRT-----LKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCC-----CCCCCEEEEEEEE
Confidence 488988864 344444455689999999986432222 6789999998744
No 218
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=75.36 E-value=12 Score=26.04 Aligned_cols=45 Identities=29% Similarity=0.469 Sum_probs=32.1
Q ss_pred EEEEEEEEEc---ceEEEEEC--CeEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 268 VIGTVQSLKP---YGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 268 v~G~V~~i~~---~G~fV~i~--gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.+|+|+...+ ||. +.-. +-+-++|.+++.... ...++.||.|+..
T Consensus 1 ~~G~V~~~~~~kgyGF-I~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~ 50 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGF-ITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFE 50 (66)
T ss_dssp EEEEEEEEETTTTEEE-EEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEE
T ss_pred CeEEEEEEECCCCceE-EEEcccceeEEeccccccccc----cccCCCCCEEEEE
Confidence 4799999985 554 5554 558999999988653 3568899999765
No 219
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=74.28 E-value=29 Score=24.81 Aligned_cols=50 Identities=16% Similarity=0.143 Sum_probs=35.3
Q ss_pred EEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 103 VKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 103 v~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
..|+|...++ +|.+-.-.++-+-|+|.+.+....... +.+|+.|++.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~-----l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKS-----LDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCC-----CCCCCEEEEEEEE
Confidence 3799999875 455444455579999999986442221 6789999998744
No 220
>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=74.27 E-value=7.2 Score=34.44 Aligned_cols=75 Identities=20% Similarity=0.165 Sum_probs=50.4
Q ss_pred CCCC--CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccc----cCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034 96 NSEL--GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEE----AGIVPGLKEEFVIIGENEADDSLVLSL 169 (318)
Q Consensus 96 ~~~~--G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~----~~~~~G~~v~v~Vl~vd~~~~~i~lS~ 169 (318)
.++. |+.+.|++.+..+.|+.++++ +...-+|.+++.--+...|.+ +.+-..-.++++++..+.. ....+|-
T Consensus 69 ~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~-~~~rltd 146 (225)
T PF09883_consen 69 SLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDG-IEARLTD 146 (225)
T ss_pred hhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccC-cccccCH
Confidence 4455 999999999999999999997 677788888883222223332 2344567788999887643 3444444
Q ss_pred eeh
Q 021034 170 RMI 172 (318)
Q Consensus 170 k~~ 172 (318)
++.
T Consensus 147 ~q~ 149 (225)
T PF09883_consen 147 EQV 149 (225)
T ss_pred HHH
Confidence 433
No 221
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=74.01 E-value=6.6 Score=27.79 Aligned_cols=58 Identities=16% Similarity=0.082 Sum_probs=38.8
Q ss_pred CEEEEEEEEEECCeEEEEeC-CCeEEEEe-CcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034 101 TKVKGTVFCTDNRGALVDIT-AKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENE 160 (318)
Q Consensus 101 ~iv~G~V~~i~~~G~~V~i~-~~~~g~lp-~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~ 160 (318)
...+++|..+.++-++|.+. .+--+++| .+++.+.+.-+ ++. +++|+.+.+.+...+.
T Consensus 2 S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~-sek-lkvG~~l~v~lk~~~~ 61 (69)
T cd05701 2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFD-SEK-LSVGQCLDVTLKDPNC 61 (69)
T ss_pred CccchhhhhhhhceEEEEeeccccEEEEEchhhcccccccc-cee-eeccceEEEEEecCcc
Confidence 34567888888999999883 23345555 45665544333 333 8999999999876554
No 222
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=72.65 E-value=34 Score=25.07 Aligned_cols=66 Identities=14% Similarity=0.179 Sum_probs=42.7
Q ss_pred CCEEEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 100 GTKVKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
.-.+.|+|.+..+++-| |.+.++..-.-+++ -. .+. ......+||.|.+....++.+++++.--.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~---GK-mr~-~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHIS---GK-MRK-NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEcc---Cc-chh-eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 44678999999998865 77765543333321 11 010 011267899999999999888888765443
No 223
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=71.99 E-value=11 Score=29.13 Aligned_cols=51 Identities=24% Similarity=0.426 Sum_probs=32.6
Q ss_pred EEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 267 VVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 267 ~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.+.|.|.++...| +|+++. | +..++..++............+..|+.|.+.
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEE
Confidence 5889999999766 899996 3 5555654443222222222337889988763
No 224
>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=71.95 E-value=19 Score=24.90 Aligned_cols=51 Identities=14% Similarity=0.196 Sum_probs=34.4
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD 162 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~ 162 (318)
-+.|+|..+.++.++++.++ +.+-++|.+.++. +..++++.+.+.-+-.++
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~~~----------l~~~~~v~l~t~~~vrEd 55 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTLSE----------LPEGGEVKLYTYLIVRED 55 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHHHT----------S-TTSEEEEEEEEEEETT
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchHHh----------CCCCCEEEEEEEEEEeec
Confidence 47899999999999999975 4677888765532 455666766664443333
No 225
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=71.25 E-value=21 Score=24.95 Aligned_cols=63 Identities=21% Similarity=0.245 Sum_probs=38.7
Q ss_pred CCEEEEEEEEEECCeEEEEeCCCeEEE-EeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034 100 GTKVKGTVFCTDNRGALVDITAKSSAY-LPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS 168 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~V~i~~~~~g~-lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS 168 (318)
|+.++-+|..+..+|-.+--++.+.|. +..+. + +.....+-+|+++++.|+.+|--.-.+-+|
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~Atr----y--H~~g~nl~pGqK~kaviLhvD~l~~~VhVS 64 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASR----Y--HKEGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEE----E--EecceecCCCceeEEEEEEEeeEEeEEEEe
Confidence 677888888877766543334445543 11111 1 111122679999999999999766666655
No 226
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=70.13 E-value=1.7e+02 Score=31.78 Aligned_cols=26 Identities=27% Similarity=0.254 Sum_probs=19.8
Q ss_pred eeEEEEEEeccchhHHHHHHHHHHHHHHHhhc
Q 021034 42 TIVSAVAISNAETREREELNQLFEEAYERCRT 73 (318)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~ 73 (318)
.||||+= +||+-...+|.+.+..-.+
T Consensus 169 ~VKC~iG------~Er~~a~~LMrK~i~~~~t 194 (1024)
T KOG1999|consen 169 IVKCKIG------REREVAFCLMRKFIELDKT 194 (1024)
T ss_pred EEEeccc------cHHHHHHHHHHHHHhhccc
Confidence 5888863 6788899999998765554
No 227
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=68.63 E-value=40 Score=29.25 Aligned_cols=70 Identities=10% Similarity=0.099 Sum_probs=47.4
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 180 (318)
.+.|+|..+.++.++++.++ +.+-++|.+.++. +..|+.+.+++.-+-.++.....-.....+.+-|..
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~~----------l~~g~~v~l~t~~~vred~~~LyGF~~~~Er~lF~~ 73 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYE----------LNLEQKAQVFTHLVVREDAELLFGFNTLEERELFKE 73 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh----------cCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHH
Confidence 57899999999999999964 5677777665531 445899999886665566554444444444334444
Q ss_pred H
Q 021034 181 C 181 (318)
Q Consensus 181 ~ 181 (318)
+
T Consensus 74 L 74 (191)
T TIGR00084 74 L 74 (191)
T ss_pred H
Confidence 4
No 228
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=68.60 E-value=5.3 Score=27.95 Aligned_cols=51 Identities=18% Similarity=0.243 Sum_probs=28.4
Q ss_pred eEEEEEEEEEEcceEEEEEC-CeEEE-EecCCcCcccccCcccccCCCCEEEEEC
Q 021034 266 SVVIGTVQSLKPYGAFIDIG-GINGL-LHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 266 ~~v~G~V~~i~~~G~fV~i~-gv~Gl-v~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
-.+.|+|.++.+.|.++++. .+.|- .-...++..... .-.+++|+.|.+.+
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~--~l~l~~G~~v~~~i 59 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA--ELGLKPGKEVYAVI 59 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh--hCCCCCCCEEEEEE
Confidence 46889999998888665553 22111 111122221111 23478999987753
No 229
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.29 E-value=46 Score=29.05 Aligned_cols=70 Identities=13% Similarity=0.031 Sum_probs=47.0
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 180 (318)
.+.|+|..+.++.++++.+| +.+-++|.+.++. +..|+.+.+++.-+-.++.....-.....+.+-|..
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~~----------l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~ 73 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLAR----------LVEGQEAELHTRLVVREDALSLYGFPDEDSLELFEL 73 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHHHHH----------cCCCCeEEEEEEEEEccCCceeeCcCCHHHHHHHHH
Confidence 57899999999999999964 4566777544321 456999999887766666655555554444333333
Q ss_pred H
Q 021034 181 C 181 (318)
Q Consensus 181 ~ 181 (318)
+
T Consensus 74 L 74 (197)
T PRK14603 74 L 74 (197)
T ss_pred H
Confidence 3
No 230
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=64.57 E-value=14 Score=25.40 Aligned_cols=46 Identities=26% Similarity=0.512 Sum_probs=30.4
Q ss_pred eEEEEEEEEEEcce----EEEEECC---eEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 266 SVVIGTVQSLKPYG----AFIDIGG---INGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 266 ~~v~G~V~~i~~~G----~fV~i~g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
-.+.|+|..+.+.| +.+++++ +...++..... .=.+++||+|.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-------~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-------ELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-------HCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-------HcCCCCCCEEEEEE
Confidence 46899999999999 6666663 66666553322 12378999998764
No 231
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.09 E-value=55 Score=28.31 Aligned_cols=63 Identities=10% Similarity=0.018 Sum_probs=42.0
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEe-CCCCeEEEEeeehhh
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN-EADDSLVLSLRMIQY 174 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd-~~~~~i~lS~k~~~~ 174 (318)
.+.|+|..+.++.++++.+| +.+-++|.+.+.. +..|+.+.+++..+- .++.....-.....+
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~~----------l~~g~~v~l~t~~~v~rEd~~~LyGF~~~~E 68 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLST----------CKIGDNIKLYIETYVNRDNVTQLYGFLNREE 68 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh----------hCCCCeEEEEEEEEEeecCCceeeCCCCHHH
Confidence 57899999999999999964 4566777644421 457999988875433 455544444444333
No 232
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=63.97 E-value=20 Score=29.41 Aligned_cols=48 Identities=21% Similarity=0.402 Sum_probs=39.8
Q ss_pred cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 264 ~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
.|..|-|.|..+...-+|++|| .+.+.|....+. .+.|+.|-.|.-|+
T Consensus 82 ~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n-------~e~Y~~GaRVrlRl 130 (173)
T KOG4078|consen 82 KGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN-------GEAYQKGARVRLRL 130 (173)
T ss_pred CCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC-------HHHhhcCceEEEEE
Confidence 4999999999999999999999 799999877654 34578888877653
No 233
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.68 E-value=60 Score=28.04 Aligned_cols=70 Identities=11% Similarity=0.126 Sum_probs=45.7
Q ss_pred EEEEEEEEEECCeEEEE-eCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHH
Q 021034 102 KVKGTVFCTDNRGALVD-ITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~-i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~ 179 (318)
.+.|+|..+.++.++++ .+| +.+-++|.+.++ . +..|+.+.+++.-+-.++.....-.....+.+-|.
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GVGY~v~i~~~~~~--------~--l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~ 73 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGVSYGIFISLFCSA--------K--IQKGEKHELFITQIIKEDSNKLYGFLDKDEQKMFE 73 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCEEEEEEecHHHHH--------H--cCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHH
Confidence 57899999999999999 454 466677764432 1 45799998888666556655544444444433344
Q ss_pred HH
Q 021034 180 RC 181 (318)
Q Consensus 180 ~~ 181 (318)
.+
T Consensus 74 ~L 75 (183)
T PRK14601 74 ML 75 (183)
T ss_pred HH
Confidence 33
No 234
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=61.62 E-value=51 Score=22.77 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=34.8
Q ss_pred EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
.|+|....+ +|.+..-.++-+-|+|.+++...... . +.+|+.|++.+..
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~----~-~~~G~~V~f~~~~ 53 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFR----S-LEEGDRVEFELEE 53 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCC----c-CCCCCEEEEEEEE
Confidence 588888876 34444434478999999999754211 2 6889999998855
No 235
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=61.19 E-value=1.3e+02 Score=27.48 Aligned_cols=129 Identities=17% Similarity=0.244 Sum_probs=70.3
Q ss_pred HHHHHHHhhhccCCCCCCEEEEEEEEEECC--eEEEE--eCCC---eEEEEeCcccccccccCccccCcCCCCEEEEEEE
Q 021034 84 EEFHSALEKYDFNSELGTKVKGTVFCTDNR--GALVD--ITAK---SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156 (318)
Q Consensus 84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~--G~~V~--i~~~---~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl 156 (318)
..+..++..+......-..+.|+|.++..+ ...|+ +..+ +.+.+...- .++..+.+|+.+.+.|-
T Consensus 111 ~~l~~~l~~~~~k~SarN~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s--------~~~L~l~~G~~v~~~Ik 182 (263)
T PRK10676 111 DSLLAAISRFSLQTSARNQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQS--------AERLGLDEGKEVLVLIK 182 (263)
T ss_pred HHHHHHHHHhccCcchhhcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHH--------HhhcCCCCCCeEEEEEE
Confidence 344456666665666777999999999865 34443 4322 334443221 12233789999988874
Q ss_pred EEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEE----EC-C--EEEEEeCcccCCcCCcchhc
Q 021034 157 GENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAE----VE-G--LRGFVPFSQISSKSTAEELL 229 (318)
Q Consensus 157 ~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~----i~-g--l~gfip~s~ls~~~~~~~~v 229 (318)
.. .+.++.-.+.. ......+.|+|.++..+|..++ ++ | +.+.++..... .+.--.
T Consensus 183 a~-----~V~l~~~~~~~----------~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~---~L~L~~ 244 (263)
T PRK10676 183 AP-----WVGITQDPAVA----------QAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAA---RLSLQQ 244 (263)
T ss_pred CC-----EEEEEcCCCCC----------CChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHH---hcCCCC
Confidence 42 35555322211 0122478999999987665443 32 2 34444432211 111115
Q ss_pred CCeEeEEEE
Q 021034 230 GKDLPLKFV 238 (318)
Q Consensus 230 Gq~v~~kVl 238 (318)
|+.|.+.+.
T Consensus 245 G~~V~a~iK 253 (263)
T PRK10676 245 GDAVTAYFN 253 (263)
T ss_pred CCEEEEEEE
Confidence 888777654
No 236
>PRK15464 cold shock-like protein CspH; Provisional
Probab=60.20 E-value=32 Score=24.75 Aligned_cols=48 Identities=21% Similarity=0.169 Sum_probs=33.9
Q ss_pred EEEEEEEEEc-CeE-EEEEC--CEEEEEeCcccCCcCCcchh-cCCeEeEEEEE
Q 021034 191 VKGKVVGANK-GGV-VAEVE--GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVE 239 (318)
Q Consensus 191 v~g~V~~v~~-~G~-~V~i~--gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~ 239 (318)
.+|+|+..+. .|+ |+.-+ +-+.|+|.+.+.... .+.+ .||.|.+.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g-~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD-AEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC-CCCCCCCCEEEEEEEE
Confidence 4799999964 444 55543 689999999996431 2223 69999988764
No 237
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.15 E-value=73 Score=27.87 Aligned_cols=70 Identities=10% Similarity=0.058 Sum_probs=44.7
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 180 (318)
.+.|+|..+.++.++++.+| +.+-++|.+-+. . +..|+.+.+++.-+-.++.....-.....+.+-+..
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~~--------~--l~~g~~v~l~t~~~vrED~~~LYGF~t~~Er~lF~~ 73 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCLA--------E--LRLLEDVEILTYLHTREDELKLFGFLNSSEREVFEE 73 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHHH--------h--cCCCCcEEEEEEEEEecCCceeeCCCCHHHHHHHHH
Confidence 57899999999999999964 456667754332 1 446898888875555555544444444433333333
Q ss_pred H
Q 021034 181 C 181 (318)
Q Consensus 181 ~ 181 (318)
+
T Consensus 74 L 74 (196)
T PRK13901 74 L 74 (196)
T ss_pred H
Confidence 3
No 238
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.97 E-value=76 Score=27.65 Aligned_cols=71 Identities=11% Similarity=0.029 Sum_probs=47.2
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 180 (318)
.+.|+|..+.++.++++.++ +.+-++|.+.+.. . ..+|+.+.+++.-+-.++.....-.....+.+-|..
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~~--------l-~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~ 74 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLAA--------I-GAIGDEVFLYTHLIVREDALTLYGFSTPAQRQLFEL 74 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHH--------h-ccCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHH
Confidence 57899999999999999965 4666777554421 1 256999999887665666555555544444333444
Q ss_pred H
Q 021034 181 C 181 (318)
Q Consensus 181 ~ 181 (318)
+
T Consensus 75 L 75 (195)
T PRK14604 75 L 75 (195)
T ss_pred H
Confidence 3
No 239
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=58.38 E-value=29 Score=23.76 Aligned_cols=43 Identities=16% Similarity=0.078 Sum_probs=27.6
Q ss_pred EEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 105 GTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 105 G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
|++....++..||.... ..+-|+|..+|.. ..-||+|.|+++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~----------A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNG----------AMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTT----------S-TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCC----------CCCCCEEEEEEec
Confidence 45555555566777754 6889999888753 3469999999987
No 240
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.15 E-value=83 Score=27.36 Aligned_cols=71 Identities=10% Similarity=0.137 Sum_probs=47.3
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~ 180 (318)
.+.|+|..+.++.++++.+| +.+-++|.+.+.. . ...|+.+.+++.-+-.++.....-.....+.+-|..
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~~--------l-~~~g~~~~l~t~~~vrEd~~~LyGF~~~~Er~lF~~ 74 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPAL--------I-GGLGQRVRVFTHLHVREDALSLFGFATTEELSLFET 74 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHHh--------c-ccCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHH
Confidence 57899999999999999964 5677777655431 1 246899998886666666655554444444333444
Q ss_pred H
Q 021034 181 C 181 (318)
Q Consensus 181 ~ 181 (318)
+
T Consensus 75 L 75 (194)
T PRK14605 75 L 75 (194)
T ss_pred H
Confidence 4
No 241
>COG1278 CspC Cold shock proteins [Transcription]
Probab=58.00 E-value=54 Score=23.46 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=32.6
Q ss_pred EEEEEEEECC--eEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034 104 KGTVFCTDNR--GALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157 (318)
Q Consensus 104 ~G~V~~i~~~--G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~ 157 (318)
+|+|.-.++. .-|+.- .+..+.|+|.|.+.-...+. +..||+|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~-----L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRT-----LREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcc-----cCCCCEEEEEEec
Confidence 4777777542 224443 44479999999986443332 6789999998844
No 242
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=57.58 E-value=25 Score=30.33 Aligned_cols=62 Identities=13% Similarity=0.114 Sum_probs=43.3
Q ss_pred CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc----------------cccCcCCCCEEEEEEEEE
Q 021034 97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------------EEAGIVPGLKEEFVIIGE 158 (318)
Q Consensus 97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~----------------~~~~~~~G~~v~v~Vl~v 158 (318)
.-.|+++.|+|.+-...|+-|.++---+-|+|.+-|.....-.+ .+.-+.+|..++++|.+.
T Consensus 79 PF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 79 PFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 34799999999999999999988766778999876644211111 111145677788877654
No 243
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=57.53 E-value=19 Score=32.67 Aligned_cols=78 Identities=23% Similarity=0.214 Sum_probs=55.3
Q ss_pred HhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc--c--c------CccccCcCCCCEEEEEEEEEe
Q 021034 90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--I--K------HVEEAGIVPGLKEEFVIIGEN 159 (318)
Q Consensus 90 ~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~--~--~------~~~~~~~~~G~~v~v~Vl~vd 159 (318)
..+| ..++|++|-|+|+.+...-+-|+++.+.++.|+.+-+.... . + ...+. |+.||.+.+.|-.+-
T Consensus 78 k~rY--~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~f-l~egDLi~AEVQ~v~ 154 (301)
T KOG3013|consen 78 KSRY--APEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSF-LKEGDLIVAEVQNVF 154 (301)
T ss_pred hhhc--CCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHH-hhccCeehHHHHHhc
Confidence 3445 67899999999999999999999999999999998774311 0 1 11123 677888877775553
Q ss_pred CCCCeEEEEeee
Q 021034 160 EADDSLVLSLRM 171 (318)
Q Consensus 160 ~~~~~i~lS~k~ 171 (318)
.+|.+.|-.|.
T Consensus 155 -~dGs~sLhTRS 165 (301)
T KOG3013|consen 155 -HDGSLSLHTRS 165 (301)
T ss_pred -cCCeEEEEecc
Confidence 35666655544
No 244
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=56.28 E-value=52 Score=22.44 Aligned_cols=55 Identities=18% Similarity=0.215 Sum_probs=30.9
Q ss_pred hhcCCeEeEEEEEEecccCeEeeehhh---hhhhhHhhcccCeEEEEEEEEEEcceEEEE
Q 021034 227 ELLGKDLPLKFVEVDEEQSRLVLSNRK---AMADSQAQLGIGSVVIGTVQSLKPYGAFID 283 (318)
Q Consensus 227 ~~vGq~v~~kVl~vd~~~~~i~lS~K~---~l~~~~~~l~~G~~v~G~V~~i~~~G~fV~ 283 (318)
.++|+++++.|.+.. +.+...--... ...+..... .|+.+...|++..++-++=+
T Consensus 2 ~~~G~~~~VlVe~~~-~~g~~~gr~~~~~~V~v~~~~~~-iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 2 SYVGKTLEVLVEELG-DEGQGIGRTDNGKVVFVPGGLPL-IGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp --TTEEEEEEEEEE--TTSEEEEEET-TEEEEETT--T---TEEEEEEEEEE-SSEEEEE
T ss_pred ccCCcEEEEEEEEec-CCCEEEEEeCCCeEEEECCCCCC-CCCEEEEEEEEeeCCcEEEE
Confidence 357999999999887 44444332221 111111222 59999999999998777643
No 245
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=55.98 E-value=47 Score=29.35 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=42.6
Q ss_pred CCCcEEEEEEEEEEcCeEEEEECC-EEEEEeCcccCC--cCC-cchhcCCeEeEEEEEEec
Q 021034 186 SEDVVVKGKVVGANKGGVVAEVEG-LRGFVPFSQISS--KST-AEELLGKDLPLKFVEVDE 242 (318)
Q Consensus 186 ~~G~iv~g~V~~v~~~G~~V~i~g-l~gfip~s~ls~--~~~-~~~~vGq~v~~kVl~vd~ 242 (318)
..|+.|-|.|+....+++-|+++| --|.+|.-.... ++| |+--+|+.|-|+|...++
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCC
Confidence 478999999999999999999986 556666544332 122 333389999999987754
No 246
>PRK10943 cold shock-like protein CspC; Provisional
Probab=55.87 E-value=55 Score=23.32 Aligned_cols=49 Identities=24% Similarity=0.385 Sum_probs=34.2
Q ss_pred EEEEEEEEEEc---CeEEEEEC-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEE
Q 021034 190 VVKGKVVGANK---GGVVAEVE-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVE 239 (318)
Q Consensus 190 iv~g~V~~v~~---~G~~V~i~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~ 239 (318)
.++|+|+..+. +|.+-.-+ +-+.|+|.+.+.... ...+ .|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g-~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG-FKTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC-CCCCCCCCEEEEEEEE
Confidence 46899999864 35444333 689999999998542 2223 69999998654
No 247
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=54.28 E-value=1e+02 Score=23.91 Aligned_cols=67 Identities=12% Similarity=-0.042 Sum_probs=42.6
Q ss_pred CCCEEEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 99 LGTKVKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
....+.|+|++..+++.| |.+.++..-+.++.- .++. ..-++.||.|.|....++..+++|+.-..+
T Consensus 19 ~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk--~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 19 EEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPG----KMKK--RMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc--cEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 344577999999998877 576555443333211 1111 112678999999998888766666655443
No 248
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=53.70 E-value=66 Score=22.89 Aligned_cols=49 Identities=24% Similarity=0.345 Sum_probs=34.0
Q ss_pred EEEEEEEEEEc---CeEEEEEC-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEE
Q 021034 190 VVKGKVVGANK---GGVVAEVE-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVE 239 (318)
Q Consensus 190 iv~g~V~~v~~---~G~~V~i~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~ 239 (318)
.++|+|+..+. +|++-.-+ +-+.|+|.+.+... ....+ .|+.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~-g~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN-GFKTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc-CCCCCCCCCEEEEEEEE
Confidence 46899999864 34443334 67999999999753 22333 79999987654
No 249
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.88 E-value=85 Score=27.19 Aligned_cols=70 Identities=11% Similarity=0.003 Sum_probs=45.7
Q ss_pred EEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHH
Q 021034 102 KVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~ 179 (318)
.+.|+|..+.++.++++. |-+.+-++|.+-+. + +..|+++.+++.-+-.++.....-.....+.+-|.
T Consensus 4 ~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~~--------~--l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~ 73 (188)
T PRK14606 4 GISGRVLKKSGNVLLVETKSGVVFEIVCDVQTSE--------E--VEEGGECFLHTFLSVSQDGITLYGFSNERKKELFL 73 (188)
T ss_pred eEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHHH--------H--cCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHH
Confidence 578999999999999994 44567777754432 1 45699999988666566655444444443333333
Q ss_pred HH
Q 021034 180 RC 181 (318)
Q Consensus 180 ~~ 181 (318)
.+
T Consensus 74 ~L 75 (188)
T PRK14606 74 SL 75 (188)
T ss_pred HH
Confidence 33
No 250
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=52.08 E-value=92 Score=22.81 Aligned_cols=60 Identities=12% Similarity=0.036 Sum_probs=38.9
Q ss_pred EEEEEEEEECCeEE-EEeCCCeE--EEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 103 VKGTVFCTDNRGAL-VDITAKSS--AYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 103 v~G~V~~i~~~G~~-V~i~~~~~--g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
+.|+|++..+++.| |...++.. |.+|-. +++ ..-++.||.|.+....+|..+++++--..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK------~rk--~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~ 64 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGK------MRK--RVWINEGDIVLVAPWDFQDDKADIIYKYT 64 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchh------hcc--cEEEcCCCEEEEEeccccCCEEEEEEEcC
Confidence 46899999988876 67655443 444431 121 12267899999998887766666655443
No 251
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=49.91 E-value=91 Score=22.85 Aligned_cols=59 Identities=24% Similarity=0.327 Sum_probs=40.1
Q ss_pred EEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCC---cchhcCCeEeEEEEEEecccCeEeeeh
Q 021034 190 VVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKST---AEELLGKDLPLKFVEVDEEQSRLVLSN 251 (318)
Q Consensus 190 iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~---~~~~vGq~v~~kVl~vd~~~~~i~lS~ 251 (318)
.+.|+|.+...++.| |.++ |.. -..|++-+.. .+-..|+.|.+.....|.++.+|.--.
T Consensus 8 e~~g~V~e~L~~~~f~v~~edg~~---~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELENGHE---RLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred EEEEEEEEecCCCEEEEEecCCcE---EEEEccCcchheeEEeCCCCEEEEEecccccccccEEEEe
Confidence 589999999887776 7775 433 3334444411 222259999999999998888876543
No 252
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=49.09 E-value=51 Score=22.51 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=25.2
Q ss_pred EEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchhcCCeEeEEEEE
Q 021034 193 GKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (318)
Q Consensus 193 g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~ 239 (318)
|++....++-.||... +-+-|||..++....+ |++|.++++.
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~~-----gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGAMD-----GDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS-T-----T-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCCCC-----CCEEEEEEec
Confidence 3444444444455554 7889999877665433 9999999987
No 253
>PRK15463 cold shock-like protein CspF; Provisional
Probab=48.79 E-value=70 Score=22.92 Aligned_cols=48 Identities=21% Similarity=0.219 Sum_probs=33.7
Q ss_pred EEEEEEEEEc-CeE-EEEE-C-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEE
Q 021034 191 VKGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVE 239 (318)
Q Consensus 191 v~g~V~~v~~-~G~-~V~i-~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~ 239 (318)
.+|+|+..+. .|+ |+.- + +-+.|+|.+.+...- ...+ .||.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g-~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD-AEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC-CCCCCCCCEEEEEEEE
Confidence 4799999964 344 4554 3 689999999997531 2223 69999997654
No 254
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=46.06 E-value=57 Score=28.36 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=36.3
Q ss_pred eEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC-CCeEEEEeeehhhhHH
Q 021034 123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA-DDSLVLSLRMIQYELA 177 (318)
Q Consensus 123 ~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~-~~~i~lS~k~~~~~~~ 177 (318)
.+|+||..++. |.+. |++|+++.+.+.++... ++++.+|+..+.....
T Consensus 2 ~~~~l~~~~~~------~~e~-~~~g~ri~~~~~~v~~~~~g~~~~srt~~~~~~~ 50 (190)
T COG0195 2 VEAILPKREQI------PGEN-FKVGDRIRALLYEVQKEAKGQIELSRTIPELLEK 50 (190)
T ss_pred ceeEcchhhcC------CCcc-cccCcEEEEEEeeeeecCcccEEEEeccHHHHHH
Confidence 57999998874 3344 89999999999998753 3468899887766433
No 255
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=45.92 E-value=1e+02 Score=21.62 Aligned_cols=45 Identities=27% Similarity=0.397 Sum_probs=31.1
Q ss_pred EEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEE
Q 021034 102 KVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~V 155 (318)
-++|+|.++.+....+.+..+-.=-+| .|+... .+++|.+|.+..
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~lp-~ef~~~--------~L~~G~kV~V~y 48 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKLP-EEFDFD--------GLKPGMKVVVFY 48 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEECC-Cccccc--------ccCCCCEEEEEE
Confidence 478999999999999999654433344 333321 278999876554
No 256
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.84 E-value=75 Score=22.26 Aligned_cols=61 Identities=20% Similarity=0.148 Sum_probs=32.6
Q ss_pred CcEEEEEEEEEEcCeEEEEE-CCEEEEE-eCcccCCcCCcchh-cCCeEeEEEEEEecccCeEeee
Q 021034 188 DVVVKGKVVGANKGGVVAEV-EGLRGFV-PFSQISSKSTAEEL-LGKDLPLKFVEVDEEQSRLVLS 250 (318)
Q Consensus 188 G~iv~g~V~~v~~~G~~V~i-~gl~gfi-p~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~~i~lS 250 (318)
|+..+-.|-.++.+|-.+-- +.+.|.- .++..- ..-..+ -||++++.|+.+|--+-.+.+|
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~AtryH--~~g~nl~pGqK~kaviLhvD~l~~~VhVS 64 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYH--KEGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEEE--ecceecCCCceeEEEEEEEeeEEeEEEEe
Confidence 34556667776554443332 3344331 111100 111223 4999999999999766666655
No 257
>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=44.98 E-value=58 Score=22.44 Aligned_cols=31 Identities=45% Similarity=0.607 Sum_probs=25.2
Q ss_pred EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccC
Q 021034 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQIS 220 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls 220 (318)
-+.|+|..+.++.++++.+ |.+-++|.+.+.
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 4789999999999999997 678888866544
No 258
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=44.75 E-value=51 Score=29.23 Aligned_cols=92 Identities=15% Similarity=0.225 Sum_probs=59.4
Q ss_pred CCCeEEEEeeehhhh-------HHHHHHhhhcCC--CcEEEEEEEEEEcCeEEEEECCEEEEEeCccc-CCc-CCc----
Q 021034 161 ADDSLVLSLRMIQYE-------LAWERCRQLQSE--DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQI-SSK-STA---- 225 (318)
Q Consensus 161 ~~~~i~lS~k~~~~~-------~~~~~~~~~~~~--G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~l-s~~-~~~---- 225 (318)
.++.+.+|..-...+ +.|-++....+. |+++.|++.+..+.|+.++++|+..-+|..+| ... ..+
T Consensus 39 ~~~wv~vtl~GeD~eva~Nll~eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~G~~~~ip~d~L~~Lg~g~~~Qi~ 118 (225)
T PF09883_consen 39 KDDWVKVTLEGEDEEVAANLLREEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVDGIFVPIPKDELKPLGPGSPRQIR 118 (225)
T ss_pred cCCceEEEEecCcHHHHHHHHHHHhCCCCchhcccCCceEEEEEEeecccceEEEeecccccCcHHHhcccCCCCHHHHH
Confidence 456677776655542 234333333345 99999999999999999999888888999998 332 122
Q ss_pred chh-c--CCeEeEEEEEEecccCeEeeehhh
Q 021034 226 EEL-L--GKDLPLKFVEVDEEQSRLVLSNRK 253 (318)
Q Consensus 226 ~~~-v--Gq~v~~kVl~vd~~~~~i~lS~K~ 253 (318)
+.| . .-.|+++|++.+.. -...||-++
T Consensus 119 ~rFG~V~hlPvev~~v~~~~~-~~~rltd~q 148 (225)
T PF09883_consen 119 RRFGLVQHLPVEVEFVKVEDG-IEARLTDEQ 148 (225)
T ss_pred HHhCcccCCceEEEEEEcccC-cccccCHHH
Confidence 223 2 34555888887653 344555443
No 259
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=43.21 E-value=43 Score=23.75 Aligned_cols=53 Identities=19% Similarity=0.224 Sum_probs=36.2
Q ss_pred EEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCcC--Ccchh-cCCeEeEEEEEEecc
Q 021034 191 VKGKVVGANKGGVVAEVE---GLRGFVPFSQISSKS--TAEEL-LGKDLPLKFVEVDEE 243 (318)
Q Consensus 191 v~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~~--~~~~~-vGq~v~~kVl~vd~~ 243 (318)
.+++|..+.+.=++|.+. .+.+|=-.||+.+-. +-+++ +||.+.+.+.+.+..
T Consensus 4 htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~~ 62 (69)
T cd05701 4 HTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCL 62 (69)
T ss_pred cchhhhhhhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCccC
Confidence 456667777777778773 455555567888653 33556 899999998776543
No 260
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=43.03 E-value=2.9e+02 Score=25.99 Aligned_cols=114 Identities=18% Similarity=0.222 Sum_probs=61.9
Q ss_pred CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhH
Q 021034 98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYEL 176 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~ 176 (318)
+.|.+++|+|..-++..-.-.+.- ...-.+|. + ...+|+.+.++|-.-| +.+.++++...
T Consensus 230 e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~--~-----------~a~~g~~~R~~I~a~D-----Vslal~~P~~~- 290 (352)
T COG4148 230 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPK--L-----------DAPVGARLRIRIQARD-----VSLALQKPEQT- 290 (352)
T ss_pred ccceEEEEEehhcCCCcceEEEecCceEEEeec--c-----------CCCCCCcEEEEEEccc-----eEEEecCcccc-
Confidence 468999999999887543333321 23333332 1 1568999999885433 67777776542
Q ss_pred HHHHHhhhcCCCcEEEEEEEEEEcCeEEEE----ECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEE
Q 021034 177 AWERCRQLQSEDVVVKGKVVGANKGGVVAE----VEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240 (318)
Q Consensus 177 ~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~----i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~v 240 (318)
..-.++.|+|+++...+--|+ ++|-.-.--.+..+.. .+.-.+||-|.+.|..+
T Consensus 291 ---------SirNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~srd-~L~l~~G~~v~AqIKsV 348 (352)
T COG4148 291 ---------SIRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWARD-ELALKPGQWVYAQIKSV 348 (352)
T ss_pred ---------chhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhhHH-hhcCCCCCeEEEEEEEE
Confidence 122367788888865443322 2343333333333321 11111566666666554
No 261
>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=42.94 E-value=54 Score=22.67 Aligned_cols=19 Identities=32% Similarity=0.324 Sum_probs=17.0
Q ss_pred EEEEEEEEECCeEEEEeCC
Q 021034 103 VKGTVFCTDNRGALVDITA 121 (318)
Q Consensus 103 v~G~V~~i~~~G~~V~i~~ 121 (318)
.+|+|.++..+.++|++..
T Consensus 16 ~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cEEEEEEEecCcEEEEEEe
Confidence 5899999999999999953
No 262
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=42.77 E-value=61 Score=29.59 Aligned_cols=110 Identities=13% Similarity=0.156 Sum_probs=59.6
Q ss_pred cEEEEEEEEEEcC--eEEEE--EC-C---EEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhhhhhhhHh
Q 021034 189 VVVKGKVVGANKG--GVVAE--VE-G---LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQA 260 (318)
Q Consensus 189 ~iv~g~V~~v~~~--G~~V~--i~-g---l~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~~ 260 (318)
..+.|+|.++..+ +..|+ +. | +.+.|...-.. .+.--.|+.+.+.|-. ..+.++.-.. .
T Consensus 128 N~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~---~L~l~~G~~v~~~Ika-----~~V~l~~~~~-----~ 194 (263)
T PRK10676 128 NQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAE---RLGLDEGKEVLVLIKA-----PWVGITQDPA-----V 194 (263)
T ss_pred hcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHh---hcCCCCCCeEEEEEEC-----CEEEEEcCCC-----C
Confidence 3689999999765 34444 42 2 44555422211 1222268888877643 3355542111 1
Q ss_pred hcccCeEEEEEEEEEEcceEEEE----EC-C--eEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 261 QLGIGSVVIGTVQSLKPYGAFID----IG-G--INGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~~~G~fV~----i~-g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
....-..+.|+|.++...|..++ ++ | +...++... .. .-.+++|+.|.+.+
T Consensus 195 ~~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s-----~~--~L~L~~G~~V~a~i 252 (263)
T PRK10676 195 AQAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNE-----AA--RLSLQQGDAVTAYF 252 (263)
T ss_pred CCChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHH-----HH--hcCCCCCCEEEEEE
Confidence 22334689999999987665443 32 2 333333221 11 12388999998753
No 263
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=42.61 E-value=96 Score=22.49 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=32.7
Q ss_pred EEEEEEEEc-CeE-EEEE-C-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEE
Q 021034 192 KGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEV 240 (318)
Q Consensus 192 ~g~V~~v~~-~G~-~V~i-~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~v 240 (318)
+|+|+..+. .|+ |+.- + +-+.|+|.+.+...- ...+ .||.|.+.+..-
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g-~~~l~~G~~V~f~~~~~ 55 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-YRTLKAGQSVQFDVHQG 55 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC-CCCCCCCCEEEEEEEEC
Confidence 588888864 343 4444 3 799999999987431 2233 699999887653
No 264
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=41.75 E-value=49 Score=28.58 Aligned_cols=54 Identities=15% Similarity=0.288 Sum_probs=40.4
Q ss_pred CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc-------------CC-----cchh---cCCeEeEEEEEE
Q 021034 187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK-------------ST-----AEEL---LGKDLPLKFVEV 240 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~-------------~~-----~~~~---vGq~v~~kVl~v 240 (318)
.|+++.|+|.+.+..|+-|.++ -=+-|+|.+-|... .. ..++ +|..|+++|.+.
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 7889999999999999998887 44678888777632 11 1232 589999998876
No 265
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.57 E-value=29 Score=30.60 Aligned_cols=45 Identities=27% Similarity=0.528 Sum_probs=33.8
Q ss_pred hhcccCeEEEEEEEEEEc--ceEEEEEC--C---eEEEEecCCcCcccccCc
Q 021034 260 AQLGIGSVVIGTVQSLKP--YGAFIDIG--G---INGLLHVSQISHDRVADI 304 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~--~G~fV~i~--g---v~Glv~~s~ls~~~~~~~ 304 (318)
.++++|+++-|+.....+ ||++|+++ | .++|+|.-++....-..|
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekp 122 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKP 122 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCc
Confidence 578899999999999986 77777776 2 678888877665543333
No 266
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=39.64 E-value=8.8 Score=37.75 Aligned_cols=62 Identities=16% Similarity=0.371 Sum_probs=47.2
Q ss_pred CCcEEEEEEEEEEcCeEEEEE--CCEEEEEeCcccCCcC-----C-------c---chh-cCCeEeEEEEEEecccCeEe
Q 021034 187 EDVVVKGKVVGANKGGVVAEV--EGLRGFVPFSQISSKS-----T-------A---EEL-LGKDLPLKFVEVDEEQSRLV 248 (318)
Q Consensus 187 ~G~iv~g~V~~v~~~G~~V~i--~gl~gfip~s~ls~~~-----~-------~---~~~-vGq~v~~kVl~vd~~~~~i~ 248 (318)
.+..+.+.|..++.+|+-|++ +|-.+|||..-+-+.+ + . ..| +|+.+.+.+.++..++|.|+
T Consensus 561 ~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRsii 640 (645)
T COG4776 561 TNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRSII 640 (645)
T ss_pred cCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhhhhh
Confidence 457789999999999999998 4999999988766431 1 1 123 68888888888887776654
No 267
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=39.50 E-value=1.8e+02 Score=23.08 Aligned_cols=68 Identities=19% Similarity=0.205 Sum_probs=35.9
Q ss_pred CEEEEEEEEEECCeEEEEeC-CCeEEE-EeCcccccccccCccc-cCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 101 TKVKGTVFCTDNRGALVDIT-AKSSAY-LPTQEACIHKIKHVEE-AGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 101 ~iv~G~V~~i~~~G~~V~i~-~~~~g~-lp~sEls~~~~~~~~~-~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
-..+|+|.+++...=.+.+. +.+.++ -|.--|... +.++.. ..+++|+.|.+.+.. .+++.++.+.++
T Consensus 43 ~~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~-v~~~~~l~~lk~G~~V~F~~~~--~~~~~~i~~i~~ 113 (115)
T PRK09838 43 ISGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFT-ITPQTKMSEIKTGDKVAFNFVQ--QGNLSLLQDIKV 113 (115)
T ss_pred EEEEEEEEEEeCCCCEEEEeecccccCCCCCcccccc-CCChhhhccCCCCCEEEEEEEE--cCCcEEEEEEee
Confidence 34589999998766333442 123333 222222211 111111 127999999998864 335556666554
No 268
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=39.29 E-value=34 Score=23.71 Aligned_cols=48 Identities=21% Similarity=0.309 Sum_probs=30.9
Q ss_pred CCEEEEEEEEEECCeEE----EEeCCC--eEEEEeCcccccccccCccccCcCCCCEEEEEE
Q 021034 100 GTKVKGTVFCTDNRGAL----VDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (318)
Q Consensus 100 G~iv~G~V~~i~~~G~~----V~i~~~--~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~V 155 (318)
...+.|+|.++...|.. ++++++ ..+.++...+ .+..+++|+.+.+.+
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~--------~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV--------AELGLKPGKEVYAVI 59 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH--------hhCCCCCCCEEEEEE
Confidence 45789999999776543 344333 4455555333 223488999998877
No 269
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.27 E-value=1.9e+02 Score=25.32 Aligned_cols=70 Identities=10% Similarity=0.102 Sum_probs=43.3
Q ss_pred EEEEEEEEEECCeE-EEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHH
Q 021034 102 KVKGTVFCTDNRGA-LVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179 (318)
Q Consensus 102 iv~G~V~~i~~~G~-~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~ 179 (318)
.+.|+|..+.++.+ +++.+| +.+-++|.+-+. .. ...|+.+.+++.-+-.++.....-.....+.+-|.
T Consensus 4 ~l~G~v~~~~~~~~vviev~GvGY~v~i~~~~~~--------~l-~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~ 74 (203)
T PRK14602 4 YLEGRVAERRENSCVVLTPGGVGYEVFLPAHTLA--------RL-PEKGGQVSFFVHTVVREDALELFGFATWDERQTFI 74 (203)
T ss_pred eEEEEEEEEcCCcEEEEEeCCEEEEEEcCHHHHH--------Hh-ccCCCeEEEEEEEEEecCcceeeCCCCHHHHHHHH
Confidence 57899999988865 678864 456666654332 11 25699999988666556655444444443333333
Q ss_pred H
Q 021034 180 R 180 (318)
Q Consensus 180 ~ 180 (318)
.
T Consensus 75 ~ 75 (203)
T PRK14602 75 V 75 (203)
T ss_pred H
Confidence 3
No 270
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=36.93 E-value=1.9e+02 Score=23.67 Aligned_cols=57 Identities=19% Similarity=0.192 Sum_probs=35.7
Q ss_pred CCCCEEEEEEEEEECCe---------EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC
Q 021034 98 ELGTKVKGTVFCTDNRG---------ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD 162 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G---------~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~ 162 (318)
..|.+.+-||+...+.| ++|++.++...+.++.. .+|++ .++|+.|++........+
T Consensus 62 ~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~------~~p~~--v~iGm~V~~v~~~~~~~~ 127 (140)
T COG1545 62 GEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD------VDPDD--VEIGMKVEAVFRKREEDG 127 (140)
T ss_pred CCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe------cCccc--ccCCCEEEEEEEEccccC
Confidence 46888888888877654 45666544445555433 22433 678999988887655433
No 271
>PRK14998 cold shock-like protein CspD; Provisional
Probab=36.58 E-value=1.3e+02 Score=21.69 Aligned_cols=48 Identities=21% Similarity=0.221 Sum_probs=32.7
Q ss_pred EEEEEEEEc-CeE-EEEE-C-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEE
Q 021034 192 KGKVVGANK-GGV-VAEV-E-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEV 240 (318)
Q Consensus 192 ~g~V~~v~~-~G~-~V~i-~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~v 240 (318)
+|+|+..+. .|+ |+.- + +-+.|+|.|.+.... ...+ .|+.|.+.+..-
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g-~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-YRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC-CCCCCCCCEEEEEEEEC
Confidence 588988864 343 4444 3 689999999987431 2223 699999987653
No 272
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=36.11 E-value=1.1e+02 Score=23.10 Aligned_cols=49 Identities=27% Similarity=0.403 Sum_probs=29.7
Q ss_pred EEEEEEEEEEcce---EEEEEC-C---eEEEEecCC--cCcccccCcccccCCCCEEEE
Q 021034 267 VVIGTVQSLKPYG---AFIDIG-G---INGLLHVSQ--ISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 267 ~v~G~V~~i~~~G---~fV~i~-g---v~Glv~~s~--ls~~~~~~~~~~~~~Gq~V~v 316 (318)
.+.|.|.++...| +|+.+. + +..++...+ .+.... .....+..|+.|.+
T Consensus 3 ~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~-~~~~~l~~es~V~V 60 (102)
T cd04320 3 LIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMV-KWAGSLSKESIVDV 60 (102)
T ss_pred EEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHH-HHHhcCCCccEEEE
Confidence 5789999999877 899996 2 555665443 111111 11123667777765
No 273
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=36.03 E-value=1.5e+02 Score=25.68 Aligned_cols=60 Identities=10% Similarity=0.035 Sum_probs=41.3
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC-CeEEEEeee
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD-DSLVLSLRM 171 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~-~~i~lS~k~ 171 (318)
.+.|+|..+.++.++++.++ +.+-++|...++. . -..|+.+.+.++..-.++ -++ .+...
T Consensus 4 ~i~G~i~~~~~~~~ii~~~gvGY~v~~~~~~~~~--------l-~~~~~~~~l~~~~~~rd~~~~l-~gF~~ 65 (192)
T PRK00116 4 YLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLYE--------L-PEVGEEVKLYTHLVVREDAILL-YGFLT 65 (192)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHh--------c-cCCCCeEEEEEEEEEechhHHH-cCcCC
Confidence 57899999999999999965 4667777655432 1 156899988886654433 344 55553
No 274
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=35.77 E-value=1.2e+02 Score=23.14 Aligned_cols=48 Identities=15% Similarity=0.265 Sum_probs=28.0
Q ss_pred EEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEE
Q 021034 267 VVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 267 ~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v 316 (318)
.+.|.|.++...| +|+.+. + +..++..+ .+.+..... ..+..|+.|.+
T Consensus 3 ~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~-~~~~~~~~~-~~l~~~s~v~V 56 (103)
T cd04319 3 TLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKD-LNEEAYREA-KKVGIESSVIV 56 (103)
T ss_pred EEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCC-CCHHHHHHH-hCCCCCCEEEE
Confidence 5789999998765 899996 3 33344332 211111111 23677887765
No 275
>PRK09890 cold shock protein CspG; Provisional
Probab=35.49 E-value=1.6e+02 Score=20.91 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=33.2
Q ss_pred EEEEEEEEEc---CeEEEEEC-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEE
Q 021034 191 VKGKVVGANK---GGVVAEVE-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVE 239 (318)
Q Consensus 191 v~g~V~~v~~---~G~~V~i~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~ 239 (318)
.+|+|+..+. +|.+-.-+ +-+.|+|.+.+.... ...+ .|+.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~-~~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE-FRTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCC-CCCCCCCCEEEEEEEE
Confidence 4799999863 35444333 689999999988542 2233 69999997643
No 276
>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=35.20 E-value=1.9e+02 Score=21.52 Aligned_cols=30 Identities=20% Similarity=0.304 Sum_probs=23.2
Q ss_pred CCCCCCEE------EEEEEEEECCeEEEEeCCCeEE
Q 021034 96 NSELGTKV------KGTVFCTDNRGALVDITAKSSA 125 (318)
Q Consensus 96 ~~~~G~iv------~G~V~~i~~~G~~V~i~~~~~g 125 (318)
++++|+.| -|+|.++.++.+.+++..+..-
T Consensus 37 ~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~i 72 (84)
T TIGR00739 37 SLKKGDKVLTIGGIIGTVTKIAENTIVIELNDNTEI 72 (84)
T ss_pred hCCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEE
Confidence 66788876 5899999999888888655443
No 277
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=35.09 E-value=1.4e+02 Score=21.61 Aligned_cols=48 Identities=21% Similarity=0.311 Sum_probs=27.9
Q ss_pred EEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 267 VVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 267 ~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.+.|.|.++...| +|+.+. + +..++..+..+. .. .-..+..|+.|.+.
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~--~~-~~~~l~~es~V~V~ 56 (84)
T cd04323 3 KVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTE--FY-DAKSLTQESSVEVT 56 (84)
T ss_pred EEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchh--HH-HHhcCCCcCEEEEE
Confidence 5789999998765 899996 2 334443332210 11 11236678877663
No 278
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=34.99 E-value=86 Score=21.96 Aligned_cols=56 Identities=16% Similarity=0.024 Sum_probs=33.0
Q ss_pred EEEEEEEEEECCeEE-EEeCCC--eEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034 102 KVKGTVFCTDNRGAL-VDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL 165 (318)
Q Consensus 102 iv~G~V~~i~~~G~~-V~i~~~--~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i 165 (318)
.+.|.|++...++.| |.+.++ ..+.+|-. +. .. .-++.|+.|.|-+-..|..++++
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK-~r----~~---iwI~~GD~V~V~~~~~d~~kG~I 62 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPGK-FR----KR---IWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-HH-HH----TC---C---TTEEEEEEESTTCTTEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccc-ee----ee---EecCCCCEEEEEecccCCCeEEE
Confidence 467999999988776 777655 44666654 21 11 12678999987774444444444
No 279
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=34.93 E-value=2.1e+02 Score=22.02 Aligned_cols=37 Identities=14% Similarity=0.186 Sum_probs=27.3
Q ss_pred CCCCCCEE------EEEEEEEECCeEEEEeCCCeEEEEeCccc
Q 021034 96 NSELGTKV------KGTVFCTDNRGALVDITAKSSAYLPTQEA 132 (318)
Q Consensus 96 ~~~~G~iv------~G~V~~i~~~G~~V~i~~~~~g~lp~sEl 132 (318)
+++.||.| .|+|.++.++.+.+.++.+.+.-+-.+-+
T Consensus 43 sL~kGD~VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~~~k~aI 85 (97)
T COG1862 43 SLKKGDEVVTIGGIVGTVTKVGDDTVEIELGDGTKIKFEKEAI 85 (97)
T ss_pred hccCCCEEEEcCCeEEEEEEEecCcEEEEECCCeEEEEEHHHH
Confidence 55677775 68999999988888888666665555444
No 280
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=34.90 E-value=1e+02 Score=28.37 Aligned_cols=49 Identities=29% Similarity=0.397 Sum_probs=39.2
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v 158 (318)
....|.+-+|.|++..++|.+|++|..--+.++. - +.+|..+.++|.+.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~-------------~-~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSS-------------P-APPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceeccC-------------C-CCCCceEEEEEEec
Confidence 3568999999999999999999998654444442 1 57899999999775
No 281
>CHL00010 infA translation initiation factor 1
Probab=34.73 E-value=1.8e+02 Score=21.21 Aligned_cols=62 Identities=15% Similarity=0.184 Sum_probs=33.8
Q ss_pred EEEEEEEEEEc-CeEEEEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeeh
Q 021034 190 VVKGKVVGANK-GGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN 251 (318)
Q Consensus 190 iv~g~V~~v~~-~G~~V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~ 251 (318)
.+.|.|++... +=+.|.+. |..-.++..--.........+|+.|.+.+...+..+++|+--.
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEe
Confidence 36789999885 44556663 4222222111111112233479999988766666666665443
No 282
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=33.69 E-value=2.4e+02 Score=23.65 Aligned_cols=69 Identities=13% Similarity=0.050 Sum_probs=42.7
Q ss_pred CCCCEEEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034 98 ELGTKVKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ 173 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~ 173 (318)
+.|+. -|+|++..+++.| |.+..+..-+.+++= .++. ..-+.+|+.|.|..-.++..+++|+.-....+
T Consensus 30 eegq~-~g~V~~~LGn~~f~V~c~dG~~rLa~I~G----KmRK--~IWI~~GD~VlVel~~yd~~KgdIi~Ry~~de 99 (155)
T PTZ00329 30 EEGQE-YAQVLRMLGNGRLEAYCFDGVKRLCHIRG----KMRK--RVWINIGDIILVSLRDFQDSKADVILKYTPDE 99 (155)
T ss_pred CCCcE-EEEEEEEcCCCEEEEEECCCCEEEEEeec----ccee--eEEecCCCEEEEeccCCCCCEEEEEEEcCHHH
Confidence 45664 5999999998876 566544443333211 1111 12267899999988777766677766555543
No 283
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=33.05 E-value=30 Score=30.36 Aligned_cols=18 Identities=28% Similarity=0.663 Sum_probs=15.7
Q ss_pred cceEEEEEC-CeEEEEecC
Q 021034 277 PYGAFIDIG-GINGLLHVS 294 (318)
Q Consensus 277 ~~G~fV~i~-gv~Glv~~s 294 (318)
+.|+||-|. |++||+-+.
T Consensus 49 DiGCFvlFDGGFsGLVviN 67 (229)
T PF11813_consen 49 DIGCFVLFDGGFSGLVVIN 67 (229)
T ss_pred CcceEEEecCCcceEEEEe
Confidence 589999998 999998764
No 284
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=32.89 E-value=1.5e+02 Score=19.63 Aligned_cols=48 Identities=10% Similarity=0.154 Sum_probs=28.8
Q ss_pred EEEEEEECCeEEEEeCCC-eEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034 105 GTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE 158 (318)
Q Consensus 105 G~V~~i~~~G~~V~i~~~-~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v 158 (318)
|+|....++..|+..... .+.|+|.+.+.. . .. .+..|+.|.|++...
T Consensus 2 G~i~~~~~g~gfv~~~~~~~~i~v~~~~~~~-~---~~--~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQG-G---LK--SLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCeeEEecCCCCccEEEEhHHhhc-C---CC--cCCCCCEEEEEEEEc
Confidence 566655554345544422 478888765321 0 11 156799999999764
No 285
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=32.62 E-value=1.8e+02 Score=20.66 Aligned_cols=40 Identities=15% Similarity=0.082 Sum_probs=31.0
Q ss_pred EEEEEEECCeEEEEeCCCe-EEEEeCcccccccccCccccCcCCCCEEEE
Q 021034 105 GTVFCTDNRGALVDITAKS-SAYLPTQEACIHKIKHVEEAGIVPGLKEEF 153 (318)
Q Consensus 105 G~V~~i~~~G~~V~i~~~~-~g~lp~sEls~~~~~~~~~~~~~~G~~v~v 153 (318)
++|-++..+-|.+.+.++. .--+|.+.+. .+ .+.|+.+.+
T Consensus 2 ~ivDRiE~~~AVl~~~~~~~~~~vp~~~LP-------~~--~keGDvl~i 42 (71)
T PF11213_consen 2 AIVDRIEGDYAVLELEDGEKEIDVPRSRLP-------EG--AKEGDVLEI 42 (71)
T ss_pred eEEEEEeCCEEEEEECCCeEEEEEEHHHCC-------CC--CCcccEEEE
Confidence 6788898888999887666 7888888773 22 688998776
No 286
>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=32.26 E-value=81 Score=20.62 Aligned_cols=34 Identities=9% Similarity=-0.028 Sum_probs=23.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE 131 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE 131 (318)
.++.|+++.-. .+..++.+.... ++..|++|.+-
T Consensus 14 s~~~Gd~i~v~-~~~~~~W~~g~~-~g~~G~~P~~y 47 (49)
T PF14604_consen 14 SFKKGDVITVL-EKSDDGWWYGRN-TGRTGLFPANY 47 (49)
T ss_dssp EB-TTEEEEEE-EESSTSEEEEEE-TTEEEEEEGGG
T ss_pred eEcCCCEEEEE-EeCCCCEEEEEE-CCEEEEECHHh
Confidence 57899999754 444556667777 56999999763
No 287
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=31.98 E-value=38 Score=30.18 Aligned_cols=58 Identities=19% Similarity=0.220 Sum_probs=42.7
Q ss_pred cCCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034 95 FNSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE 160 (318)
Q Consensus 95 ~~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~ 160 (318)
...++|++++|.|-.+.+. |+++ .+-..+-+|..+++..+. . ...+++.++.|...|.
T Consensus 103 f~Pk~Gd~LeG~Vn~vS~sHIglLI--hg~FNASIpk~nip~dw~-----f-I~md~eee~~v~ntD~ 162 (253)
T KOG4134|consen 103 FRPKAGDILEGVVNHVSRSHIGLLI--HGVFNASIPKTNIPADWE-----F-IAMDQEEEIRVKNTDI 162 (253)
T ss_pred ECCCCCCeeeeeeeecchhhhceee--hhhhhccCCCCCCcccee-----e-ecCCchhhhceeeccc
Confidence 5678999999999988764 5554 333447788888765543 1 5679999999988774
No 288
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=31.98 E-value=1.7e+02 Score=21.72 Aligned_cols=43 Identities=16% Similarity=0.129 Sum_probs=27.6
Q ss_pred EEEEEEEEECC--eEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEE
Q 021034 103 VKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155 (318)
Q Consensus 103 v~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~V 155 (318)
+.|.|..+.++ -+.|+++| +.=-+.++-+.. + .++||-|-+++
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gG-vkreV~l~Lv~~-------~--v~~GdyVLVHv 49 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGG-VKREVNLDLVGE-------E--VKVGDYVLVHV 49 (82)
T ss_pred cccEEEEEeCCCceEEEEecc-EeEEEEeeeecC-------c--cccCCEEEEEe
Confidence 46899999885 38999975 332222222211 1 67899998876
No 289
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=31.52 E-value=2e+02 Score=20.68 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=29.7
Q ss_pred EEEEEEEEEEcc--eEEEEEC---C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 267 VVIGTVQSLKPY--GAFIDIG---G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 267 ~v~G~V~~i~~~--G~fV~i~---g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.+.|.|.++... -+|+.+. + +..++..+...+. ....+..|+.|.+.
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~----~~~~l~~gs~V~v~ 57 (82)
T cd04318 3 TVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFK----EILKLSTGSSIRVE 57 (82)
T ss_pred EEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHH----HHhcCCCceEEEEE
Confidence 578999999865 4799994 3 5666655433211 12346778877663
No 290
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=31.44 E-value=84 Score=28.87 Aligned_cols=46 Identities=24% Similarity=0.276 Sum_probs=35.2
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V 318 (318)
..-.+|..-+|.|.+..+.|.+|++| +-.+.++.. +.+|..|+++|
T Consensus 101 ~~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~~-------------~~~~~RvTvri 147 (272)
T COG2106 101 TSPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSSP-------------APPGARVTVRI 147 (272)
T ss_pred CCccceeecceEEEEecCCceEEEecCCcceeccCC-------------CCCCceEEEEE
Confidence 35678999999999999999999998 555554422 56777777764
No 291
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=31.11 E-value=2.6e+02 Score=21.98 Aligned_cols=37 Identities=11% Similarity=0.123 Sum_probs=26.9
Q ss_pred CCCCCCEE------EEEEEEEECCeEEEEeCCCeEEEEeCccc
Q 021034 96 NSELGTKV------KGTVFCTDNRGALVDITAKSSAYLPTQEA 132 (318)
Q Consensus 96 ~~~~G~iv------~G~V~~i~~~G~~V~i~~~~~g~lp~sEl 132 (318)
++++|+.| -|+|.++.++-+.+++..+..--+..+-+
T Consensus 38 ~Lk~GD~VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~r~AI 80 (109)
T PRK05886 38 SLQPGDRVHTTSGLQATIVGITDDTVDLEIAPGVVTTWMKLAV 80 (109)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhhhe
Confidence 56788876 59999999998889987655544444433
No 292
>PLN00208 translation initiation factor (eIF); Provisional
Probab=31.04 E-value=3.1e+02 Score=22.78 Aligned_cols=65 Identities=11% Similarity=0.041 Sum_probs=40.7
Q ss_pred CCCCEEEEEEEEEECCeEE-EEeCCCeE--EEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034 98 ELGTKVKGTVFCTDNRGAL-VDITAKSS--AYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171 (318)
Q Consensus 98 ~~G~iv~G~V~~i~~~G~~-V~i~~~~~--g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~ 171 (318)
..|+ +-|+|++...++.| |....+.. |.+|-. ++. ..-++.|+.|.|.+-.++..++.|+.-...
T Consensus 30 ~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGK------mRK--rIWI~~GD~VlVel~~~d~~KgdIv~ry~~ 97 (145)
T PLN00208 30 EDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCHIRGK------MRK--KVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
T ss_pred CCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEEecc------cee--eEEecCCCEEEEEccCCCCCEEEEEEEcCH
Confidence 4566 45999999998876 56655443 444421 111 112678999999987777666666554443
No 293
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=30.55 E-value=2.3e+02 Score=21.04 Aligned_cols=63 Identities=14% Similarity=0.082 Sum_probs=39.3
Q ss_pred CCCEEEEEEEEEECCeEE-EEeCCCeE--EEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034 99 LGTKVKGTVFCTDNRGAL-VDITAKSS--AYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 99 ~G~iv~G~V~~i~~~G~~-V~i~~~~~--g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
.|+ +.|+|++...++.| |...++.. |.+|-. +++ ..-++.||.|.+.....+..++.|+--..
T Consensus 4 e~q-~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK------~Rk--~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 4 DGQ-EIAQVVKMLGNGRLEVMCADGKERLARIPGK------MRK--KVWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred CCc-EEEEEEEEcCCCEEEEEECCCCEEEEEEchh------hcc--cEEEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 344 66999999988876 56655443 444421 111 11267899999988777666666554443
No 294
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=30.14 E-value=1.6e+02 Score=22.60 Aligned_cols=50 Identities=14% Similarity=0.240 Sum_probs=28.5
Q ss_pred eEEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEE
Q 021034 266 SVVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 266 ~~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v 316 (318)
-.+.|.|.++...| +|+.+. + +..++..++.+..... ....+..|+.|.+
T Consensus 15 V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~-~~~~l~~es~V~V 70 (108)
T cd04316 15 VTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFK-TVRKLSRESVISV 70 (108)
T ss_pred EEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHH-HHhCCCCcCEEEE
Confidence 34789999988766 688885 3 4455543332211111 1124677777765
No 295
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=30.05 E-value=1.5e+02 Score=22.73 Aligned_cols=25 Identities=36% Similarity=0.379 Sum_probs=17.2
Q ss_pred hhcccCeEEEEEEEEEEcceEEEEECC
Q 021034 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG 286 (318)
Q Consensus 260 ~~l~~G~~v~G~V~~i~~~G~fV~i~g 286 (318)
+.-++-.++.|+|.+..| +-|++.+
T Consensus 12 ~~~~p~~i~~G~V~s~~P--L~I~i~~ 36 (100)
T PF10844_consen 12 EASNPVDIVIGTVVSVPP--LKIKIDQ 36 (100)
T ss_pred hcCCCceeEEEEEEeccc--EEEEECC
Confidence 344455667888888888 6677764
No 296
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=28.45 E-value=2.4e+02 Score=20.59 Aligned_cols=48 Identities=25% Similarity=0.406 Sum_probs=34.6
Q ss_pred cCCCcEEEEEEEEEEcCe-EEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEec
Q 021034 185 QSEDVVVKGKVVGANKGG-VVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDE 242 (318)
Q Consensus 185 ~~~G~iv~g~V~~v~~~G-~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~ 242 (318)
.+.|+.++..|..+.+.| =...++|..-|+|-.+ .|++++++|.++-+
T Consensus 13 VeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~----------~Gd~V~vkI~~v~~ 61 (73)
T COG3269 13 VEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAE----------VGDEVKVKITKVKP 61 (73)
T ss_pred cccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCC----------CCCeeeEEEEEeec
Confidence 357889999999886543 2334558888888433 69999999988754
No 297
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=27.29 E-value=85 Score=21.35 Aligned_cols=49 Identities=20% Similarity=0.347 Sum_probs=30.0
Q ss_pred eEEEEEEEEEEcceEEEEEC-C-e-EEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 266 SVVIGTVQSLKPYGAFIDIG-G-I-NGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 266 ~~v~G~V~~i~~~G~fV~i~-g-v-~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
.-+.+.|..+...|..+.+. . . .|=.---+|+.+. ..-.+..||+|-++
T Consensus 5 ~~l~a~V~~v~~~G~~vRlEl~~~~~~~~iEvel~~~~---~~l~l~~G~~V~l~ 56 (58)
T PF12857_consen 5 GGLPARVRRVRPVGPEVRLELKRLDDGEPIEVELPRER---RQLGLQPGDRVYLR 56 (58)
T ss_pred CcEeEEEEEEEecCCeEEEEEEECCCCCEEEEEeCHhH---HhcCCCCCCEEEEE
Confidence 45788999999999888775 1 1 1111112333332 22347779999765
No 298
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=26.98 E-value=2.1e+02 Score=20.94 Aligned_cols=40 Identities=20% Similarity=0.331 Sum_probs=27.6
Q ss_pred EEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCCCEEEE
Q 021034 268 VIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 268 v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v 316 (318)
+.|.|..+.+..+.|+++|..--+...-++ ..++||.|-+
T Consensus 5 iP~~V~~i~~~~A~v~~~G~~~~v~l~lv~---------~~~vGD~VLV 44 (76)
T TIGR00074 5 IPGQVVEIDENIALVEFCGIKRDVSLDLVG---------EVKVGDYVLV 44 (76)
T ss_pred cceEEEEEcCCEEEEEcCCeEEEEEEEeeC---------CCCCCCEEEE
Confidence 567888898888999998765444443332 1568888765
No 299
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=26.72 E-value=6.6e+02 Score=30.05 Aligned_cols=142 Identities=12% Similarity=0.082 Sum_probs=76.5
Q ss_pred ccchhHHHHHHHHHHHHHHHhhcCCCCC--------CCCCHHHHHHHHhhhccCCCCCCEEE-----------EEEEEEE
Q 021034 51 NAETREREELNQLFEEAYERCRTAPMEG--------VSFTLEEFHSALEKYDFNSELGTKVK-----------GTVFCTD 111 (318)
Q Consensus 51 ~~~~~~~~~~~~~i~e~~~~~~~~~~~~--------~~~s~~~~~~~~~~~~~~~~~G~iv~-----------G~V~~i~ 111 (318)
.+.+++|..|-..+.+.+..--....+. +.+|.++.. +...+++|+++. ++|..+.
T Consensus 633 ~~t~~dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r-----~~~~Yr~Gdvv~~y~~~~~~~~~y~V~~V~ 707 (1960)
T TIGR02760 633 ATTHREQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRR-----NAAHYKQGMVIRFWQKGKIPHDDYVVTNVN 707 (1960)
T ss_pred cCCcHHHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHh-----hHhhcCCCCEEEeecccCccCCcEEEEEEe
Confidence 3455789999999999885432211111 123333333 223456777776 5677776
Q ss_pred C--CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCc
Q 021034 112 N--RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDV 189 (318)
Q Consensus 112 ~--~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~ 189 (318)
+ +.+.|....+..-.+..+++.+.. .. + +......+.+- ...++.++...... .+..|+
T Consensus 708 ~~~n~L~l~~~dG~~~~~~p~~l~~~~----~~--~---svy~~~~l~ia-~Gdrl~~trn~~~~---------gl~ng~ 768 (1960)
T TIGR02760 708 KHNNTLTLKDAQGKTQKFKPSSLKDLE----RP--F---SVYRPEQLEVA-AGERLQVTGNHFHS---------RVRNGE 768 (1960)
T ss_pred CCCCEEEEEcCCCCEEEECHHHhcccc----cc--e---eeecccccccc-CCCEEEEccCCccc---------CccCCC
Confidence 5 556666543444444444442200 00 1 11222233332 24567777654322 134777
Q ss_pred EEEEEEEEEEcCeEEEEEC-CEEEEEeCcc
Q 021034 190 VVKGKVVGANKGGVVAEVE-GLRGFVPFSQ 218 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ 218 (318)
.+. |.++...++.+... |-.-.||.++
T Consensus 769 ~~t--V~~i~~~~i~l~~~~g~~~~L~~~~ 796 (1960)
T TIGR02760 769 LLT--VSSINNEGITLITEDGQTLHLPHGA 796 (1960)
T ss_pred EEE--EEEEcCCeEEEEeCCCceEEccCCC
Confidence 554 88999999988875 6566676654
No 300
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.98 E-value=2.5e+02 Score=20.02 Aligned_cols=61 Identities=20% Similarity=0.254 Sum_probs=33.6
Q ss_pred cEEEEEEEEEEcCe-EEEEE-CCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEee
Q 021034 189 VVVKGKVVGANKGG-VVAEV-EGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVL 249 (318)
Q Consensus 189 ~iv~g~V~~v~~~G-~~V~i-~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~l 249 (318)
-..+|.|++...++ +.|.+ +|..-.++..---.....+..+||.|.+.+...+..+++|+.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 35679999988774 45655 343222221111111122234799999887666665666553
No 301
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=25.74 E-value=1.4e+02 Score=29.84 Aligned_cols=51 Identities=22% Similarity=0.350 Sum_probs=33.9
Q ss_pred eEEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 266 SVVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 266 ~~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
-.+.|.|.++...| +|+.+. + +..++....+.......... +..|+.|.|.
T Consensus 57 v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v~ 113 (491)
T PRK00484 57 VSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKK-LDLGDIIGVE 113 (491)
T ss_pred EEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhc-CCCCCEEEEE
Confidence 46899999999877 899995 2 56666655443222222222 7889988764
No 302
>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=25.52 E-value=1.9e+02 Score=19.09 Aligned_cols=35 Identities=14% Similarity=0.024 Sum_probs=23.4
Q ss_pred hcccCeEEEEEEEEEE-cceEEEEECCeEEEEecCCc
Q 021034 261 QLGIGSVVIGTVQSLK-PYGAFIDIGGINGLLHVSQI 296 (318)
Q Consensus 261 ~l~~G~~v~G~V~~i~-~~G~fV~i~gv~Glv~~s~l 296 (318)
.++.|+++.-. ..-. +.-.++..+|-.|++|.+.+
T Consensus 17 s~~~Gd~i~v~-~~~~~~~ww~~~~~g~~G~~P~~~v 52 (55)
T PF07653_consen 17 SFKKGDVIEVL-GEKDDDGWWLGENNGRRGWFPSSYV 52 (55)
T ss_dssp EB-TTEEEEEE-EEECSTSEEEEEETTEEEEEEGGGE
T ss_pred EEecCCEEEEE-EeecCCCEEEEEECCcEEEEcHHHE
Confidence 57789988754 2333 33366777799999998765
No 303
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=25.41 E-value=1.4e+02 Score=23.86 Aligned_cols=48 Identities=21% Similarity=0.360 Sum_probs=27.4
Q ss_pred eEEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEE
Q 021034 266 SVVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 266 ~~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v 316 (318)
-.+.|+|.++...| +|+.+. | +..++..+.... . .....+..|+.|.|
T Consensus 17 V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~--~-~~~~~l~~gs~V~V 70 (135)
T cd04317 17 VTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPE--F-ELAEKLRNESVIQV 70 (135)
T ss_pred EEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhH--H-HHHhCCCCccEEEE
Confidence 45788999888765 888885 3 444443332210 0 01123667777765
No 304
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.75 E-value=2.1e+02 Score=24.86 Aligned_cols=47 Identities=19% Similarity=0.252 Sum_probs=33.9
Q ss_pred EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchhcCCeEeEEEEEE
Q 021034 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~v 240 (318)
.+.|+|..+.++.++++++ |..-++|.+.+..-.+ .|+.+...+-.+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~~l~~----~g~~~~l~t~~~ 52 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGVGFRCYMPATSPALIGG----LGQRVRVFTHLH 52 (194)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEeCHHHHHhccc----CCCeEEEEEEEE
Confidence 5799999999999999997 6778888655432111 477777775444
No 305
>PRK13605 endoribonuclease SymE; Provisional
Probab=24.40 E-value=1.5e+02 Score=23.51 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=32.6
Q ss_pred EeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh--hHHHHHHhh
Q 021034 127 LPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY--ELAWERCRQ 183 (318)
Q Consensus 127 lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~--~~~~~~~~~ 183 (318)
.|.-.|...+++ +.+|..|+.+.++| ++|+|+++...... .+-|..+.+
T Consensus 37 ~PaI~LkG~WLe---eAGF~tG~~V~V~V-----~~G~LVIt~~~~~~~~~el~~~l~~ 87 (113)
T PRK13605 37 IPAITLKGQWLE---AAGFATGTAVDVRV-----MEGCIVLTAQPPAAEESELMQSLRQ 87 (113)
T ss_pred CCceeECchhHH---hhCCCCCCeEEEEE-----eCCEEEEEeCCCCcccHHHHHHHHH
Confidence 444445555544 45699999999888 35899999888733 345555544
No 306
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.33 E-value=2.1e+02 Score=24.90 Aligned_cols=47 Identities=17% Similarity=0.320 Sum_probs=33.8
Q ss_pred EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchhcCCeEeEEEEEE
Q 021034 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~v 240 (318)
.++|+|..+..+.++++++ |..-++|.+.+..-.+ +|+.++..+-.+
T Consensus 4 ~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~~l~~----~g~~v~l~t~~~ 52 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLAAIGA----IGDEVFLYTHLI 52 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHHHhcc----CCCeEEEEEEEE
Confidence 5799999999999999997 6777787554432111 588887775444
No 307
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=23.89 E-value=1.7e+02 Score=21.18 Aligned_cols=48 Identities=23% Similarity=0.385 Sum_probs=27.9
Q ss_pred EEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEE
Q 021034 267 VVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKV 316 (318)
Q Consensus 267 ~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v 316 (318)
.+.|.|.++...| +|+.+. + +..++..+.... .......+..|+.|.+
T Consensus 3 ~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~--~~~~~~~l~~~s~V~v 56 (85)
T cd04100 3 TLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGE--FFEEAEKLRTESVVGV 56 (85)
T ss_pred EEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChH--HHHHHhCCCCCCEEEE
Confidence 5789999887654 788885 3 455554433211 0011234678888776
No 308
>PRK04950 ProP expression regulator; Provisional
Probab=23.62 E-value=82 Score=27.89 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=26.8
Q ss_pred cEEEEEEEEEEcCeEEEEEC-CEEEEEeCccc
Q 021034 189 VVVKGKVVGANKGGVVAEVE-GLRGFVPFSQI 219 (318)
Q Consensus 189 ~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~l 219 (318)
..+.|+|++++++|+-|++. |+...+...||
T Consensus 180 ~~~~a~i~ei~kd~v~vql~~Gl~~~v~ae~l 211 (213)
T PRK04950 180 SAMDATVLEITKDDVRVQLDSGLSMIVRAEHL 211 (213)
T ss_pred CCCceEEEEEecCcEEEEcCCCcEEEEeHhhh
Confidence 45678999999999999997 99888887775
No 309
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=23.45 E-value=3e+02 Score=20.12 Aligned_cols=64 Identities=11% Similarity=-0.047 Sum_probs=38.7
Q ss_pred EEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE-eCCCCeEEEEeeeh
Q 021034 103 VKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE-NEADDSLVLSLRMI 172 (318)
Q Consensus 103 v~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v-d~~~~~i~lS~k~~ 172 (318)
.-|+|++..+++.| |...++..-++++.- ..-++ .-++.|+.|.+....+ ++.++.++--..+.
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~g---K~Rk~---iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPG---KLRKN---IWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEch---hhccC---EEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 35889999888876 676655443333311 11111 1267899999988777 55566665544443
No 310
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.43 E-value=2.6e+02 Score=24.49 Aligned_cols=54 Identities=9% Similarity=0.060 Sum_probs=39.6
Q ss_pred EEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034 102 KVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS 164 (318)
Q Consensus 102 iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~ 164 (318)
.+.|+|..+.+..+.++.++ +..-++|.+.+.. . ..+|+.+..++..+-.++..
T Consensus 4 ~l~G~v~~~~~~~ivie~~GVGY~i~~~~~~~~~--------l-~~~g~~~~l~t~~~vREd~~ 58 (201)
T COG0632 4 YLRGKVTEKNPDYIVIEVNGVGYEINVPMRTLAE--------L-PEVGEEVKLFTHLVVREDAH 58 (201)
T ss_pred eeEEEEEEecCCEEEEEeCCEEEEEEcChHHHhh--------c-ccCCCeEEEEEEEeehhhHH
Confidence 57899999999999999964 4666777655421 1 24699999988777666543
No 311
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=23.26 E-value=97 Score=26.55 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=25.9
Q ss_pred EEEEEEEEEEcCeEEEEEC-CEEEEEeCccc
Q 021034 190 VVKGKVVGANKGGVVAEVE-GLRGFVPFSQI 219 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~-gl~gfip~s~l 219 (318)
--.++|.+++++|+-|.++ |+...+...||
T Consensus 176 a~~AtvlEv~Kd~vRVqL~~Gl~m~V~AehL 206 (208)
T COG3109 176 AMDATVLEITKDGVRVQLNSGLSMIVRAEHL 206 (208)
T ss_pred cccceEEEEeccceEEeecCCceEEEehhhh
Confidence 3468999999999999997 99988887776
No 312
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=23.08 E-value=1.7e+02 Score=28.66 Aligned_cols=51 Identities=16% Similarity=0.185 Sum_probs=32.9
Q ss_pred eEEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 266 SVVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 266 ~~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
-.+.|.|.++...| +|+.+- + +...+..++.+....... ..+..|+.|.|.
T Consensus 15 v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v~ 71 (428)
T TIGR00458 15 VTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWA-KKLNLESVVAVR 71 (428)
T ss_pred EEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHH-hCCCCCcEEEEE
Confidence 45789999999877 899985 2 566666555433211111 347788888763
No 313
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=23.03 E-value=1.5e+02 Score=21.52 Aligned_cols=42 Identities=21% Similarity=0.321 Sum_probs=25.8
Q ss_pred EEEEEEEEEc----ceEEEEECC-------eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 268 VIGTVQSLKP----YGAFIDIGG-------INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 268 v~G~V~~i~~----~G~fV~i~g-------v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
|+|.|+...+ .|.|++=.. -.|+.-... . ...+++||.|.+.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~-------~-~~~~~~Gd~V~vt 54 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTG-------S-GADVAVGDLVRVT 54 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecC-------C-CCCCCCCCEEEEE
Confidence 7899999887 688887641 233322110 0 3447889998763
No 314
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=22.57 E-value=6.6e+02 Score=23.72 Aligned_cols=132 Identities=17% Similarity=0.268 Sum_probs=75.1
Q ss_pred CCCeEEEEeeehhhhHHHHHH-----hhhcCCCcEEEEEEEEEE-cCeEE-EEECCEEEEEeCcccCCcCCcchhcCCeE
Q 021034 161 ADDSLVLSLRMIQYELAWERC-----RQLQSEDVVVKGKVVGAN-KGGVV-AEVEGLRGFVPFSQISSKSTAEELLGKDL 233 (318)
Q Consensus 161 ~~~~i~lS~k~~~~~~~~~~~-----~~~~~~G~iv~g~V~~v~-~~G~~-V~i~gl~gfip~s~ls~~~~~~~~vGq~v 233 (318)
++|++..|-+-. +-|.+. ...-+.|.+++|+|..-. .+|+. +.++...-.+|.-.+ -+|+.+
T Consensus 203 e~GkV~A~g~~e---~v~~~~~~~p~~~~~e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~~~a--------~~g~~~ 271 (352)
T COG4148 203 ENGKVKASGPLE---EVWGSPDFPPWLPREEQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKLDA--------PVGARL 271 (352)
T ss_pred cCCeEEecCcHH---HHhcCcccCcccCccccceEEEEEehhcCCCcceEEEecCceEEEeeccCC--------CCCCcE
Confidence 356776665432 234322 111246889999998874 46664 344544444442221 168888
Q ss_pred eEEEEEEecccCeEeeehhhhhhhhHhhcccCeEEEEEEEEEEcce----EEEEECCeEEEEecCCcCcccccCcccccC
Q 021034 234 PLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYG----AFIDIGGINGLLHVSQISHDRVADIATVLQ 309 (318)
Q Consensus 234 ~~kVl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i~~~G----~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~ 309 (318)
+++|-. +-+.+++++.. ....-.++.|+|..|.+.+ ++++++|-.=...++..+.+ +=.++
T Consensus 272 R~~I~a-----~DVslal~~P~-----~~SirNiLp~~v~~i~~~~~~V~v~ld~~g~~l~Arit~~srd-----~L~l~ 336 (352)
T COG4148 272 RIRIQA-----RDVSLALQKPE-----QTSIRNILPGKVVGIEDDDGQVDVQLDCGGKTLWARITPWARD-----ELALK 336 (352)
T ss_pred EEEEEc-----cceEEEecCcc-----ccchhhccceeEEEEEcCCCcEEEEEEcCCcEEEEEccHhhHH-----hhcCC
Confidence 887753 33556655432 2334467888899888655 33444454444455554443 23489
Q ss_pred CCCEEEEEC
Q 021034 310 PGDTLKVCL 318 (318)
Q Consensus 310 ~Gq~V~v~V 318 (318)
+||.|-|.|
T Consensus 337 ~G~~v~AqI 345 (352)
T COG4148 337 PGQWVYAQI 345 (352)
T ss_pred CCCeEEEEE
Confidence 999998764
No 315
>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=22.39 E-value=1.8e+02 Score=19.81 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=21.2
Q ss_pred EEEEEcCeEEEEECCEEEEEeCcccCCc
Q 021034 195 VVGANKGGVVAEVEGLRGFVPFSQISSK 222 (318)
Q Consensus 195 V~~v~~~G~~V~i~gl~gfip~s~ls~~ 222 (318)
|++.+..|++|.-++---+||.++|+..
T Consensus 14 I~~~~~~gy~vpHgdH~HyI~k~dLs~~ 41 (53)
T PF04270_consen 14 IISETGDGYVVPHGDHFHYIPKSDLSAS 41 (53)
T ss_dssp --EE-SSEEEEEETTEEEEEEGGGS-HH
T ss_pred ccccCCCeEEeeCCCcccCCchhhCCHH
Confidence 4556689999999999999999999853
No 316
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=22.34 E-value=3e+02 Score=19.61 Aligned_cols=59 Identities=17% Similarity=0.148 Sum_probs=33.4
Q ss_pred EEEEEEEEEECC-eEEEEeCCC--eEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEE
Q 021034 102 KVKGTVFCTDNR-GALVDITAK--SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL 167 (318)
Q Consensus 102 iv~G~V~~i~~~-G~~V~i~~~--~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~l 167 (318)
..+|.|++...+ .+.|...++ ..+.++- .++.. .....+||.|.+.+-..++.++.|+.
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~G------klr~~-~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISG------KMRKN-YIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEcc------ceeeC-CcccCCCCEEEEEEcccCCCeEEEEE
Confidence 456999999877 455655333 2233221 11111 11156899999987556655565543
No 317
>COG0307 RibC Riboflavin synthase alpha chain [Coenzyme metabolism]
Probab=22.31 E-value=5.4e+02 Score=22.64 Aligned_cols=131 Identities=17% Similarity=0.175 Sum_probs=67.1
Q ss_pred CCCCCCEEE-----EEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEE-----------EEEEEe
Q 021034 96 NSELGTKVK-----GTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEF-----------VIIGEN 159 (318)
Q Consensus 96 ~~~~G~iv~-----G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v-----------~Vl~vd 159 (318)
+++.|+-+. -||+.+.+++..+|+-......--+.++....--+.+.. ++.|+++-- .|+++.
T Consensus 32 d~~lGdSIAvnGvCLTVt~~~~~~f~~dv~~ETl~~TnL~~~~~G~~VNLERA-l~~~~r~GGH~VsGHVDg~g~I~~i~ 110 (204)
T COG0307 32 DVKLGDSIAVNGVCLTVTEFNEDGFSVDVMPETLRRTNLGDLKVGDKVNLERA-LKLGDRLGGHLVSGHVDGTGEIVKIE 110 (204)
T ss_pred cCccCCeEEECCEEEEEEEECCCcEEEEecHHHhhhcchhhcccCCEEeeehh-ccCCCccccEEEEeEEeeEEEEEEEE
Confidence 566777664 289999999988888543211111122211111122322 455544433 345566
Q ss_pred CCCCeEEEEeeehhhhHHHHHHhhhcCCCcE-E---EEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchh-cCCeEe
Q 021034 160 EADDSLVLSLRMIQYELAWERCRQLQSEDVV-V---KGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEEL-LGKDLP 234 (318)
Q Consensus 160 ~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~i-v---~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~-vGq~v~ 234 (318)
++.+...+..+.+.....+. ..+.|.+ + +-+|.++.++.+.|.+ ||...-. ..+..+ +|+.|+
T Consensus 111 ~~~na~~~~~~~~~~~l~ky----iv~KGsIavDGiSLTV~~v~~~~F~V~l------IPhT~~~--T~l~~~~~Gd~VN 178 (204)
T COG0307 111 KDGNAVRFWFKAPPEELAKY----IVEKGSIAVDGISLTVNEVEDDTFSVSL------IPHTLER--TTLGEKKVGDRVN 178 (204)
T ss_pred EcCCeEEEEEEcCCHHHHhh----hcccceEEEeeEEEEEEEEcCCEEEEEE------Eecchhh--cchhhccCCCEEE
Confidence 66666677765443221111 2345643 3 4456666655665654 7754422 223333 799888
Q ss_pred EEEEEEec
Q 021034 235 LKFVEVDE 242 (318)
Q Consensus 235 ~kVl~vd~ 242 (318)
+++|.
T Consensus 179 ---iE~D~ 183 (204)
T COG0307 179 ---IEIDV 183 (204)
T ss_pred ---EeEcH
Confidence 45664
No 318
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=22.17 E-value=2.3e+02 Score=26.16 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=38.1
Q ss_pred ccCCCCCCEE-----EEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCcc
Q 021034 94 DFNSELGTKV-----KGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141 (318)
Q Consensus 94 ~~~~~~G~iv-----~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~ 141 (318)
++.+++||.+ .|+|.++.-....+.-..+..-.+|++.+....+.+.+
T Consensus 127 ~rpf~vGD~I~i~~~~G~V~~I~~r~T~i~t~d~~~v~IPNs~~~~~~i~N~s 179 (286)
T PRK10334 127 FRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFS 179 (286)
T ss_pred cCCCCCCCEEEECCEEEEEEEEEeEEEEEEcCCCCEEEEcchHhcCCeeEEcC
Confidence 3678899987 68999988777777766778899999999887666644
No 319
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=22.07 E-value=1.9e+02 Score=29.12 Aligned_cols=52 Identities=19% Similarity=0.298 Sum_probs=34.1
Q ss_pred eEEEEEEEEEEcce--EEEEEC-C---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034 266 SVVIGTVQSLKPYG--AFIDIG-G---INGLLHVSQISHDRVADIATVLQPGDTLKVC 317 (318)
Q Consensus 266 ~~v~G~V~~i~~~G--~fV~i~-g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~ 317 (318)
-.|.|.|.++...| +|+.+. + +..++..+.++.+........+..||.|.|.
T Consensus 56 v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~ 113 (496)
T TIGR00499 56 VSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVT 113 (496)
T ss_pred EEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEE
Confidence 46789999999766 899996 2 6666766655433211112247889988763
No 320
>PRK01712 carbon storage regulator; Provisional
Probab=21.93 E-value=2.5e+02 Score=19.87 Aligned_cols=32 Identities=16% Similarity=0.301 Sum_probs=25.4
Q ss_pred ccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 140 VEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 140 ~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
+.+. +..|+.+.+.|+++. ++++.+....+..
T Consensus 8 ~gE~-I~Igd~I~I~V~~i~--~~~VrlGI~AP~~ 39 (64)
T PRK01712 8 VGES-LMIGDDIEVTVLGVK--GNQVRIGINAPKE 39 (64)
T ss_pred CCCE-EEeCCCEEEEEEEEe--CCEEEEEEECCCC
Confidence 4444 778999999999887 6789998887765
No 321
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=21.58 E-value=2.5e+02 Score=19.69 Aligned_cols=36 Identities=22% Similarity=0.360 Sum_probs=29.7
Q ss_pred cccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcC
Q 021034 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQIS 297 (318)
Q Consensus 262 l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls 297 (318)
|.-|-.++|.|.+..+|-+.++.+|-.=|+.+.-+|
T Consensus 18 L~NG~~l~G~I~~fD~ftVll~~~g~qqLIYKhAIS 53 (61)
T cd01716 18 LVNGVQLKGQIESFDNFTVLLESDGKQQLVYKHAIS 53 (61)
T ss_pred EeCCcEEEEEEEEEcceEEEEEECCcEEEEEeeeeE
Confidence 445999999999999999999988766677776665
No 322
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=21.47 E-value=2.7e+02 Score=24.08 Aligned_cols=46 Identities=24% Similarity=0.260 Sum_probs=33.5
Q ss_pred EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchhcCCeEeEEEEEE
Q 021034 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~v 240 (318)
.+.|+|..+.++.++++.+ |..-++|.+.+..- . .|+.++..+-..
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~~l---~--~g~~v~l~t~~~ 51 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYEL---N--LEQKAQVFTHLV 51 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHhc---C--CCCeEEEEEEEE
Confidence 4789999999999999997 67788876554421 1 377777775433
No 323
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=21.44 E-value=1.3e+02 Score=29.78 Aligned_cols=30 Identities=17% Similarity=0.256 Sum_probs=26.8
Q ss_pred cCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034 145 IVPGLKEEFVIIGENEADDSLVLSLRMIQY 174 (318)
Q Consensus 145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~ 174 (318)
++=|++++..|++.|+++++..||++.-..
T Consensus 45 LkWGDEiEy~vV~fDd~~kk~rv~l~~e~i 74 (640)
T KOG3754|consen 45 LKWGDEIEYMVVKFDDKNKKARVSLRAEKI 74 (640)
T ss_pred ccccceeEEEEEecccccceeeeeeeHHHH
Confidence 677999999999999999999999987654
No 324
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=21.41 E-value=4e+02 Score=20.75 Aligned_cols=34 Identities=12% Similarity=0.203 Sum_probs=25.5
Q ss_pred CCCCCCEE------EEEEEEEECCeEEEEeCCCeEEEEeC
Q 021034 96 NSELGTKV------KGTVFCTDNRGALVDITAKSSAYLPT 129 (318)
Q Consensus 96 ~~~~G~iv------~G~V~~i~~~G~~V~i~~~~~g~lp~ 129 (318)
++++|+.| -|+|+++.++-+.+++..+..--+..
T Consensus 52 ~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r 91 (106)
T PRK05585 52 SLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQK 91 (106)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 66788887 69999999998889987654443333
No 325
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.29 E-value=2.4e+02 Score=24.31 Aligned_cols=45 Identities=16% Similarity=0.267 Sum_probs=33.8
Q ss_pred EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchhcCCeEeEEEEE
Q 021034 190 VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239 (318)
Q Consensus 190 iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~ 239 (318)
.+.|+|..+..+.++++.+ |..-++|.+.+.. + -.|+.++..+-.
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~~~---l--~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLST---C--KIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHHHh---h--CCCCeEEEEEEE
Confidence 5799999999999999997 6677777555442 1 168888888643
No 326
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=20.68 E-value=3.6e+02 Score=21.02 Aligned_cols=40 Identities=23% Similarity=0.261 Sum_probs=31.0
Q ss_pred hHhhcccCeEE------EEEEEEEEcceEEEEEC-CeEEEEecCCcC
Q 021034 258 SQAQLGIGSVV------IGTVQSLKPYGAFIDIG-GINGLLHVSQIS 297 (318)
Q Consensus 258 ~~~~l~~G~~v------~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls 297 (318)
..+.+++|+.| .|+|.++.+.-+-++++ |..--+.++-++
T Consensus 49 ~~~~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r~aI~ 95 (106)
T PRK05585 49 MLSSLAKGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQKSAIA 95 (106)
T ss_pred HHHhcCCCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhHHhh
Confidence 45789999987 79999999988888887 766555555444
No 327
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=20.60 E-value=4.1e+02 Score=20.53 Aligned_cols=63 Identities=11% Similarity=0.002 Sum_probs=39.8
Q ss_pred cEEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehh
Q 021034 189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252 (318)
Q Consensus 189 ~iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K 252 (318)
..+.|+|+....++.| |.+. |..-+.+.+-=.. +..+-..|+.|.+.....|..+++|+.-..
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~R-k~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 85 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMK-KRMWIREGDVVIVAPWDFQDEKADIIWRYT 85 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhc-ccEEecCCCEEEEEecccCCCEEEEEEEcC
Confidence 3588999999888877 5765 5444433221111 112222599999998888877777765444
No 328
>PRK00143 mnmA tRNA-specific 2-thiouridylase MnmA; Reviewed
Probab=20.24 E-value=5.4e+02 Score=24.36 Aligned_cols=93 Identities=18% Similarity=0.326 Sum_probs=58.9
Q ss_pred HHHHHHHHHHH-HHHhhcCCCCCCCCCH-HHHHHHHhhhccCCCCCCEEE--EEEEEEECCeEEEEeCCCeEEEEeCccc
Q 021034 57 REELNQLFEEA-YERCRTAPMEGVSFTL-EEFHSALEKYDFNSELGTKVK--GTVFCTDNRGALVDITAKSSAYLPTQEA 132 (318)
Q Consensus 57 ~~~~~~~i~e~-~~~~~~~~~~~~~~s~-~~~~~~~~~~~~~~~~G~iv~--G~V~~i~~~G~~V~i~~~~~g~lp~sEl 132 (318)
|.+++++.++. +...+..+..++-|.. .++.+.++++. ...+|.++. |+|....++-.+-.+|- .+|+
T Consensus 168 K~eVr~~A~~~gl~~~~k~~s~~icf~~~~~~~~fl~~~~-~~~pG~~~~~~g~~~g~H~G~~~yTiGQ-r~gl------ 239 (346)
T PRK00143 168 KPEVREIAEEAGLPVAKKKDSQGICFIGERDYRDFLKRYL-PAQPGEIVDLDGKVLGEHKGLMYYTIGQ-RKGL------ 239 (346)
T ss_pred HHHHHHHHHHcCCCcCCCCCCCcccCCCchhHHHHHHHhc-ccCCCCEEccCCCEEEEECCEEeEecCC-cCCC------
Confidence 56777777662 2222323333333443 47888888886 447898885 78887777767777764 3343
Q ss_pred ccccccCccccCcCCC-CEEEEEEEEEeCCCCeEEEEee
Q 021034 133 CIHKIKHVEEAGIVPG-LKEEFVIIGENEADDSLVLSLR 170 (318)
Q Consensus 133 s~~~~~~~~~~~~~~G-~~v~v~Vl~vd~~~~~i~lS~k 170 (318)
-++ ..-...|+++|++++.++++-+
T Consensus 240 -------------~~~~~~~p~yV~~~d~~~n~v~v~~~ 265 (346)
T PRK00143 240 -------------GIGGDGEPWYVVGKDPETNTVVVGQG 265 (346)
T ss_pred -------------CCCCCCcceEEEEEcCCCCEEEEECh
Confidence 111 1123678899999999999876
No 329
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 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 family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=20.02 E-value=2e+02 Score=18.96 Aligned_cols=35 Identities=14% Similarity=0.099 Sum_probs=25.7
Q ss_pred CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccc
Q 021034 96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC 133 (318)
Q Consensus 96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls 133 (318)
.++.|..+. |..-..+.+.|. ..+..|+++.++++
T Consensus 20 ~l~~g~~v~--v~~~~~~W~~V~-~~g~~GWv~~~~lw 54 (55)
T PF06347_consen 20 RLEPGVPVR--VIECRGGWCKVR-ADGRTGWVHKSLLW 54 (55)
T ss_pred EECCCCEEE--EEEccCCeEEEE-ECCeEEeEEeeecc
Confidence 455676654 456677888899 66789999998875
Done!