Query 044309
Match_columns 259
No_of_seqs 291 out of 2249
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 13:23:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044309.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044309hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00248 eukaryotic translatio 100.0 9E-38 1.9E-42 288.3 17.7 164 73-236 3-166 (319)
2 COG1093 SUI2 Translation initi 100.0 5.2E-35 1.1E-39 260.4 5.1 163 77-239 1-163 (269)
3 KOG2916 Translation initiation 100.0 5E-31 1.1E-35 234.5 3.9 158 73-231 2-159 (304)
4 PRK03987 translation initiatio 100.0 2.1E-29 4.6E-34 228.2 10.1 158 82-239 3-160 (262)
5 COG0539 RpsA Ribosomal protein 99.9 2.5E-27 5.4E-32 231.2 10.5 179 48-243 245-443 (541)
6 COG0539 RpsA Ribosomal protein 99.9 9E-27 1.9E-31 227.3 11.4 192 33-243 145-357 (541)
7 PRK12269 bifunctional cytidyla 99.9 2.9E-23 6.4E-28 213.3 10.5 143 48-204 546-701 (863)
8 PRK13806 rpsA 30S ribosomal pr 99.9 1.1E-22 2.3E-27 199.0 11.7 151 49-216 257-424 (491)
9 PRK07899 rpsA 30S ribosomal pr 99.9 9E-22 2E-26 191.9 10.4 150 36-204 164-329 (486)
10 PRK12269 bifunctional cytidyla 99.9 2.2E-21 4.7E-26 199.6 12.1 143 48-204 633-788 (863)
11 PHA02945 interferon resistance 99.8 3.6E-20 7.8E-25 140.7 9.5 79 83-164 7-87 (88)
12 PRK13806 rpsA 30S ribosomal pr 99.8 2.2E-20 4.8E-25 182.7 9.2 162 36-217 158-339 (491)
13 PRK06299 rpsA 30S ribosomal pr 99.8 1.6E-19 3.4E-24 178.8 12.6 161 35-216 156-332 (565)
14 TIGR00717 rpsA ribosomal prote 99.8 1.3E-19 2.7E-24 177.4 10.0 141 50-204 242-395 (516)
15 TIGR00717 rpsA ribosomal prote 99.8 1.5E-19 3.2E-24 176.9 9.9 141 50-204 329-482 (516)
16 PRK06299 rpsA 30S ribosomal pr 99.8 7.9E-19 1.7E-23 173.9 12.3 132 49-194 342-478 (565)
17 COG1098 VacB Predicted RNA bin 99.8 1.3E-19 2.8E-24 145.6 5.2 78 87-167 5-82 (129)
18 PRK06676 rpsA 30S ribosomal pr 99.8 8.6E-19 1.9E-23 166.3 9.6 149 50-216 158-322 (390)
19 PRK00087 4-hydroxy-3-methylbut 99.7 9.2E-18 2E-22 169.1 10.7 149 50-216 442-607 (647)
20 PRK07400 30S ribosomal protein 99.7 1.2E-16 2.6E-21 148.7 11.6 117 33-170 156-276 (318)
21 cd05705 S1_Rrp5_repeat_hs14 S1 99.7 1.6E-16 3.4E-21 118.1 8.9 69 87-157 3-74 (74)
22 PRK07400 30S ribosomal protein 99.7 2.5E-16 5.4E-21 146.6 12.0 118 83-204 28-153 (318)
23 PRK07899 rpsA 30S ribosomal pr 99.7 1.6E-16 3.5E-21 155.1 10.4 146 51-217 92-253 (486)
24 cd04452 S1_IF2_alpha S1_IF2_al 99.7 6.5E-16 1.4E-20 113.6 10.4 75 86-160 2-76 (76)
25 PRK08582 hypothetical protein; 99.6 8.7E-16 1.9E-20 127.3 10.5 80 87-169 5-84 (139)
26 PRK06676 rpsA 30S ribosomal pr 99.6 1.5E-15 3.2E-20 144.2 11.1 110 50-172 247-360 (390)
27 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 2.4E-15 5.3E-20 110.8 9.6 71 86-158 2-72 (73)
28 cd05698 S1_Rrp5_repeat_hs6_sc5 99.6 2.1E-15 4.6E-20 109.4 9.0 70 88-159 1-70 (70)
29 PF00575 S1: S1 RNA binding do 99.6 3.6E-15 7.9E-20 109.2 10.3 71 87-159 4-74 (74)
30 cd05703 S1_Rrp5_repeat_hs12_sc 99.6 3.2E-15 6.8E-20 110.6 9.5 70 88-159 1-72 (73)
31 cd05704 S1_Rrp5_repeat_hs13 S1 99.6 4.1E-15 8.9E-20 109.6 8.7 69 87-159 3-72 (72)
32 PLN00207 polyribonucleotide nu 99.6 2.7E-15 5.8E-20 154.1 10.4 108 42-171 727-835 (891)
33 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.6 5.9E-15 1.3E-19 107.1 9.2 69 88-158 1-69 (69)
34 cd04461 S1_Rrp5_repeat_hs8_sc7 99.6 5.2E-15 1.1E-19 111.4 8.9 72 84-158 12-83 (83)
35 PRK07252 hypothetical protein; 99.6 8.1E-15 1.8E-19 118.7 10.4 80 87-168 3-83 (120)
36 cd05706 S1_Rrp5_repeat_sc10 S1 99.6 1.3E-14 2.8E-19 106.2 10.3 71 87-159 3-73 (73)
37 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.6 1E-14 2.2E-19 107.2 9.1 69 88-158 1-71 (71)
38 cd05691 S1_RPS1_repeat_ec6 S1_ 99.6 1.8E-14 3.8E-19 104.8 10.0 72 88-161 1-72 (73)
39 cd05707 S1_Rrp5_repeat_sc11 S1 99.6 9.2E-15 2E-19 105.8 8.3 68 88-157 1-68 (68)
40 cd05684 S1_DHX8_helicase S1_DH 99.6 1.7E-14 3.8E-19 107.4 10.0 75 88-164 1-77 (79)
41 cd05708 S1_Rrp5_repeat_sc12 S1 99.6 2.2E-14 4.7E-19 105.2 10.3 74 87-161 2-75 (77)
42 cd05690 S1_RPS1_repeat_ec5 S1_ 99.6 1.5E-14 3.3E-19 104.3 8.2 68 88-157 1-69 (69)
43 cd05694 S1_Rrp5_repeat_hs2_sc2 99.6 3.8E-14 8.3E-19 105.3 10.4 70 87-163 4-73 (74)
44 cd05687 S1_RPS1_repeat_ec1_hs1 99.5 4.4E-14 9.6E-19 102.5 9.6 70 88-159 1-70 (70)
45 cd05692 S1_RPS1_repeat_hs4 S1_ 99.5 4.8E-14 1E-18 100.5 9.0 69 88-159 1-69 (69)
46 cd05689 S1_RPS1_repeat_ec4 S1_ 99.5 4.8E-14 1E-18 102.9 8.8 71 84-157 1-72 (72)
47 PRK05807 hypothetical protein; 99.5 6.6E-14 1.4E-18 115.6 10.5 72 87-162 5-76 (136)
48 PRK08059 general stress protei 99.5 6.9E-14 1.5E-18 113.4 10.2 80 83-165 4-83 (123)
49 PRK00087 4-hydroxy-3-methylbut 99.5 4.7E-14 1E-18 142.4 10.2 103 50-165 532-638 (647)
50 cd05685 S1_Tex S1_Tex: The C-t 99.5 1.4E-13 3E-18 98.0 8.1 68 88-157 1-68 (68)
51 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.5 2E-13 4.3E-18 103.1 8.8 76 84-162 3-82 (86)
52 cd05688 S1_RPS1_repeat_ec3 S1_ 99.5 3.8E-13 8.2E-18 96.0 8.8 68 87-157 1-68 (68)
53 cd04472 S1_PNPase S1_PNPase: P 99.4 4.5E-13 9.7E-18 95.8 8.4 68 88-158 1-68 (68)
54 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.4 5.3E-13 1.2E-17 96.8 8.7 66 88-157 1-66 (66)
55 cd04465 S1_RPS1_repeat_ec2_hs2 99.4 1.5E-12 3.3E-17 94.0 9.5 67 88-159 1-67 (67)
56 smart00316 S1 Ribosomal protei 99.4 2.3E-12 4.9E-17 91.6 9.5 71 87-159 2-72 (72)
57 TIGR02696 pppGpp_PNP guanosine 99.4 8.9E-13 1.9E-17 133.2 9.9 70 85-157 645-718 (719)
58 PRK11824 polynucleotide phosph 99.4 1.6E-12 3.5E-17 132.2 11.5 73 86-161 620-692 (693)
59 cd05693 S1_Rrp5_repeat_hs1_sc1 99.4 1.2E-12 2.5E-17 102.8 7.9 72 87-160 3-96 (100)
60 PRK09521 exosome complex RNA-b 99.4 2.9E-12 6.2E-17 111.0 10.7 122 37-194 30-159 (189)
61 cd04454 S1_Rrp4_like S1_Rrp4_l 99.4 2.5E-12 5.4E-17 96.5 9.0 75 84-161 3-77 (82)
62 PHA02858 EIF2a-like PKR inhibi 99.4 2.1E-12 4.5E-17 97.5 7.4 73 83-158 12-85 (86)
63 cd04453 S1_RNase_E S1_RNase_E: 99.4 3.9E-12 8.4E-17 97.6 9.0 70 87-158 7-81 (88)
64 cd04471 S1_RNase_R S1_RNase_R: 99.4 6.1E-12 1.3E-16 93.5 9.6 71 87-158 1-82 (83)
65 COG2996 Predicted RNA-bindinin 99.3 6E-12 1.3E-16 113.6 6.0 113 87-222 155-269 (287)
66 cd00164 S1_like S1_like: Ribos 99.2 2.9E-11 6.2E-16 84.3 7.2 65 91-157 1-65 (65)
67 cd04473 S1_RecJ_like S1_RecJ_l 99.2 8.2E-11 1.8E-15 87.6 10.0 64 83-158 13-76 (77)
68 cd05702 S1_Rrp5_repeat_hs11_sc 99.2 4.2E-11 9.1E-16 87.3 8.1 62 88-151 1-64 (70)
69 TIGR03591 polynuc_phos polyrib 99.2 2.5E-11 5.4E-16 123.4 9.0 69 85-156 616-684 (684)
70 COG1185 Pnp Polyribonucleotide 99.2 3E-11 6.5E-16 120.5 7.6 79 80-162 613-691 (692)
71 KOG1067 Predicted RNA-binding 99.2 3E-11 6.4E-16 117.9 7.2 81 83-167 665-745 (760)
72 COG2183 Tex Transcriptional ac 99.2 5.8E-11 1.3E-15 120.0 7.7 78 83-163 655-732 (780)
73 cd04460 S1_RpoE S1_RpoE: RpoE, 99.1 6.5E-10 1.4E-14 86.5 9.4 78 89-169 1-94 (99)
74 PRK04163 exosome complex RNA-b 99.1 4.2E-10 9.2E-15 100.8 9.2 76 83-161 59-138 (235)
75 cd04455 S1_NusA S1_NusA: N-uti 99.0 1.6E-09 3.5E-14 78.5 9.0 63 87-158 3-67 (67)
76 TIGR02063 RNase_R ribonuclease 99.0 1.4E-09 3E-14 111.1 10.4 81 74-158 617-708 (709)
77 TIGR00358 3_prime_RNase VacB a 98.9 5.3E-09 1.2E-13 106.0 10.6 81 74-158 562-653 (654)
78 PRK11642 exoribonuclease R; Pr 98.9 5.6E-09 1.2E-13 108.0 10.5 82 75-160 634-726 (813)
79 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.9 8.2E-09 1.8E-13 79.8 8.0 75 84-161 3-87 (92)
80 TIGR00448 rpoE DNA-directed RN 98.9 1.3E-08 2.8E-13 87.5 9.6 74 87-163 81-170 (179)
81 PRK09202 nusA transcription el 98.7 9.1E-08 2E-12 93.6 11.0 67 86-161 133-201 (470)
82 KOG1070 rRNA processing protei 98.7 1.3E-07 2.9E-12 100.1 12.3 110 81-194 1157-1269(1710)
83 PRK08563 DNA-directed RNA poly 98.7 1.3E-07 2.9E-12 81.5 9.9 75 85-162 79-169 (187)
84 COG1095 RPB7 DNA-directed RNA 98.7 9.2E-08 2E-12 82.4 8.1 81 85-168 79-177 (183)
85 KOG1070 rRNA processing protei 98.6 1.6E-07 3.5E-12 99.5 8.8 79 80-162 594-672 (1710)
86 PRK05054 exoribonuclease II; P 98.5 6.6E-07 1.4E-11 90.8 10.1 83 74-158 549-643 (644)
87 TIGR01953 NusA transcription t 98.4 2.3E-06 5E-11 80.8 11.1 67 86-161 130-199 (341)
88 PRK12327 nusA transcription el 98.4 2.4E-06 5.2E-11 81.2 10.8 66 86-160 133-200 (362)
89 TIGR00757 RNaseEG ribonuclease 98.3 5.7E-06 1.2E-10 80.0 12.6 58 87-146 25-96 (414)
90 COG1097 RRP4 RNA-binding prote 98.3 3E-06 6.5E-11 75.9 8.6 77 83-162 60-140 (239)
91 cd05790 S1_Rrp40 S1_Rrp40: Rrp 98.3 5E-06 1.1E-10 63.7 8.6 74 84-161 3-76 (86)
92 COG1096 Predicted RNA-binding 98.2 8.1E-06 1.7E-10 70.6 9.6 94 82-195 59-160 (188)
93 TIGR02062 RNase_B exoribonucle 98.2 7E-06 1.5E-10 83.3 9.3 82 74-157 545-638 (639)
94 COG0557 VacB Exoribonuclease R 98.1 1.2E-05 2.6E-10 82.5 9.1 81 75-159 613-704 (706)
95 PF10447 EXOSC1: Exosome compo 98.0 1.7E-05 3.7E-10 60.3 7.0 64 84-147 1-82 (82)
96 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.0 4E-05 8.6E-10 58.8 9.0 63 87-152 1-74 (88)
97 cd05699 S1_Rrp5_repeat_hs7 S1_ 98.0 3E-05 6.4E-10 57.5 7.2 68 88-159 1-72 (72)
98 PTZ00162 DNA-directed RNA poly 97.9 7.2E-05 1.6E-09 64.5 9.4 72 87-161 81-166 (176)
99 PRK12328 nusA transcription el 97.9 9.4E-05 2E-09 70.5 10.3 68 84-160 135-206 (374)
100 PF13509 S1_2: S1 domain; PDB: 97.8 0.00014 3E-09 51.9 8.0 61 87-159 1-61 (61)
101 PF07541 EIF_2_alpha: Eukaryot 97.8 2E-05 4.4E-10 63.3 3.3 44 196-239 1-45 (114)
102 COG1107 Archaea-specific RecJ- 97.7 6.6E-05 1.4E-09 74.6 5.7 101 83-192 119-231 (715)
103 COG2996 Predicted RNA-bindinin 97.7 0.00029 6.2E-09 64.3 9.2 97 87-194 73-173 (287)
104 PRK11712 ribonuclease G; Provi 97.5 0.001 2.2E-08 65.7 11.8 126 87-218 38-202 (489)
105 PRK12329 nusA transcription el 97.5 0.00086 1.9E-08 65.2 10.6 70 85-160 150-225 (449)
106 PRK10811 rne ribonuclease E; R 97.3 0.002 4.3E-08 67.7 11.9 59 87-147 38-107 (1068)
107 KOG1856 Transcription elongati 97.2 0.00037 8E-09 73.6 5.1 75 84-161 983-1060(1299)
108 PTZ00248 eukaryotic translatio 96.7 0.00012 2.5E-09 68.6 -3.7 92 37-145 66-171 (319)
109 KOG3409 Exosomal 3'-5' exoribo 96.0 0.035 7.6E-07 47.8 7.7 97 80-194 61-165 (193)
110 KOG3298 DNA-directed RNA polym 95.2 0.072 1.6E-06 45.4 6.8 62 87-151 81-153 (170)
111 PF08292 RNA_pol_Rbc25: RNA po 94.8 0.21 4.6E-06 40.6 8.4 61 87-149 3-76 (122)
112 COG1530 CafA Ribonucleases G a 94.4 0.06 1.3E-06 53.4 5.2 59 87-148 37-102 (487)
113 cd05705 S1_Rrp5_repeat_hs14 S1 92.8 0.036 7.8E-07 40.8 0.3 31 173-204 1-39 (74)
114 PRK12442 translation initiatio 92.5 0.88 1.9E-05 35.0 7.5 65 90-160 8-73 (87)
115 COG1098 VacB Predicted RNA bin 91.3 0.1 2.2E-06 42.7 1.3 55 172-234 2-65 (129)
116 TIGR00008 infA translation ini 91.2 1.2 2.6E-05 32.7 6.8 60 90-155 6-66 (68)
117 PF00313 CSD: 'Cold-shock' DNA 90.4 4.6 0.0001 28.4 9.3 50 91-146 1-53 (66)
118 KOG3013 Exosomal 3'-5' exoribo 90.3 0.27 5.9E-06 44.9 3.3 76 83-161 81-166 (301)
119 cd04453 S1_RNase_E S1_RNase_E: 89.6 0.12 2.7E-06 39.3 0.4 46 171-216 3-57 (88)
120 PF10246 MRP-S35: Mitochondria 89.1 2.3 5E-05 33.7 7.2 52 87-147 23-74 (104)
121 PRK15463 cold shock-like prote 89.1 1.9 4.1E-05 31.6 6.4 51 91-146 5-57 (70)
122 PRK15464 cold shock-like prote 88.5 1.9 4.1E-05 31.6 6.1 51 91-146 5-57 (70)
123 cd04454 S1_Rrp4_like S1_Rrp4_l 87.6 2 4.4E-05 31.5 5.9 55 134-188 4-66 (82)
124 PRK10943 cold shock-like prote 87.2 3 6.4E-05 30.4 6.5 52 90-146 3-56 (69)
125 PRK09507 cspE cold shock prote 86.7 3.4 7.4E-05 30.0 6.5 53 90-147 3-57 (69)
126 PRK09890 cold shock protein Cs 85.8 4.2 9.2E-05 29.6 6.7 51 91-146 5-57 (70)
127 PRK09937 stationary phase/star 85.5 3.8 8.2E-05 30.3 6.4 63 92-161 3-67 (74)
128 cd05704 S1_Rrp5_repeat_hs13 S1 84.8 0.47 1E-05 34.4 1.2 41 174-217 2-50 (72)
129 cd05706 S1_Rrp5_repeat_sc10 S1 84.5 3.7 8E-05 29.2 5.8 53 134-188 1-63 (73)
130 COG4776 Rnb Exoribonuclease II 84.0 0.37 8.1E-06 47.5 0.4 76 75-152 550-637 (645)
131 PRK09521 exosome complex RNA-b 82.8 5.9 0.00013 34.1 7.4 57 131-187 59-133 (189)
132 PRK09202 nusA transcription el 82.5 0.37 8E-06 47.7 -0.3 75 113-195 71-153 (470)
133 PRK10354 RNA chaperone/anti-te 82.0 6.5 0.00014 28.6 6.3 51 91-146 5-57 (70)
134 cd04458 CSP_CDS Cold-Shock Pro 81.7 11 0.00024 26.4 7.3 51 92-147 2-54 (65)
135 TIGR02381 cspD cold shock doma 81.4 5.5 0.00012 28.8 5.7 50 92-146 3-54 (68)
136 PRK14998 cold shock-like prote 81.2 6.9 0.00015 28.9 6.2 61 92-159 3-65 (73)
137 cd05703 S1_Rrp5_repeat_hs12_sc 81.2 2.6 5.7E-05 30.6 4.0 50 137-188 1-62 (73)
138 cd05686 S1_pNO40 S1_pNO40: pNO 80.9 0.45 9.8E-06 34.4 -0.2 39 174-216 2-49 (73)
139 TIGR02696 pppGpp_PNP guanosine 80.6 1.4 3E-05 45.8 3.1 81 145-233 611-710 (719)
140 cd05700 S1_Rrp5_repeat_hs9 S1_ 80.5 7.4 0.00016 28.0 5.8 65 88-158 1-65 (65)
141 KOG1004 Exosomal 3'-5' exoribo 80.4 7.6 0.00016 34.7 7.2 63 84-149 62-124 (230)
142 cd05687 S1_RPS1_repeat_ec1_hs1 78.1 4.5 9.7E-05 28.5 4.3 51 137-189 1-61 (70)
143 cd05702 S1_Rrp5_repeat_hs11_sc 76.9 6.2 0.00013 28.0 4.8 50 137-188 1-62 (70)
144 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 76.3 8.3 0.00018 28.3 5.5 55 134-188 4-70 (86)
145 cd05690 S1_RPS1_repeat_ec5 S1_ 76.3 0.77 1.7E-05 32.3 -0.2 28 176-204 1-36 (69)
146 cd05691 S1_RPS1_repeat_ec6 S1_ 76.0 7.3 0.00016 27.3 4.9 52 137-188 1-60 (73)
147 cd05697 S1_Rrp5_repeat_hs5 S1_ 74.6 7.4 0.00016 27.4 4.6 50 137-188 1-60 (69)
148 COG1278 CspC Cold shock protei 74.5 7.2 0.00016 28.6 4.5 50 92-146 3-54 (67)
149 PF10447 EXOSC1: Exosome compo 72.3 8.8 0.00019 29.1 4.7 50 135-186 3-82 (82)
150 cd05689 S1_RPS1_repeat_ec4 S1_ 71.7 2.1 4.6E-05 30.4 1.2 22 173-195 1-22 (72)
151 PF03459 TOBE: TOBE domain; I 71.3 17 0.00036 25.1 5.8 48 89-144 5-57 (64)
152 cd05791 S1_CSL4 S1_CSL4: CSL4, 71.2 10 0.00023 28.9 5.0 53 134-188 4-76 (92)
153 cd04461 S1_Rrp5_repeat_hs8_sc7 70.2 16 0.00034 26.8 5.7 55 134-188 12-74 (83)
154 cd04322 LysRS_N LysRS_N: N-ter 69.4 40 0.00086 26.0 8.1 54 90-143 3-59 (108)
155 PF00575 S1: S1 RNA binding do 69.3 4.8 0.0001 28.6 2.6 54 134-189 2-65 (74)
156 cd05707 S1_Rrp5_repeat_sc11 S1 68.9 14 0.00031 25.8 5.0 50 137-188 1-60 (68)
157 cd05708 S1_Rrp5_repeat_sc12 S1 68.1 12 0.00027 26.3 4.6 54 135-188 1-63 (77)
158 PF13742 tRNA_anti_2: OB-fold 68.0 53 0.0011 25.2 9.0 70 88-163 23-99 (99)
159 PRK04012 translation initiatio 66.4 42 0.00091 26.3 7.6 67 84-158 17-84 (100)
160 smart00316 S1 Ribosomal protei 66.1 10 0.00022 25.7 3.7 52 135-188 1-62 (72)
161 cd04452 S1_IF2_alpha S1_IF2_al 65.3 16 0.00036 25.8 4.8 54 135-188 2-65 (76)
162 cd05693 S1_Rrp5_repeat_hs1_sc1 64.8 23 0.00049 27.4 5.8 53 134-188 1-82 (100)
163 TIGR03591 polynuc_phos polyrib 63.6 6.5 0.00014 40.8 3.2 67 145-216 584-663 (684)
164 COG0361 InfA Translation initi 61.8 65 0.0014 24.1 7.8 66 88-159 6-72 (75)
165 smart00652 eIF1a eukaryotic tr 61.4 55 0.0012 24.7 7.2 64 88-158 4-68 (83)
166 COG4044 Uncharacterized protei 59.8 22 0.00047 31.9 5.3 90 83-177 72-171 (247)
167 cd05695 S1_Rrp5_repeat_hs3 S1_ 59.6 20 0.00043 25.3 4.3 49 137-188 1-58 (66)
168 cd05793 S1_IF1A S1_IF1A: Trans 59.5 40 0.00088 25.0 6.1 61 91-158 2-63 (77)
169 TIGR01953 NusA transcription t 59.5 2.2 4.9E-05 40.5 -0.9 64 128-194 78-150 (341)
170 cd05698 S1_Rrp5_repeat_hs6_sc5 56.3 40 0.00087 23.4 5.5 50 137-188 1-60 (70)
171 COG1096 Predicted RNA-binding 54.8 1.1E+02 0.0024 26.8 8.9 58 131-188 59-134 (188)
172 PRK08059 general stress protei 54.7 26 0.00056 28.1 4.7 55 134-188 5-67 (123)
173 COG1185 Pnp Polyribonucleotide 53.7 18 0.00039 37.4 4.4 58 145-204 585-655 (692)
174 PRK00484 lysS lysyl-tRNA synth 53.0 1.2E+02 0.0026 30.2 10.0 71 90-161 58-131 (491)
175 cd05694 S1_Rrp5_repeat_hs2_sc2 52.4 30 0.00066 25.1 4.4 56 134-189 2-60 (74)
176 PRK05807 hypothetical protein; 52.3 8.4 0.00018 31.7 1.5 32 172-204 2-40 (136)
177 TIGR00638 Mop molybdenum-pteri 51.9 23 0.00049 24.6 3.5 50 89-145 7-60 (69)
178 cd04473 S1_RecJ_like S1_RecJ_l 51.9 29 0.00063 25.1 4.2 52 134-187 14-67 (77)
179 cd04455 S1_NusA S1_NusA: N-uti 51.4 28 0.0006 24.5 4.0 52 135-188 2-56 (67)
180 COG1545 Predicted nucleic-acid 50.7 1E+02 0.0023 25.3 7.8 62 83-153 59-129 (140)
181 PRK12327 nusA transcription el 50.5 3.2 7E-05 39.8 -1.4 63 131-195 84-153 (362)
182 PF06196 DUF997: Protein of un 48.7 10 0.00022 28.6 1.3 16 1-16 36-51 (80)
183 cd05701 S1_Rrp5_repeat_hs10 S1 48.7 31 0.00067 25.2 3.7 59 91-150 4-62 (69)
184 cd05688 S1_RPS1_repeat_ec3 S1_ 48.5 41 0.00089 22.8 4.4 51 136-188 1-60 (68)
185 PTZ00329 eukaryotic translatio 46.5 90 0.002 26.6 6.8 67 84-158 28-95 (155)
186 PF02599 CsrA: Global regulato 46.2 33 0.00072 23.9 3.5 32 130-163 8-39 (54)
187 PRK08582 hypothetical protein; 45.6 55 0.0012 27.0 5.4 55 134-188 3-65 (139)
188 PRK11824 polynucleotide phosph 45.2 8.7 0.00019 39.9 0.6 62 151-216 592-666 (693)
189 KOG4078 Putative mitochondrial 43.4 70 0.0015 27.0 5.6 52 87-147 82-133 (173)
190 CHL00010 infA translation init 43.3 1.3E+02 0.0029 22.2 7.6 65 91-161 9-74 (78)
191 PLN00207 polyribonucleotide nu 42.2 10 0.00022 40.5 0.7 42 171-216 749-799 (891)
192 PRK03987 translation initiatio 40.6 54 0.0012 30.0 5.0 58 132-191 4-73 (262)
193 PRK00276 infA translation init 40.5 1.4E+02 0.003 21.6 7.7 61 90-156 8-69 (72)
194 cd04456 S1_IF1A_like S1_IF1A_l 40.4 1.5E+02 0.0033 22.0 6.9 62 91-159 2-65 (78)
195 PRK04163 exosome complex RNA-b 40.3 1.2E+02 0.0026 27.0 7.2 55 134-188 61-127 (235)
196 cd05685 S1_Tex S1_Tex: The C-t 40.2 80 0.0017 21.2 4.8 52 137-188 1-60 (68)
197 PF01176 eIF-1a: Translation i 40.0 67 0.0015 22.8 4.5 58 90-154 4-62 (65)
198 KOG3297 DNA-directed RNA polym 39.9 84 0.0018 27.6 5.7 61 87-149 81-158 (202)
199 cd03524 RPA2_OBF_family RPA2_O 39.4 1.1E+02 0.0024 20.1 6.3 66 91-160 2-72 (75)
200 PRK01712 carbon storage regula 39.2 60 0.0013 23.6 4.0 33 129-163 7-39 (64)
201 cd04487 RecJ_OBF2_like RecJ_OB 38.6 1.5E+02 0.0033 21.5 7.7 66 90-161 2-70 (73)
202 COG2106 Uncharacterized conser 38.6 60 0.0013 30.0 4.9 49 84-147 102-150 (272)
203 COG5009 MrcA Membrane carboxyp 38.5 1.1E+02 0.0024 32.4 7.3 58 84-143 342-404 (797)
204 COG0195 NusA Transcription elo 37.9 59 0.0013 28.5 4.6 43 113-161 2-45 (190)
205 COG2183 Tex Transcriptional ac 37.8 32 0.0007 36.2 3.4 44 169-216 652-703 (780)
206 TIGR00499 lysS_bact lysyl-tRNA 37.0 1.9E+02 0.004 28.9 8.5 71 90-160 57-130 (496)
207 cd04489 ExoVII_LU_OBF ExoVII_L 36.8 1.5E+02 0.0032 20.8 7.6 67 90-161 3-74 (78)
208 PF01336 tRNA_anti-codon: OB-f 36.4 1.4E+02 0.003 20.4 5.7 67 90-161 2-72 (75)
209 PRK02983 lysS lysyl-tRNA synth 33.8 3.1E+02 0.0067 30.3 10.2 95 61-157 626-725 (1094)
210 PRK07252 hypothetical protein; 33.7 1E+02 0.0022 24.7 5.1 54 135-188 2-63 (120)
211 PF07076 DUF1344: Protein of u 33.3 1.4E+02 0.0031 21.4 5.2 50 89-148 3-52 (61)
212 COG1190 LysU Lysyl-tRNA synthe 33.0 1.6E+02 0.0036 29.6 7.3 72 89-160 64-138 (502)
213 PRK00568 carbon storage regula 31.6 81 0.0018 23.7 3.8 33 129-163 7-39 (76)
214 PF00970 FAD_binding_6: Oxidor 31.4 1.3E+02 0.0027 22.2 5.0 47 133-179 29-88 (99)
215 KOG4134 DNA-dependent RNA poly 31.4 37 0.0008 30.7 2.3 57 84-149 104-162 (253)
216 KOG3409 Exosomal 3'-5' exoribo 30.6 97 0.0021 27.0 4.6 57 132-188 64-138 (193)
217 cd04508 TUDOR Tudor domains ar 30.5 1.2E+02 0.0025 19.4 4.1 35 87-122 11-46 (48)
218 PRK12445 lysyl-tRNA synthetase 30.0 2.8E+02 0.006 27.8 8.5 71 90-160 69-142 (505)
219 PLN00208 translation initiatio 29.1 2.5E+02 0.0054 23.6 6.7 65 84-156 28-93 (145)
220 TIGR00202 csrA carbon storage 28.8 1.1E+02 0.0023 22.6 4.0 33 129-163 7-39 (69)
221 PRK14605 ruvA Holliday junctio 28.6 3.8E+02 0.0082 23.2 8.2 55 90-153 4-58 (194)
222 TIGR00084 ruvA Holliday juncti 28.6 3.8E+02 0.0082 23.2 8.2 54 90-153 4-57 (191)
223 smart00333 TUDOR Tudor domain. 27.9 1.6E+02 0.0034 19.5 4.6 36 87-123 15-51 (57)
224 cd04485 DnaE_OBF DnaE_OBF: A s 27.7 2.1E+02 0.0045 19.7 5.6 58 100-162 15-75 (84)
225 PRK00286 xseA exodeoxyribonucl 27.5 3.3E+02 0.0073 26.3 8.4 71 88-163 25-100 (438)
226 PRK06763 F0F1 ATP synthase sub 27.3 2E+02 0.0044 25.6 6.1 25 88-112 39-63 (213)
227 TIGR00523 eIF-1A eukaryotic/ar 26.2 3.2E+02 0.0069 21.3 6.9 51 88-145 18-69 (99)
228 COG1551 CsrA RNA-binding globa 26.2 98 0.0021 23.0 3.4 31 130-162 8-38 (73)
229 TIGR00458 aspS_arch aspartyl-t 26.1 3E+02 0.0064 26.9 7.8 53 90-143 16-71 (428)
230 PLN02502 lysyl-tRNA synthetase 26.0 3.7E+02 0.0081 27.3 8.6 71 90-160 112-187 (553)
231 PF08206 OB_RNB: Ribonuclease 25.9 2.2E+02 0.0049 19.5 6.7 43 93-146 1-44 (58)
232 PRK14603 ruvA Holliday junctio 25.2 4.3E+02 0.0092 23.0 7.9 60 90-159 4-63 (197)
233 cd04319 PhAsnRS_like_N PhAsnRS 25.2 2.3E+02 0.0049 21.5 5.6 52 90-143 3-57 (103)
234 PRK14600 ruvA Holliday junctio 24.3 4.7E+02 0.01 22.6 8.2 47 90-146 4-50 (186)
235 PF07238 PilZ: PilZ domain; I 24.2 2.7E+02 0.0058 19.8 6.4 22 87-108 21-42 (102)
236 PF14444 S1-like: S1-like 24.1 2.7E+02 0.0059 19.8 5.9 43 90-146 3-46 (58)
237 PF02237 BPL_C: Biotin protein 24.0 1.2E+02 0.0026 20.0 3.4 22 87-108 11-33 (48)
238 smart00357 CSP Cold shock prot 23.6 2.2E+02 0.0049 18.7 7.4 48 93-147 2-50 (64)
239 PF01835 A2M_N: MG2 domain; I 21.9 1.4E+02 0.0031 22.1 3.8 31 131-161 8-45 (99)
240 PRK14604 ruvA Holliday junctio 21.8 5.4E+02 0.012 22.4 8.2 55 90-153 4-58 (195)
241 cd04482 RPA2_OBF_like RPA2_OBF 21.6 2.4E+02 0.0052 21.3 5.0 54 90-149 2-62 (91)
242 PF01938 TRAM: TRAM domain; I 21.5 2.7E+02 0.0059 18.9 6.8 50 87-149 4-53 (61)
243 PRK10334 mechanosensitive chan 21.0 2.4E+02 0.0051 26.0 5.7 49 80-131 126-179 (286)
244 cd00210 PTS_IIA_glc PTS_IIA, P 20.7 2.7E+02 0.0058 22.6 5.3 56 91-148 42-102 (124)
No 1
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=100.00 E-value=9e-38 Score=288.27 Aligned_cols=164 Identities=62% Similarity=1.017 Sum_probs=158.5
Q ss_pred CchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC
Q 044309 73 PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG 152 (259)
Q Consensus 73 ~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g 152 (259)
+.+.|||+.++||++|++|.|+|++|.+|||||+|.+|+|++||||+||+||+|++++++++++||.+.|+|++||+++|
T Consensus 3 ~~~~cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg 82 (319)
T PTZ00248 3 DLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG 82 (319)
T ss_pred CcccccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence 46789999999998999999999999999999999999899999999999999999999999999999999999999999
Q ss_pred eEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCC
Q 044309 153 YIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTR 232 (259)
Q Consensus 153 kI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~ 232 (259)
+|+||+|++.++||..+.++|+.|++++|+|.+++++||+|++++|..++||+.+.|+|+|+||+.++.+|.++|.++++
T Consensus 83 ~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i 162 (319)
T PTZ00248 83 YIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDI 162 (319)
T ss_pred EEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCC
Confidence 99999999999999999999999999999999999889999999999999999999999999999999999999999998
Q ss_pred cccc
Q 044309 233 EVKE 236 (259)
Q Consensus 233 ~~~~ 236 (259)
.+..
T Consensus 163 ~~ev 166 (319)
T PTZ00248 163 PEEV 166 (319)
T ss_pred CHHH
Confidence 7543
No 2
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-35 Score=260.41 Aligned_cols=163 Identities=34% Similarity=0.512 Sum_probs=156.9
Q ss_pred hhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309 77 CRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL 156 (259)
Q Consensus 77 ~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L 156 (259)
||+..+.||++|++|.|+|++|.+|||||.|+||+|.+||+|+||++.+|++|+++++++||.+.|+|++||+.+|.|+|
T Consensus 1 m~~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDL 80 (269)
T COG1093 1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDL 80 (269)
T ss_pred CcccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEee
Confidence 67788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCcccc
Q 044309 157 SKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKE 236 (259)
Q Consensus 157 SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~ 236 (259)
|+|++.+++..++.+.|+..+.+..+++.+++++|.+++++|.+++|+|.+.||++|+||+.|+.+|.++|.++..++..
T Consensus 81 SlkrV~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~ 160 (269)
T COG1093 81 SLKRVTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEW 160 (269)
T ss_pred ehhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999987665
Q ss_pred CCC
Q 044309 237 IGP 239 (259)
Q Consensus 237 ~~~ 239 (259)
+++
T Consensus 161 ~~~ 163 (269)
T COG1093 161 KEV 163 (269)
T ss_pred HHH
Confidence 544
No 3
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5e-31 Score=234.55 Aligned_cols=158 Identities=73% Similarity=1.166 Sum_probs=153.9
Q ss_pred CchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC
Q 044309 73 PNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG 152 (259)
Q Consensus 73 ~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g 152 (259)
+.+.|||+..+||+++++|.+.|.+|.+.||||.|.||++++|||-+||||.+|++++++..++|..-.|.|++||+++|
T Consensus 2 ~~~~cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekG 81 (304)
T KOG2916|consen 2 STLECRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKG 81 (304)
T ss_pred CcceeehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCC
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCC
Q 044309 153 YIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLT 231 (259)
Q Consensus 153 kI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~ 231 (259)
+|+||.+++.+++..+|.++|.+...++.++.++++++|..+++||..++||++++|||+|+|||+++.+|. +|..|+
T Consensus 82 YIDLSkrrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW~~~rk~g~aYdaFK~~vtd~t-V~d~l~ 159 (304)
T KOG2916|consen 82 YIDLSKRRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGWPLERKYGHAYDAFKIAVTDPT-VLDELD 159 (304)
T ss_pred ceechhccCCHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCcHHHHHHHhCCchhhhhchHHHHHHHhccCcc-cccccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999955 999888
No 4
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.96 E-value=2.1e-29 Score=228.23 Aligned_cols=158 Identities=29% Similarity=0.457 Sum_probs=149.3
Q ss_pred hcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 82 ARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 82 ~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
+.+|++|++|.|+|++|.++|+||+|.+|++++||||+|+++++++.++++.+++||.+.|+|+++|+++++|+||+|++
T Consensus 3 ~~~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 3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 46888999999999999999999999987789999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHhccccceEEEEEEecccccCCchHHHHHhhchhhHHhhcCHHHHHHHHhcCcchhhccCCCccccCCC
Q 044309 162 SEEDIQACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYWKYGHAFEAFKIIVTDPDSVLNSLTREVKEIGP 239 (259)
Q Consensus 162 ~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~~~~~~~~~fk~a~~~~~~~l~~l~~~~~~~~~ 239 (259)
.+++..++.++|+..+.++.++..+++++|..++++|..++|||.++|||+|+||+.|+.+++++|.++++++...++
T Consensus 83 ~~~e~~~~~~~~~~~~~~~~il~~~a~~~~~~~e~~~~~~~~~l~~~yg~~y~af~~~~~~~~~~l~~~~~~~~~~~~ 160 (262)
T PRK03987 83 NEHQRREKIQEWKNEQKADKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVPEEWADA 160 (262)
T ss_pred ccchHHHHHHHHHHHhhHhhHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChhhhccCCCCHHHHHH
Confidence 998888899999999999999999999999999999999999999999999999999998778899999988766554
No 5
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.5e-27 Score=231.20 Aligned_cols=179 Identities=25% Similarity=0.389 Sum_probs=152.4
Q ss_pred Cccccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309 48 TPFEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS 123 (259)
Q Consensus 48 ~~~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls 123 (259)
.++++|++++| ||++.++||.. +.+++| +|+.+.|+|+++++|||||++. +|++||+|+||+|
T Consensus 245 kVi~~D~e~~RVsLSlK~l~~dPw~~----------i~~~~~-~g~~v~G~Vt~i~~~GafVei~--~GvEGlvhvSEis 311 (541)
T COG0539 245 KVISLDEERGRVSLSLKQLEEDPWEG----------IEKKYP-VGDKVEGKVTNLTDYGAFVEIE--EGVEGLVHVSEIS 311 (541)
T ss_pred EEEEEccCCCeEEEEehhcccCcHHH----------HhhhcC-CCCEEEEEEEEeecCcEEEEec--CCccceeechhhc
Confidence 44689999999 59999999998 889999 9999999999999999999998 6999999999999
Q ss_pred cccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH
Q 044309 124 RRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL 197 (259)
Q Consensus 124 ~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~ 197 (259)
|.+...|++++++||+|.|+|+++|++++||+||+|++..+||+...+.|+.|+.++|.|.++++ +|+|+ +++
T Consensus 312 w~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~-~g~fv~le~gidG~ 390 (541)
T COG0539 312 WTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITD-FGAFVELEGGIDGL 390 (541)
T ss_pred ccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecc-cceEEccCCCccce
Confidence 99988899999999999999999999999999999999999999999999999999999999987 99997 344
Q ss_pred --HHhhchhhHHhhcCHHHHHHHHh--------cCcchhhccCCCccccCCCCCcc
Q 044309 198 --YVNIGWPLYWKYGHAFEAFKIIV--------TDPDSVLNSLTREVKEIGPDGQE 243 (259)
Q Consensus 198 --~~~~sw~l~~~~~~~~~~fk~a~--------~~~~~~l~~l~~~~~~~~~~~~~ 243 (259)
.+++||. +-+....-||..- -++..--.+|+++.-+-+|+...
T Consensus 391 vh~~d~sw~---~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~ 443 (541)
T COG0539 391 VHLSDLSWD---RPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEF 443 (541)
T ss_pred EEHHhcCcc---ccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhh
Confidence 8999995 3334444555432 12222344566666666776543
No 6
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=9e-27 Score=227.31 Aligned_cols=192 Identities=26% Similarity=0.365 Sum_probs=150.0
Q ss_pred cccccceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhh-hhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309 33 ADSLSGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRM-YEARYPEVDMAVMIQVKNIADMGAYVSL 107 (259)
Q Consensus 33 ~~~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~-~~~~~~~~G~iv~G~V~~I~~~GafV~L 107 (259)
.+.+.|..... .++++|++++++ +.+.+. .....|. +.+.++ +|+++.|+|+++++|||||+|
T Consensus 145 ~~~~~Gk~~~~----kiie~d~~~n~vv~SrR~~~e~-------~~~~~r~e~~~~l~-~G~vV~G~V~~It~~GafVdi 212 (541)
T COG0539 145 LDPLIGKELEF----KILELDKKRNNVVLSRRAVLEE-------ERSEQREELLNKLE-VGEVVEGVVKNITDYGAFVDI 212 (541)
T ss_pred ccccCCceEEE----EEEEEccccCcEEEEhHHHhhH-------HHHHHHHHHHhcCC-CCceEEEEEEEeecCcEEEEe
Confidence 45566766664 457999999985 222210 0111111 345677 999999999999999999999
Q ss_pred ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecc
Q 044309 108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187 (259)
Q Consensus 108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~ 187 (259)
. |++||||+|||||.++.+|+++|++||+|+|+|+++|++++||+||+|++.++||+...++|++|+.+.|+|+++.
T Consensus 213 g---GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~ 289 (541)
T COG0539 213 G---GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLT 289 (541)
T ss_pred c---CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEee
Confidence 4 7999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccCCch------HHH--HHhhchhhHHhhcCHHHHHHHHh--------cCcchhhccCCCccccCCCCCcc
Q 044309 188 ETLGIDL------EEL--YVNIGWPLYWKYGHAFEAFKIIV--------TDPDSVLNSLTREVKEIGPDGQE 243 (259)
Q Consensus 188 ~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~fk~a~--------~~~~~~l~~l~~~~~~~~~~~~~ 243 (259)
+ ||+|+ ++| .+++||. +...+.+.++.-= .++++--.+|++++-.-+|+.+.
T Consensus 290 ~-~GafVei~~GvEGlvhvSEisw~---~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~ 357 (541)
T COG0539 290 D-YGAFVEIEEGVEGLVHVSEISWT---KKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEF 357 (541)
T ss_pred c-CcEEEEecCCccceeechhhccc---ccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhh
Confidence 7 99997 456 9999995 5555777774211 22333344555555555664443
No 7
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.89 E-value=2.9e-23 Score=213.35 Aligned_cols=143 Identities=23% Similarity=0.434 Sum_probs=131.4
Q ss_pred Cccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309 48 TPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS 123 (259)
Q Consensus 48 ~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls 123 (259)
.++++|++++|+ |++.++||.. +.+.++ +|+++.|+|+++++||+||+|. +|++||+|+||++
T Consensus 546 kVi~iD~e~~rI~LSlK~l~~~p~~~----------~~~~~~-vG~iV~G~V~~I~~fG~fVeL~--~gveGLvhiSEls 612 (863)
T PRK12269 546 KVIRLDQAEKRINLSLKHFQPDPWLE----------FENKFG-VNDVVKGRVTKIADFGAFIELA--EGIEGLAHISEFS 612 (863)
T ss_pred EEEEEecCCCeEEEEEeccccchhhh----------hhccCC-CCCEEEEEEEEEeCCeEEEEec--CCceeeeEHHHhc
Confidence 346889998884 8899999997 777888 9999999999999999999997 5899999999999
Q ss_pred c-ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HH
Q 044309 124 R-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EE 196 (259)
Q Consensus 124 ~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~ 196 (259)
| .++.+|.+.|++||+|+|+|+++|+++++|.||+|++.++||....++|+.|++++|+|.++.+ ||+|+ ++
T Consensus 613 ~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~-~G~fV~l~~gV~G 691 (863)
T PRK12269 613 WVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTN-AGAFIEMEEGIDG 691 (863)
T ss_pred CccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEec-ceEEEEeCCCcEE
Confidence 9 6889999999999999999999999999999999999999999999999999999999999987 99997 33
Q ss_pred H--HHhhchh
Q 044309 197 L--YVNIGWP 204 (259)
Q Consensus 197 ~--~~~~sw~ 204 (259)
+ .++++|.
T Consensus 692 lIh~sels~~ 701 (863)
T PRK12269 692 FLHVDDLSWV 701 (863)
T ss_pred EEEhHHhhcc
Confidence 4 8899994
No 8
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.88 E-value=1.1e-22 Score=198.96 Aligned_cols=151 Identities=23% Similarity=0.327 Sum_probs=131.9
Q ss_pred ccccchhh----hh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309 49 PFEFSREN----AK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS 120 (259)
Q Consensus 49 ~~eid~e~----~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis 120 (259)
++++|.++ +| +|++.++||.. +.+.++ +|+++.|+|+++++||+||++. +|++||+|+|
T Consensus 257 Vl~id~~~~~~~~ri~lS~K~~~~~p~~~----------~~~~~~-~G~~v~G~V~~v~~~G~fV~l~--~gv~Glvh~s 323 (491)
T PRK13806 257 VLGIERAKKGKGLRISLSIKQAGGDPWDT----------VGDRLK-AGDKVTGKVVRLAPFGAFVEIL--PGIEGLVHVS 323 (491)
T ss_pred EEEEecccCCcceEEEEEehhhhcccchh----------hhccCC-CCCEEEEEEEEEeCceEEEEeC--CCcEEEEEHH
Confidence 34677776 35 38889999997 777888 9999999999999999999997 5899999999
Q ss_pred cccc-ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch-----
Q 044309 121 ELSR-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL----- 194 (259)
Q Consensus 121 Els~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv----- 194 (259)
+++| .++.++.+.+++||.|.|+|+++|+++++|.||+|++..+||....+.|++|++++|+|+++.+ ||+|+
T Consensus 324 els~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~-~G~FV~l~~g 402 (491)
T PRK13806 324 EMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQ-FGLFVNLAPG 402 (491)
T ss_pred HcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEec-CceEEEcCCC
Confidence 9999 6788899999999999999999999999999999999999999999999999999999999976 99997
Q ss_pred -HHH--HHhhchhhHHhhcCHHHHH
Q 044309 195 -EEL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 195 -e~~--~~~~sw~l~~~~~~~~~~f 216 (259)
++| .++++|. +...+.+.|
T Consensus 403 v~Gli~~se~s~~---~~~~~~~~~ 424 (491)
T PRK13806 403 VTGLLPASVISRA---GKPATYEKL 424 (491)
T ss_pred cEEEEEHHHcCcc---cccchhhcC
Confidence 234 8899984 334444444
No 9
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.86 E-value=9e-22 Score=191.85 Aligned_cols=150 Identities=19% Similarity=0.259 Sum_probs=128.9
Q ss_pred ccceeEEEeecCCccccchhhhhh----hh----cccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309 36 LSGCLKTLILVPTPFEFSRENAKA----KK----LSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSL 107 (259)
Q Consensus 36 l~g~~~~~~~~~~~~eid~e~~ri----K~----l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L 107 (259)
..|..... .++++|++++++ |. ....+|.. +...++ +|+++.|+|+++++||+||+|
T Consensus 164 ~vGq~V~v----kVleid~~~~~ivLSrr~~l~~~~~~~~~~----------~~~~lk-~G~iv~G~V~~i~~~G~FVdl 228 (486)
T PRK07899 164 YIGQEIEA----KIIELDKNRNNVVLSRRAWLEQTQSEVRSE----------FLNQLQ-KGQVRKGVVSSIVNFGAFVDL 228 (486)
T ss_pred cCCCEEEE----EEEEEECCCCEEEEEhHHHHHhhhHHHHHH----------HHHhcc-CCCEEEEEEEEEECCeEEEEE
Confidence 45665554 346788888874 32 23356665 556777 999999999999999999999
Q ss_pred ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecc
Q 044309 108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVA 187 (259)
Q Consensus 108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~ 187 (259)
. +++||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....++++.|+++.|+|+++.
T Consensus 229 g---gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~ 305 (486)
T PRK07899 229 G---GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLV 305 (486)
T ss_pred C---CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEe
Confidence 4 7999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred cccCCchH------HH--HHhhchh
Q 044309 188 ETLGIDLE------EL--YVNIGWP 204 (259)
Q Consensus 188 ~~~G~fve------~~--~~~~sw~ 204 (259)
+ +|+|++ +| .++++|.
T Consensus 306 ~-fGvFVeL~~gieGLvh~SeLs~~ 329 (486)
T PRK07899 306 P-FGAFVRVEEGIEGLVHISELAER 329 (486)
T ss_pred c-cEEEEEeCCCcEEEEEHHHcCcc
Confidence 6 999972 34 8888884
No 10
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.85 E-value=2.2e-21 Score=199.61 Aligned_cols=143 Identities=22% Similarity=0.375 Sum_probs=128.1
Q ss_pred Cccccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc
Q 044309 48 TPFEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS 123 (259)
Q Consensus 48 ~~~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls 123 (259)
.++.+|.+++| +|++.++||.. +.+.++ +|+++.|+|+++++||+||+|. +|++||||.||++
T Consensus 633 kVl~iD~e~~rIsLS~K~l~~~Pw~~----------~~~~~~-vG~~v~G~V~~i~~~G~fV~l~--~gV~GlIh~sels 699 (863)
T PRK12269 633 MILGYDIQAGRVSLGLKQVTANPWEE----------IEARYP-VGARFTRRIVKVTNAGAFIEME--EGIDGFLHVDDLS 699 (863)
T ss_pred EEEEEecccCceEEEehhcccCchHH----------HHHhCC-CCCEEEEEEEEEecceEEEEeC--CCcEEEEEhHHhh
Confidence 44678999888 48999999998 778888 9999999999999999999997 6999999999999
Q ss_pred cccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HH
Q 044309 124 RRRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EE 196 (259)
Q Consensus 124 ~~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~ 196 (259)
|.+. .++...|++||.|+|+|+++|+++++|.||+|++..+||....+.|+.|++++|+|..+.+ +|+|+ ++
T Consensus 700 ~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~-~GvFVeL~~gVeG 778 (863)
T PRK12269 700 WVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTD-FGIFVRVPGGVEG 778 (863)
T ss_pred ccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEec-CeEEEEcCCCeEE
Confidence 9664 4455689999999999999999999999999999999999999999999999999999976 99997 23
Q ss_pred H--HHhhchh
Q 044309 197 L--YVNIGWP 204 (259)
Q Consensus 197 ~--~~~~sw~ 204 (259)
+ .++++|.
T Consensus 779 lI~~s~lsdd 788 (863)
T PRK12269 779 LVRKQHLVEN 788 (863)
T ss_pred EEEHHHcCCc
Confidence 3 8888885
No 11
>PHA02945 interferon resistance protein; Provisional
Probab=99.83 E-value=3.6e-20 Score=140.69 Aligned_cols=79 Identities=28% Similarity=0.451 Sum_probs=75.4
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccc--ccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSEL--SRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEl--s~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+|++|+++.|+|+. .+|||||.|+||+|.+||||+||+ +.+|+++ ++++ .||++.|+|+++|+.+|.|+||+|+
T Consensus 7 ~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 7 SLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred cCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 588899999999999 999999999999999999999955 9999999 9999 9999999999999999999999999
Q ss_pred cchh
Q 044309 161 VSEE 164 (259)
Q Consensus 161 ~~~~ 164 (259)
+.++
T Consensus 84 V~~~ 87 (88)
T PHA02945 84 MCRH 87 (88)
T ss_pred cccC
Confidence 8764
No 12
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.82 E-value=2.2e-20 Score=182.66 Aligned_cols=162 Identities=21% Similarity=0.301 Sum_probs=132.4
Q ss_pred ccceeEEEeecCCccccchhhhhh----hhcc----cCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEE
Q 044309 36 LSGCLKTLILVPTPFEFSRENAKA----KKLS----EQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSL 107 (259)
Q Consensus 36 l~g~~~~~~~~~~~~eid~e~~ri----K~l~----~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L 107 (259)
+.|+.... .++++|++++++ +++. +.+|.. +...+. +|+++.|+|+++.++|+||+|
T Consensus 158 ~vG~~i~~----~V~~id~~~~~v~lSrk~~~~~~~~~~~~~----------~~~~l~-~G~iv~G~V~~v~~~G~fV~l 222 (491)
T PRK13806 158 YVGQTFQF----LITRVEENGRNIVVSRRALLEREQKEALEA----------FMETVK-EGDVVEGTVTRLAPFGAFVEL 222 (491)
T ss_pred cCCCeEEE----EEEEEECCCCeEEEEeehhhhhhhHHHHHH----------HHhhCC-CCCEEEEEEEEEeCCeEEEEc
Confidence 45665554 235788888774 3332 244554 445566 999999999999999999999
Q ss_pred ccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC----CeEEEEEeecchhhHHHHHHhccccceEEEEE
Q 044309 108 LEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK----GYIDLSKRRVSEEDIQACEERYNKSKLVHSIM 183 (259)
Q Consensus 108 ~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~----gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V 183 (259)
. ++++||||+|+++|.++.++.+.|++||.|.|+|+++|.++ ++|.||+|++.++||....++|+.|+++.|+|
T Consensus 223 ~--~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V 300 (491)
T PRK13806 223 A--PGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKV 300 (491)
T ss_pred C--CCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEE
Confidence 6 58999999999999999999999999999999999999875 47999999999999999999999999999999
Q ss_pred EecccccCCchH------HH--HHhhchhhHHhhcCHHHHHH
Q 044309 184 RHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFK 217 (259)
Q Consensus 184 ~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk 217 (259)
+.+.+ +|+|++ ++ .++++|. ++..++.+.|+
T Consensus 301 ~~v~~-~G~fV~l~~gv~Glvh~sels~~--~~~~~~~~~~~ 339 (491)
T PRK13806 301 VRLAP-FGAFVEILPGIEGLVHVSEMSWT--RRVNKPEDVVA 339 (491)
T ss_pred EEEeC-ceEEEEeCCCcEEEEEHHHcCcc--cccCCHHHcCC
Confidence 99976 999972 34 8899994 34455555553
No 13
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.81 E-value=1.6e-19 Score=178.81 Aligned_cols=161 Identities=24% Similarity=0.377 Sum_probs=133.1
Q ss_pred cccceeEEEeecCCccccchhhhhh----hhcccC----ccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEE
Q 044309 35 SLSGCLKTLILVPTPFEFSRENAKA----KKLSEQ----PIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVS 106 (259)
Q Consensus 35 ~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~----pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~ 106 (259)
.+.|+.... .++++|++++++ |++.+. +|.. +...+. +|+++.|+|++++++|+||+
T Consensus 156 ~~vG~~i~~----~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~----------~~~~l~-~G~iv~g~V~~v~~~G~~V~ 220 (565)
T PRK06299 156 PLEGKELEF----KVIKLDKKRNNIVVSRRAVLEEERAEEREE----------LLENLE-EGQVVEGVVKNITDYGAFVD 220 (565)
T ss_pred HhCCCEEEE----EEEEEECCCCEEEEEhHHhhhhhhhhHHHH----------HHhcCC-CCCEEEEEEEEEeCCeEEEE
Confidence 346666654 335889888884 555443 3433 445666 99999999999999999999
Q ss_pred EccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEec
Q 044309 107 LLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHV 186 (259)
Q Consensus 107 L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i 186 (259)
++ |.+||+|++|++|.++.++.+.|++||.|.|+|+++|++++++.||+|++.++||....+.|+.|+++.|+|..+
T Consensus 221 i~---g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i 297 (565)
T PRK06299 221 LG---GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNI 297 (565)
T ss_pred EC---CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEE
Confidence 94 899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCchH------HH--HHhhchhhHHhhcCHHHHH
Q 044309 187 AETLGIDLE------EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 187 ~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~f 216 (259)
.+ +|+|++ ++ .++++|. ....++.+.|
T Consensus 298 ~~-~G~fV~l~~~v~Glv~~sel~~~--~~~~~~~~~~ 332 (565)
T PRK06299 298 TD-YGAFVELEEGIEGLVHVSEMSWT--KKNKHPSKVV 332 (565)
T ss_pred eC-CeEEEEeCCCCEEEEEHHHcCcc--ccccCHHHhc
Confidence 66 999973 33 7889885 3334554444
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=99.80 E-value=1.3e-19 Score=177.44 Aligned_cols=141 Identities=26% Similarity=0.481 Sum_probs=125.2
Q ss_pred cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309 50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR 125 (259)
Q Consensus 50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~ 125 (259)
+.+|++++++ |++.++||+. +...++ +|+++.|+|+++.++|+||++. ++++||+|+|+++|.
T Consensus 242 l~~d~~~~~i~lS~k~~~~~p~~~----------~~~~~~-~G~i~~g~V~~v~~~G~fV~l~--~~v~g~v~~sels~~ 308 (516)
T TIGR00717 242 IKFDKEKGRISLSLKQLGEDPWEA----------IEKKFP-VGDKITGRVTNLTDYGVFVEIE--EGIEGLVHVSEMSWV 308 (516)
T ss_pred EEEECCCCcEEEEEEecchhHHHH----------HHhhcc-CCCEEEEEEEEeeCCcEEEEeC--CCCEEEEEHHHcCCc
Confidence 4678888874 6777899987 666777 8999999999999999999997 589999999999985
Q ss_pred -cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH-
Q 044309 126 -RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL- 197 (259)
Q Consensus 126 -~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~- 197 (259)
...++.+.+++||.+.|+|+++|++++++.||+|++..+||....+.+..|+++.|+|..+.+ +|+|+ +++
T Consensus 309 ~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~-~G~fV~l~~~v~glv 387 (516)
T TIGR00717 309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITD-FGAFVELEGGIDGLI 387 (516)
T ss_pred cccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEec-ceEEEECCCCCEEEE
Confidence 466777889999999999999999999999999999999999999999999999999999966 99997 233
Q ss_pred -HHhhchh
Q 044309 198 -YVNIGWP 204 (259)
Q Consensus 198 -~~~~sw~ 204 (259)
.++++|.
T Consensus 388 ~~s~ls~~ 395 (516)
T TIGR00717 388 HLSDISWD 395 (516)
T ss_pred EHHHCcCc
Confidence 8899995
No 15
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.80 E-value=1.5e-19 Score=176.91 Aligned_cols=141 Identities=27% Similarity=0.427 Sum_probs=124.8
Q ss_pred cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309 50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR 125 (259)
Q Consensus 50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~ 125 (259)
+++|++++|+ |++.++||.. +.+.++ +|+++.|+|++++++|+||+|+ ++++||+|+++++|.
T Consensus 329 ~~id~~~~~i~lS~k~~~~~p~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~--~~v~glv~~s~ls~~ 395 (516)
T TIGR00717 329 LDIDPERRRLSLGLKQCKANPWEQ----------FEEKHP-VGDRVTGKIKKITDFGAFVELE--GGIDGLIHLSDISWD 395 (516)
T ss_pred EEEcCCCCEEEEEehhcccCcHHH----------HHHhCC-CCCEEEEEEEEEecceEEEECC--CCCEEEEEHHHCcCc
Confidence 4688888884 7788899987 666777 8999999999999999999997 589999999999986
Q ss_pred cc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch------HHH-
Q 044309 126 RI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL- 197 (259)
Q Consensus 126 ~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~- 197 (259)
+. .++...|++||.|.|+|+++|+++++|.||+|++.++||....+.++.|++++|+|+++.+ +|+|+ +++
T Consensus 396 ~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~-~G~fV~l~~~~~Glv 474 (516)
T TIGR00717 396 KDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKD-FGAFVELPGGVEGLI 474 (516)
T ss_pred ccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEec-ceEEEEcCCCeEEEE
Confidence 53 4567889999999999999999999999999999999999998899999999999999976 99997 233
Q ss_pred -HHhhchh
Q 044309 198 -YVNIGWP 204 (259)
Q Consensus 198 -~~~~sw~ 204 (259)
.++++|.
T Consensus 475 ~~s~l~~~ 482 (516)
T TIGR00717 475 RNSELSEN 482 (516)
T ss_pred EHHHcCcc
Confidence 7888884
No 16
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.78 E-value=7.9e-19 Score=173.88 Aligned_cols=132 Identities=29% Similarity=0.464 Sum_probs=121.0
Q ss_pred ccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc
Q 044309 49 PFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR 124 (259)
Q Consensus 49 ~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~ 124 (259)
++++|++++|+ |++..+||.. +...++ +|+++.|+|++++++|+||+|+ .+++||+|+++++|
T Consensus 342 V~~id~~~~~i~ls~k~~~~~p~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~--~~v~g~i~~s~l~~ 408 (565)
T PRK06299 342 VLEIDEEKRRISLGLKQCKENPWEE----------FAEKYP-VGDVVEGKVKNITDFGAFVGLE--GGIDGLVHLSDISW 408 (565)
T ss_pred EEEEcCCCCEEEEehHHhccchhhh----------HHHhCC-CCCEEEEEEEEEecceEEEECC--CCCEEEEEHHHcCc
Confidence 35788888884 7788899987 666777 8999999999999999999997 48999999999999
Q ss_pred ccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309 125 RRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL 194 (259)
Q Consensus 125 ~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv 194 (259)
.+. .++.+.|++||.|.|+|+++|+++++|.||+|+...+||....+.++.|+++.|+|.++.+ +|+|+
T Consensus 409 ~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~-~G~fV 478 (565)
T PRK06299 409 DKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKD-KGAFV 478 (565)
T ss_pred cccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEec-CceEE
Confidence 876 8888999999999999999999999999999999999999999999999999999999976 89987
No 17
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=1.3e-19 Score=145.65 Aligned_cols=78 Identities=29% Similarity=0.460 Sum_probs=74.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI 166 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~ 166 (259)
+|++++|+|++|++|||||+|+ ++..|||||||++.++++++.+++++||.|.|+|+++|. +|+|+||+|.+.+.|-
T Consensus 5 vG~~l~GkItgI~~yGAFV~l~--~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~pe 81 (129)
T COG1098 5 VGSKLKGKITGITPYGAFVELE--GGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEPE 81 (129)
T ss_pred ccceEEEEEEeeEecceEEEec--CCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhCcc
Confidence 8999999999999999999998 689999999999999999999999999999999999998 8999999999877554
Q ss_pred H
Q 044309 167 Q 167 (259)
Q Consensus 167 ~ 167 (259)
.
T Consensus 82 ~ 82 (129)
T COG1098 82 K 82 (129)
T ss_pred c
Confidence 3
No 18
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.77 E-value=8.6e-19 Score=166.28 Aligned_cols=149 Identities=22% Similarity=0.338 Sum_probs=123.7
Q ss_pred cccchhhhhh----hhccc----CccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccc
Q 044309 50 FEFSRENAKA----KKLSE----QPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSE 121 (259)
Q Consensus 50 ~eid~e~~ri----K~l~~----~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisE 121 (259)
+++|++++++ |++.. ++|.. ....+. +|+++.|+|+++.++|+||++. +++||||+|+
T Consensus 158 l~~d~~~~~i~lS~k~~~~~~~~~~~~~----------~~~~~~-~G~~v~g~V~~v~~~G~fV~l~---~v~g~v~~se 223 (390)
T PRK06676 158 IELDPEKNRVILSRRAVVEEERAAKKEE----------LLSSLK-EGDVVEGTVARLTDFGAFVDIG---GVDGLVHISE 223 (390)
T ss_pred EEEECCCCEEEEEeHHHhhhhhhhHHHH----------HHhhCC-CCCEEEEEEEEEecceEEEEeC---CeEEEEEHHH
Confidence 4678877774 44322 34443 444566 8999999999999999999994 7999999999
Q ss_pred cccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH------
Q 044309 122 LSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE------ 195 (259)
Q Consensus 122 ls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------ 195 (259)
++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++..+||....+.+..|+++.|.|+.+.+ +|+|++
T Consensus 224 ls~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~-~G~fV~l~~gi~ 302 (390)
T PRK06676 224 LSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTD-FGAFVEVLPGVE 302 (390)
T ss_pred cCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeC-ceEEEEECCCCe
Confidence 9999999999999999999999999999999999999999999999999999999999999999976 999973
Q ss_pred HH--HHhhchhhHHhhcCHHHHH
Q 044309 196 EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 196 ~~--~~~~sw~l~~~~~~~~~~f 216 (259)
++ .++++|. +..++.+.|
T Consensus 303 Glv~~se~~~~---~~~~~~~~~ 322 (390)
T PRK06676 303 GLVHISQISHK---HIATPSEVL 322 (390)
T ss_pred EEEEhHHcCcc---ccCChhhcc
Confidence 23 7788774 333444444
No 19
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.73 E-value=9.2e-18 Score=169.11 Aligned_cols=149 Identities=26% Similarity=0.420 Sum_probs=124.5
Q ss_pred cccchhhhh-h----hhcc----cCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309 50 FEFSRENAK-A----KKLS----EQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFS 120 (259)
Q Consensus 50 ~eid~e~~r-i----K~l~----~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhis 120 (259)
+++|+++++ + |.+. ..+|.. ..+.+. +|+++.|+|+++.++|+||++ ++++||||+|
T Consensus 442 l~vd~e~~~~l~lS~k~~~~~~~~~~~~~----------~~~~l~-~G~iV~g~V~~v~~~G~fV~l---~gv~Gll~~s 507 (647)
T PRK00087 442 IEFNRKRRKKVVLSRKAILEEEKEKKKEE----------TWNSLE-EGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVS 507 (647)
T ss_pred EEEEcCCCcEEEEEeHHHhhhhhhhHHHH----------HHHhCC-CCCEEEEEEEEEeCCcEEEEE---CCEEEEEEHH
Confidence 577888777 4 3321 233333 334465 899999999999999999999 3899999999
Q ss_pred ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH-----
Q 044309 121 ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE----- 195 (259)
Q Consensus 121 Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve----- 195 (259)
+++|.++.++.+.|++||.+.|+|+++|++++++.||+|++.++||....++++.|+++.|+|.++.+ +|+|++
T Consensus 508 els~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~-~G~fV~l~~~i 586 (647)
T PRK00087 508 EISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAP-FGAFVELEPGV 586 (647)
T ss_pred HcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEEC-CeEEEEECCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999976 999982
Q ss_pred -HH--HHhhchhhHHhhcCHHHHH
Q 044309 196 -EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 196 -~~--~~~~sw~l~~~~~~~~~~f 216 (259)
++ .++++|. +..++.+.|
T Consensus 587 ~Gli~~sel~~~---~~~~~~~~~ 607 (647)
T PRK00087 587 DGLVHISQISWK---RIDKPEDVL 607 (647)
T ss_pred EEEEEhhhcCcc---ccCCHhhcC
Confidence 33 7888884 344555555
No 20
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.69 E-value=1.2e-16 Score=148.75 Aligned_cols=117 Identities=24% Similarity=0.372 Sum_probs=98.8
Q ss_pred cccccceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEc
Q 044309 33 ADSLSGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLL 108 (259)
Q Consensus 33 ~~~l~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ 108 (259)
.+.+.|..... .++++|++++|+ |+.... . ....++ +|+++.|+|+++++||+||++
T Consensus 156 ~~~~vG~~i~~----kVl~id~~~~~i~lS~K~~~~~---~----------~~~~~k-~G~vv~G~V~~I~~~G~fV~i- 216 (318)
T PRK07400 156 KEELVGEELPL----KFLEVDEERNRLVLSHRRALVE---R----------KMNRLE-VGEVVVGTVRGIKPYGAFIDI- 216 (318)
T ss_pred ccccCCCEEEE----EEEEEEcccCEEEEEhhHhhhh---h----------hhccCC-CCCEEEEEEEEEECCeEEEEE-
Confidence 34567777764 447899999995 433221 1 223566 899999999999999999999
Q ss_pred cCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHH
Q 044309 109 EYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACE 170 (259)
Q Consensus 109 ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~ 170 (259)
++++||||+++++|.++.++.+.|++||.|+|+|+++|.++++|.||+|++.++||+...
T Consensus 217 --~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~ 276 (318)
T PRK07400 217 --GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLK 276 (318)
T ss_pred --CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhh
Confidence 489999999999999999999999999999999999999999999999999999998653
No 21
>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=99.68 E-value=1.6e-16 Score=118.08 Aligned_cols=69 Identities=22% Similarity=0.384 Sum_probs=64.8
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCc---cccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSV---SSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~---~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
+|+++.|+|++++++|+||+|. ++++|+||+++++|.++.++ .+.|++||.+.|+|+++|+++++|.||
T Consensus 3 ~G~~V~g~V~~i~~~G~fV~l~--~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 3 EGQLLRGYVSSVTKQGVFFRLS--SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCEEEEEEEEEeCCcEEEEeC--CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 8999999999999999999997 58999999999999987775 588999999999999999999999986
No 22
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.68 E-value=2.5e-16 Score=146.61 Aligned_cols=118 Identities=15% Similarity=0.177 Sum_probs=107.7
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.+. .|+++.|+|+++.++|+||+|+ ++.+||||.+|+++.++.++.+.+++||.+.|+|++++.+++++.||+|++.
T Consensus 28 ~~~-~G~iv~G~V~~i~~~g~~Vdig--~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~ 104 (318)
T PRK07400 28 HFK-PGDIVNGTVFSLEPRGALIDIG--AKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIE 104 (318)
T ss_pred hcC-CCCEEEEEEEEEECCEEEEEEC--CCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhh
Confidence 355 8999999999999999999996 5799999999999999999999999999999999999999999999999986
Q ss_pred h-hhHHHHHHhccccceEEEEEEecccccCCchH-----HH--HHhhchh
Q 044309 163 E-EDIQACEERYNKSKLVHSIMRHVAETLGIDLE-----EL--YVNIGWP 204 (259)
Q Consensus 163 ~-~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve-----~~--~~~~sw~ 204 (259)
. ++|+...+.+..|+.+.|+|..+.+ +|+|++ +| .++++|.
T Consensus 105 ~~~~w~~l~~~~~~~~~V~g~V~~~~~-~G~~V~l~Gv~gfip~s~ls~~ 153 (318)
T PRK07400 105 YMRAWERVRQLQKEDATVRSEVFATNR-GGALVRIEGLRGFIPGSHISTR 153 (318)
T ss_pred hhhHHHHHHHhccCCCEEEEEEEEEEC-CeEEEEECCEEEEEEHHHcCcc
Confidence 4 8999999999999999999999976 899873 33 7889984
No 23
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.67 E-value=1.6e-16 Score=155.14 Aligned_cols=146 Identities=17% Similarity=0.280 Sum_probs=121.5
Q ss_pred ccchhhhhh----hhc-ccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309 51 EFSRENAKA----KKL-SEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR 125 (259)
Q Consensus 51 eid~e~~ri----K~l-~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~ 125 (259)
.++.+++++ |++ .+++|.. +.+.+. .|+++.|+|+++.++|+||++ |++||||.|++++.
T Consensus 92 ~~~~~~g~liLS~k~~~~~~~w~~----------ie~~~e-~g~~V~G~V~~v~k~G~~Vdl----Gi~gflP~Sel~~~ 156 (486)
T PRK07899 92 QKEDKEGRLILSKKRAQYERAWGT----------IEKIKE-KDGVVTGTVIEVVKGGLILDI----GLRGFLPASLVEMR 156 (486)
T ss_pred EEECCCCeEEEEehhhcccchHHH----------HHHHhc-CCCEEEEEEEEEECCeEEEEE----CCEEEEEhhHhccc
Confidence 456666663 433 3688987 766665 799999999999999999999 58999999999998
Q ss_pred cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc----hhhHHHHHHhccccceEEEEEEecccccCCch-----HH
Q 044309 126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS----EEDIQACEERYNKSKLVHSIMRHVAETLGIDL-----EE 196 (259)
Q Consensus 126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~----~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv-----e~ 196 (259)
++.++..+ +||.|.|+|+++|++++++.||+|.+. ..+|......++.|+++.|+|+.+.+ +|+|+ ++
T Consensus 157 ~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~-~G~FVdlggv~G 233 (486)
T PRK07899 157 RVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVN-FGAFVDLGGVDG 233 (486)
T ss_pred ccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEEC-CeEEEEECCEEE
Confidence 88887764 899999999999999999999999653 36788888999999999999999976 99997 34
Q ss_pred H--HHhhchhhHHhhcCHHHHHH
Q 044309 197 L--YVNIGWPLYWKYGHAFEAFK 217 (259)
Q Consensus 197 ~--~~~~sw~l~~~~~~~~~~fk 217 (259)
+ .++++|. ++.++.+.|+
T Consensus 234 lv~~Sels~~---~v~~~~~~~k 253 (486)
T PRK07899 234 LVHVSELSWK---HIDHPSEVVE 253 (486)
T ss_pred EEEHHHCCCc---ccCCHHHhcC
Confidence 4 8999994 5667766664
No 24
>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=99.67 E-value=6.5e-16 Score=113.57 Aligned_cols=75 Identities=75% Similarity=1.064 Sum_probs=70.3
Q ss_pred CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
+.|+++.|+|+++.++|+||++.++++.+||||+|+++++++.++.+.|++||.+.|+|+++|.+++++.||+|+
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 479999999999999999999975456999999999999999999999999999999999999989999999984
No 25
>PRK08582 hypothetical protein; Provisional
Probab=99.65 E-value=8.7e-16 Score=127.30 Aligned_cols=80 Identities=26% Similarity=0.433 Sum_probs=75.8
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI 166 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~ 166 (259)
+|++|.|+|++|++||+||+|+ ++++||||+|++++.++.++.+.|++||.|.|+|+++|. +++|.||++++.++||
T Consensus 5 vG~iv~G~V~~I~~fG~fV~L~--~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~~ 81 (139)
T PRK08582 5 VGSKLQGKVTGITNFGAFVELP--EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRPK 81 (139)
T ss_pred CCCEEEEEEEEEECCeEEEEEC--CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCch
Confidence 8999999999999999999998 589999999999999999999999999999999999997 5999999999999998
Q ss_pred HHH
Q 044309 167 QAC 169 (259)
Q Consensus 167 ~~~ 169 (259)
...
T Consensus 82 ~~~ 84 (139)
T PRK08582 82 RQH 84 (139)
T ss_pred hhc
Confidence 754
No 26
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.63 E-value=1.5e-15 Score=144.23 Aligned_cols=110 Identities=26% Similarity=0.421 Sum_probs=99.8
Q ss_pred cccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309 50 FEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR 125 (259)
Q Consensus 50 ~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~ 125 (259)
+++|++++|+ |++.++||.. +.+.+. +|+++.|+|+++.++|+||++. ++++||+|+|++++.
T Consensus 247 l~vd~~~~~i~lS~k~~~~~~~~~----------~~~~~~-~G~~v~g~V~~i~~~G~fV~l~--~gi~Glv~~se~~~~ 313 (390)
T PRK06676 247 LSIDWETERISLSLKDTLPGPWEG----------VEEKLP-EGDVIEGTVKRLTDFGAFVEVL--PGVEGLVHISQISHK 313 (390)
T ss_pred EEEeCCCCEEEEEEeecccCcccc----------chhhhc-CCcEEEEEEEEEeCceEEEEEC--CCCeEEEEhHHcCcc
Confidence 4778888884 7788899987 666777 8999999999999999999997 589999999999999
Q ss_pred cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHh
Q 044309 126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEER 172 (259)
Q Consensus 126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~ 172 (259)
++.++.+.|++||.|.|+|+++|++++++.||+|++..+||+...++
T Consensus 314 ~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~ 360 (390)
T PRK06676 314 HIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR 360 (390)
T ss_pred ccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence 98899999999999999999999999999999999999999987654
No 27
>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=99.63 E-value=2.4e-15 Score=110.83 Aligned_cols=71 Identities=21% Similarity=0.288 Sum_probs=65.1
Q ss_pred CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
++|+++.|+|+++++||+||++.++ +.+||+|+|++++.++.++.+.+++||.+.|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~-~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGC-RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCC-CeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 4899999999999999999999531 3799999999999999999999999999999999999964 999986
No 28
>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=99.62 E-value=2.1e-15 Score=109.41 Aligned_cols=70 Identities=29% Similarity=0.376 Sum_probs=66.8
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
|+++.|+|+++.++|+||++. ++.+||+|+|+++++++.++.+.+++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFY--NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC--CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999997 5799999999999988999999999999999999999999999999986
No 29
>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=99.62 E-value=3.6e-15 Score=109.16 Aligned_cols=71 Identities=44% Similarity=0.573 Sum_probs=68.6
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|+++.|+|+++.++|+||+|. ++++||||.+++++.+..++.+.+++||.+.|+|+++|++++++.||+|
T Consensus 4 ~G~iv~g~V~~v~~~g~~V~l~--~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 4 EGDIVEGKVTSVEDFGVFVDLG--NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp TTSEEEEEEEEEETTEEEEEES--TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCEEEEEEEEEECCEEEEEEC--CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 8999999999999999999997 5899999999999999999999999999999999999999999999986
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=99.62 E-value=3.2e-15 Score=110.63 Aligned_cols=70 Identities=23% Similarity=0.306 Sum_probs=66.1
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc--ccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR--IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~--v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
|+++.|+|+++.++|+||+|. ++++|+||++++++.. .+++.+.|++||.++|+|+++|+++++|.||+|
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 GQEVTGFVNNVSKEFVWLTIS--PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 789999999999999999997 5899999999999864 888999999999999999999999999999987
No 31
>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=99.60 E-value=4.1e-15 Score=109.59 Aligned_cols=69 Identities=22% Similarity=0.198 Sum_probs=65.2
Q ss_pred CCcEEEEEEEEEeC-ceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 87 VDMAVMIQVKNIAD-MGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 87 ~G~iv~G~V~~I~~-~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|++|.|+|+++.+ +|+||+|. ++.+|++|+|+++++++.++.+.|++||.++|+|+++|. +++.||+|
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l~--~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQLP--FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEECC--CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 79999999999985 89999997 689999999999999999999999999999999999984 89999986
No 32
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.60 E-value=2.7e-15 Score=154.14 Aligned_cols=108 Identities=26% Similarity=0.314 Sum_probs=91.0
Q ss_pred EEeecCCccccchhhhhhhhcccCccccCCCCchhhhhhhhcCCCCCcEEE-EEEEEEeCceEEEEEccCCCEEEEEEcc
Q 044309 42 TLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVM-IQVKNIADMGAYVSLLEYNNIEGMILFS 120 (259)
Q Consensus 42 ~~~~~~~~~eid~e~~riK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~-G~V~~I~~~GafV~L~ey~~~eGllhis 120 (259)
..+++++...++..+.+|+++.. .+++|++|. |+|++|.+||+||+|. ++.+||||+|
T Consensus 727 V~I~a~d~~~i~~A~~~I~~l~~-------------------~~~vG~iy~~g~V~~I~~FGaFVeL~--~g~EGLVHIS 785 (891)
T PLN00207 727 VKITAKDLSSLEKSKAIISSLTM-------------------VPTVGDIYRNCEIKSIAPYGAFVEIA--PGREGLCHIS 785 (891)
T ss_pred EEEEeCCHHHHHHHHHHHHHHhc-------------------CcCCCcEEECcEEEEEeccEEEEEeC--CCCEEEEEhh
Confidence 33455555555555555655531 234899995 6999999999999997 5899999999
Q ss_pred ccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHH
Q 044309 121 ELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEE 171 (259)
Q Consensus 121 Els~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~ 171 (259)
+++|+++.++.+.|++||.|+|+|+++|+ +++|.||+|++.++||++..+
T Consensus 786 eLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~~~~ 835 (891)
T PLN00207 786 ELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLPEANSEKSS 835 (891)
T ss_pred hcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEeccccCchhhhhh
Confidence 99999999999999999999999999997 799999999999999998764
No 33
>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=99.60 E-value=5.9e-15 Score=107.12 Aligned_cols=69 Identities=22% Similarity=0.305 Sum_probs=65.7
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
|+++.|+|+++.++|+||+|+ ++++||+|++++++.+..++.+.+++||.+.|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLS--DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec--CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999997 579999999999999888899999999999999999999999999985
No 34
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.59 E-value=5.2e-15 Score=111.35 Aligned_cols=72 Identities=29% Similarity=0.277 Sum_probs=68.5
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
+. +|+++.|+|+++.++|+||+|. ++.+||+|+++++++++.++.+.|++||.+.|+|+++|.++++|.||+
T Consensus 12 ~~-~G~i~~g~V~~v~~~G~fv~l~--~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 12 LK-PGMVVHGYVRNITPYGVFVEFL--GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred CC-CCCEEEEEEEEEeeceEEEEcC--CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 45 8999999999999999999997 589999999999999999999999999999999999999999999986
No 35
>PRK07252 hypothetical protein; Provisional
Probab=99.59 E-value=8.1e-15 Score=118.71 Aligned_cols=80 Identities=29% Similarity=0.376 Sum_probs=74.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch-hh
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE-ED 165 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~-~~ 165 (259)
+|+++.|+|++|+++|+||+|. ++.+||+|++++++.++.++.+.+++||.|.|+|+++|.+++++.||++++.+ .+
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~--~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~ 80 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALE--NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQ 80 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEEC--CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc
Confidence 7999999999999999999997 57999999999999999999999999999999999999999999999999986 34
Q ss_pred HHH
Q 044309 166 IQA 168 (259)
Q Consensus 166 ~~~ 168 (259)
|..
T Consensus 81 ~~~ 83 (120)
T PRK07252 81 HFP 83 (120)
T ss_pred ccC
Confidence 443
No 36
>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=99.59 E-value=1.3e-14 Score=106.21 Aligned_cols=71 Identities=24% Similarity=0.195 Sum_probs=67.4
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|+++.|+|++++++|+||+|+ ++++|++|++++++++..++.+.|++||.++|+|+++|..++++.||++
T Consensus 3 ~G~iv~g~V~~v~~~gi~v~l~--~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 3 VGDILPGRVTKVNDRYVLVQLG--NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCEEEEEEEEEeCCeEEEEeC--CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 8999999999999999999998 5899999999999988888889999999999999999998999999985
No 37
>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=99.58 E-value=1e-14 Score=107.25 Aligned_cols=69 Identities=23% Similarity=0.386 Sum_probs=65.2
Q ss_pred CcEEE-EEEEEE-eCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 88 DMAVM-IQVKNI-ADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 88 G~iv~-G~V~~I-~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
|++|. |+|+++ .++|+||+|. ++++||+|+|++++.++.++.+.|++||.+.|+|+++|+.+++|.||+
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 GAVVDSVKVTKVEPDLGAVFELK--DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeC--CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 6999999997 589999999999999999999999999999999999999999999985
No 38
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.58 E-value=1.8e-14 Score=104.81 Aligned_cols=72 Identities=29% Similarity=0.377 Sum_probs=68.5
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
|+++.|+|+++.++|+||+|. ++++|++|+++++++++.++.+.|++||.+.|+|+++|++++++.||+|+.
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 GSIVTGKVTEVDAKGATVKLG--DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC--CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999997 579999999999999999999999999999999999999889999999975
No 39
>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=99.57 E-value=9.2e-15 Score=105.81 Aligned_cols=68 Identities=28% Similarity=0.417 Sum_probs=65.0
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|+++.|+|+++.++|+||++. ++++||+|++++++++..++.+.+++||.+.|+|+++|+++++|.||
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 GDVVRGFVKNIANNGVFVTLG--RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC--CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999997 57999999999999999999999999999999999999999999886
No 40
>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=99.57 E-value=1.7e-14 Score=107.41 Aligned_cols=75 Identities=28% Similarity=0.394 Sum_probs=68.6
Q ss_pred CcEEEEEEEEEeCceEEEEEccC-CCEEEEEEccccccccc-cCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchh
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEY-NNIEGMILFSELSRRRI-RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEE 164 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey-~~~eGllhisEls~~~v-~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~ 164 (259)
|+++.|+|+++++||+||+|.++ ++.+||+|++++++.+. .++.+.|++||.|.|+|+++| ++++.||+|++.++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~~ 77 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQD 77 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecccC
Confidence 78999999999999999999743 26999999999999886 899999999999999999999 79999999998764
No 41
>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=99.57 E-value=2.2e-14 Score=105.23 Aligned_cols=74 Identities=28% Similarity=0.439 Sum_probs=69.2
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
+|+++.|+|++++++|+||++.+ .+.+|++|++++++.+..++.+.|++||.|.|+|+++|.+++++.||+|+.
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 VGQKIDGTVRRVEDYGVFIDIDG-TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECC-CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 69999999999999999999973 369999999999999888899999999999999999999999999999974
No 42
>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=99.56 E-value=1.5e-14 Score=104.33 Aligned_cols=68 Identities=32% Similarity=0.530 Sum_probs=63.5
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc-ccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR-RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~-~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|+++.|+|+++++||+||+|+ ++.+||+|+++++| .+..++.+.|++||.+.|+|+++|.++++|+||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~--~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD--GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC--CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 789999999999999999997 58999999999997 577888899999999999999999999999885
No 43
>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=99.56 E-value=3.8e-14 Score=105.30 Aligned_cols=70 Identities=19% Similarity=0.209 Sum_probs=64.4
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE 163 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~ 163 (259)
+|+++.|+|++|+++|+||+++ +++++||+|.+++++. +.+++||.+.|+|+++|++++++.||+|+..+
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~g-~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDIG-IPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEeC-CCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 8999999999999999999995 2589999999999976 77999999999999999999999999998653
No 44
>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=99.54 E-value=4.4e-14 Score=102.54 Aligned_cols=70 Identities=36% Similarity=0.387 Sum_probs=66.6
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
|++|.|+|.++.++|+||+|. ++.+|+||.+|+++.+..++.+.+++||.++|+|+++|++.+++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~--~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG--YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999996 5799999999999999999999999999999999999988899999985
No 45
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.53 E-value=4.8e-14 Score=100.52 Aligned_cols=69 Identities=30% Similarity=0.512 Sum_probs=65.5
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
|+++.|+|+++.++|+||++. ++.+||+|.++++++++.++.+.+++||.+.|+|+++|. ++++.||+|
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 GSVVEGTVTRLKPFGAFVELG--GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999997 589999999999999999999999999999999999998 899999986
No 46
>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=99.53 E-value=4.8e-14 Score=102.88 Aligned_cols=71 Identities=31% Similarity=0.531 Sum_probs=64.0
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-cccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|| +|+++.|+|++++++|+||+|. ++.+||+|+++++|. +..++.+.|++||.+.|+|+++|.+++++.||
T Consensus 1 ~~-~g~~~~g~V~~i~~~G~fv~l~--~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YP-EGTRLFGKVTNLTDYGCFVELE--EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred Cc-CCCEEEEEEEEEEeeEEEEEcC--CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 45 8999999999999999999998 479999999999975 55577788999999999999999999999875
No 47
>PRK05807 hypothetical protein; Provisional
Probab=99.53 E-value=6.6e-14 Score=115.64 Aligned_cols=72 Identities=24% Similarity=0.367 Sum_probs=69.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
+|++|.|+|++++++|+||+|+ +.+||||+|++++.++.++.+.+++||.|.|+|+++|. +++|.||+|++.
T Consensus 5 vG~vv~G~Vt~i~~~GafV~L~---~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 5 AGSILEGTVVNITNFGAFVEVE---GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred CCCEEEEEEEEEECCeEEEEEC---CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 8999999999999999999994 68999999999999999999999999999999999998 799999999986
No 48
>PRK08059 general stress protein 13; Validated
Probab=99.52 E-value=6.9e-14 Score=113.44 Aligned_cols=80 Identities=34% Similarity=0.509 Sum_probs=74.7
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.+. +|++|.|+|+++.++|+||++. ++.+|++|++++++.++.++.+.+++||.|.|+|+++|.+++++.||++++.
T Consensus 4 ~~k-~G~iv~G~V~~i~~~G~fV~i~--~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~ 80 (123)
T PRK08059 4 QYE-VGSVVTGKVTGIQPYGAFVALD--EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATE 80 (123)
T ss_pred cCC-CCCEEEEEEEEEecceEEEEEC--CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcc
Confidence 355 8999999999999999999997 5899999999999999999999999999999999999999999999999998
Q ss_pred hhh
Q 044309 163 EED 165 (259)
Q Consensus 163 ~~~ 165 (259)
.+|
T Consensus 81 ~~~ 83 (123)
T PRK08059 81 EAP 83 (123)
T ss_pred cCc
Confidence 766
No 49
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.51 E-value=4.7e-14 Score=142.38 Aligned_cols=103 Identities=34% Similarity=0.515 Sum_probs=94.5
Q ss_pred cccchhhhh----hhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc
Q 044309 50 FEFSRENAK----AKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR 125 (259)
Q Consensus 50 ~eid~e~~r----iK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~ 125 (259)
+++|+++++ +|++.++||.. +.+.++ +|+++.|+|++++++|+||++. ++++||+|++++++.
T Consensus 532 ~~id~~~~~I~lS~K~~~~~p~~~----------~~~~~~-~G~~v~g~V~~i~~~G~fV~l~--~~i~Gli~~sel~~~ 598 (647)
T PRK00087 532 LDIDKENKKLSLSLKKLLPDPWEN----------VEEKYP-VGSIVLGKVVRIAPFGAFVELE--PGVDGLVHISQISWK 598 (647)
T ss_pred EEEECCCCEEEEEeeccccChhhh----------hhhhcc-CCeEEEEEEEEEECCeEEEEEC--CCCEEEEEhhhcCcc
Confidence 467888888 38888999997 666777 8999999999999999999997 689999999999999
Q ss_pred cccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhh
Q 044309 126 RIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEED 165 (259)
Q Consensus 126 ~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~ 165 (259)
++.++.+.|++||.|+|+|+++|++++++.||+|++.++|
T Consensus 599 ~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 599 RIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred ccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 9999999999999999999999999999999999999877
No 50
>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=99.49 E-value=1.4e-13 Score=98.01 Aligned_cols=68 Identities=34% Similarity=0.545 Sum_probs=64.2
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|+++.|+|++++++|+||++. ++.+||+|.+++++.++.++.+.+++||.+.|+|+++|++++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~--~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG--VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC--CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789999999999999999997 57999999999999888899999999999999999999989999886
No 51
>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=99.48 E-value=2e-13 Score=103.15 Aligned_cols=76 Identities=21% Similarity=0.269 Sum_probs=67.7
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc----ccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR----RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~----~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
.|++|++|.|+|+++.++|++|++. ++.+|+||++++++ .+..++.+.+++||.+.|+|+++|++ +++.||++
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~--~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~ 79 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDIN--SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTR 79 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECC--CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeC
Confidence 3458999999999999999999997 58999999999996 45567788899999999999999885 99999999
Q ss_pred ecc
Q 044309 160 RVS 162 (259)
Q Consensus 160 ~~~ 162 (259)
+..
T Consensus 80 ~~~ 82 (86)
T cd05789 80 SLK 82 (86)
T ss_pred ccc
Confidence 753
No 52
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.46 E-value=3.8e-13 Score=96.04 Aligned_cols=68 Identities=35% Similarity=0.538 Sum_probs=64.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
+|+++.|+|+++.++|+||++. +.+|++|.+++++.++.++.+.|++||.+.|+|+++|.+++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG---GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC---CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999994 6999999999999889899999999999999999999999999986
No 53
>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=99.45 E-value=4.5e-13 Score=95.80 Aligned_cols=68 Identities=37% Similarity=0.566 Sum_probs=64.1
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
|+++.|+|+++.++|+||++. ++.+||+|++++++.++.++.+.|++||.+.|+|+++|+ ++++.||+
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 GKIYEGKVVKIKDFGAFVEIL--PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC--CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 789999999999999999997 579999999999999988889999999999999999999 89999985
No 54
>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=99.44 E-value=5.3e-13 Score=96.77 Aligned_cols=66 Identities=26% Similarity=0.340 Sum_probs=59.7
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|+++.|+|+++.++|+||+|. ++++|++|.++++..+.. .+.|++||.+.|+|+++|+++++|.||
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 GMLVNARVKKVLSNGLILDFL--SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc--CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999997 579999999999765443 778999999999999999999999886
No 55
>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=99.42 E-value=1.5e-12 Score=93.97 Aligned_cols=67 Identities=21% Similarity=0.340 Sum_probs=61.5
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
|+++.|+|+++.++|+||++ ++++||||.|++++.+..++.+. +||.+.|+|+++|.++++|.||+|
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---EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE---CCEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 37999999999998887777663 899999999999998999999975
No 56
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.40 E-value=2.3e-12 Score=91.55 Aligned_cols=71 Identities=44% Similarity=0.571 Sum_probs=66.5
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|+++.|+|++++++|+||++. ++.+|++|.+++++.+..++.+.|++||.+.|+|++++..++++.||++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~--~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLG--NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeC--CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 6999999999999999999997 5899999999999888888888899999999999999998899999975
No 57
>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=99.40 E-value=8.9e-13 Score=133.24 Aligned_cols=70 Identities=29% Similarity=0.528 Sum_probs=65.1
Q ss_pred CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc----cccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS----RRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls----~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
|++|++|.|+|++|++||+||+|. +|.+||||+||++ ++++.++.+++++||.|+|+|+++|. ++||.|+
T Consensus 645 ~~vG~i~~GkV~~I~dfGaFVel~--~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 645 PEVGERFLGTVVKTTAFGAFVSLL--PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred CCCCCEEEEEEEEEECceEEEEec--CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 459999999999999999999997 6899999999996 47899999999999999999999996 7999986
No 58
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.39 E-value=1.6e-12 Score=132.15 Aligned_cols=73 Identities=36% Similarity=0.549 Sum_probs=69.6
Q ss_pred CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
++|+++.|+|++|.+||+||+|. ++.+||+|+|++++++++++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus 620 ~vG~v~~G~V~~I~~fGafVei~--~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 620 EVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred cCCeEEEEEEEEEECCeEEEEEC--CCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 38999999999999999999997 6899999999999999999999999999999999999986 9999999975
No 59
>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=99.39 E-value=1.2e-12 Score=102.82 Aligned_cols=72 Identities=29% Similarity=0.408 Sum_probs=65.4
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-------------------cCccccccCCCeEEEEEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-------------------RSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-------------------~~~~~~~kvGd~V~vkVi~v 147 (259)
+|++|.|+|++|.++|+||+|. ++++|++|++++++.+. .++.+.|++||.|.|+|+++
T Consensus 3 ~G~vV~G~V~~v~~~gl~v~L~--~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 3 EGMLVLGQVKEITKLDLVISLP--NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEECC--CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 7999999999999999999997 58999999999998652 34778899999999999999
Q ss_pred eCC---CCeEEEEEee
Q 044309 148 DKE---KGYIDLSKRR 160 (259)
Q Consensus 148 D~~---~gkI~LSlK~ 160 (259)
|++ +++|.||+|.
T Consensus 81 d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 81 DKSKSGKKRIELSLEP 96 (100)
T ss_pred cCCcCCCcEEEEEecH
Confidence 997 7899999984
No 60
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.38 E-value=2.9e-12 Score=111.03 Aligned_cols=122 Identities=16% Similarity=0.159 Sum_probs=96.1
Q ss_pred cceeEEEeecCCccccchhhhhhhhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccC------
Q 044309 37 SGCLKTLILVPTPFEFSRENAKAKKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEY------ 110 (259)
Q Consensus 37 ~g~~~~~~~~~~~~eid~e~~riK~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey------ 110 (259)
.|++...++. .+++|.++++++- +||.. +. ..|++|++|.|+|+++.++|+||+|..+
T Consensus 30 ~~~i~as~~G--~~~id~~~~~Isv---~P~~~----------~~-~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~ 93 (189)
T PRK09521 30 NGEVYASVVG--KVFIDDINRKISV---IPFKK----------TP-PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERE 93 (189)
T ss_pred CCEEEEEeeE--EEEEcCCCCEEEE---ecCcC----------CC-CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccc
Confidence 3555554442 3467887777543 58875 33 3444999999999999999999999632
Q ss_pred --CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 111 --NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 111 --~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
.+.+|++|.+++++.+..++.+.|++||.|.|+|++++ +++.||+|+.. -|.|...+.
T Consensus 94 l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~~-----------------lGvv~a~~~ 153 (189)
T PRK09521 94 LATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGKD-----------------LGVIYAMCS 153 (189)
T ss_pred cCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecCC-----------------ceEEEEEcc
Confidence 26899999999999888889999999999999999998 78999998532 388888888
Q ss_pred ccCCch
Q 044309 189 TLGIDL 194 (259)
Q Consensus 189 ~~G~fv 194 (259)
.+|..+
T Consensus 154 ~~g~~~ 159 (189)
T PRK09521 154 RCRTPL 159 (189)
T ss_pred ccCCce
Confidence 788865
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=99.38 E-value=2.5e-12 Score=96.49 Aligned_cols=75 Identities=13% Similarity=0.120 Sum_probs=69.2
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
+|++|++|.|+|+++.+.|++|++. .+.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~--~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDIL--SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeC--CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 4569999999999999999999997 5899999999999888888899999999999999999986 8999999863
No 62
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=99.36 E-value=2.1e-12 Score=97.52 Aligned_cols=73 Identities=29% Similarity=0.563 Sum_probs=69.4
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEE-ccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMIL-FSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllh-isEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
.||++|+++. .|+.+.+.|+||.|.||+ .+|+|. .+|++.++++++++.+ +|..+.|+|+++|+++|.|+||.
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 5899999999 777999999999999996 999998 9999999999999999 99999999999999999999985
No 63
>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=99.36 E-value=3.9e-12 Score=97.58 Aligned_cols=70 Identities=20% Similarity=0.240 Sum_probs=61.3
Q ss_pred CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEcccccc---ccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSR---RRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~---~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
+|+++.|+|+++.++ ||||+|. ++.+||||+||++| .++.++.+.+++||.|.|+|++......-..||.
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~--~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIG--LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeC--CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence 899999999999997 9999998 58999999999999 6788899999999999999999776544444443
No 64
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.35 E-value=6.1e-12 Score=93.54 Aligned_cols=71 Identities=23% Similarity=0.361 Sum_probs=62.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEeCCCCeEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVDKEKGYID 155 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD~~~gkI~ 155 (259)
+|+++.|+|++++++|+||+|..| +.+|++|++++++.++. +..+.+++||.|+|+|.++|.+++++.
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 VGEEFDGVISGVTSFGLFVELDNL-TVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCC-CEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEE
Confidence 389999999999999999999742 79999999999875422 345789999999999999999899999
Q ss_pred EEE
Q 044309 156 LSK 158 (259)
Q Consensus 156 LSl 158 (259)
+++
T Consensus 80 ~~l 82 (83)
T cd04471 80 FEL 82 (83)
T ss_pred EEE
Confidence 986
No 65
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.26 E-value=6e-12 Score=113.62 Aligned_cols=113 Identities=20% Similarity=0.219 Sum_probs=99.6
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhhH
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEEDI 166 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~~ 166 (259)
.|+.+.|+|++....|.||-++ ++.-||||-||.. ...+.|+++.++|+++.+ +|+|.||++....+..
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e--~~~~GfIh~sEr~--------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l 223 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITE--NGYLGFIHKSERF--------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEML 223 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEc--CCeEEEEcchhhc--------ccccCCceEEEEEEEEcc-CCeeecccccccHHhh
Confidence 4999999999999999999996 7999999999976 457899999999999998 8999999999988777
Q ss_pred HHHHHhccccceEEEEEEecccccCCchHHHHHhhchh--hHHhhcCHHHHHHHHhcC
Q 044309 167 QACEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWP--LYWKYGHAFEAFKIIVTD 222 (259)
Q Consensus 167 ~~~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~--l~~~~~~~~~~fk~a~~~ 222 (259)
+..+ +.+++.+.+ .|-|+. |+|.|-| |.+.|+.++.+||+|+|.
T Consensus 224 ~~da---------q~Il~yL~~-~gG~mp--f~DKSsPEdIk~~FgiSKg~FKrAiGg 269 (287)
T COG2996 224 DEDA---------QMILTYLES-NGGFMP--FNDKSSPEDIKATFGISKGQFKRAIGG 269 (287)
T ss_pred hhhH---------HHHHHHHHH-cCCccc--cCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 7665 356677766 555678 9999999 999999999999999985
No 66
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=99.24 E-value=2.9e-11 Score=84.30 Aligned_cols=65 Identities=42% Similarity=0.590 Sum_probs=60.2
Q ss_pred EEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE
Q 044309 91 VMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 91 v~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS 157 (259)
+.|+|+++.++|+||++. ++.+|++|.+++++.+..++.+.+++||.+.|+|+++|++++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~--~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELE--DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEec--CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999997 58999999999999888888899999999999999999988999876
No 67
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=99.24 E-value=8.2e-11 Score=87.62 Aligned_cols=64 Identities=30% Similarity=0.352 Sum_probs=58.1
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
.+. +|+.+.|+|++++++|+||++. ++.+||+|.+++. +.+++||.++++|.++ .+++++++|+
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 DLE-VGKLYKGKVNGVAKYGVFVDLN--DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hCC-CCCEEEEEEEeEecceEEEEEC--CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 455 8999999999999999999998 5799999999974 5699999999999999 7789999986
No 68
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.23 E-value=4.2e-11 Score=87.30 Aligned_cols=62 Identities=24% Similarity=0.216 Sum_probs=57.5
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc--ccCccccccCCCeEEEEEEEEeCCC
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR--IRSVSSLIKVGRIEPVMVLRVDKEK 151 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~--v~~~~~~~kvGd~V~vkVi~vD~~~ 151 (259)
|++|.|+|+++.++|+||++. ++++|++|++++++++ ..++.+.|++||.+.|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~--~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA--DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC--CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 789999999999999999997 5899999999999874 7888899999999999999999854
No 69
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.23 E-value=2.5e-11 Score=123.38 Aligned_cols=69 Identities=36% Similarity=0.578 Sum_probs=64.5
Q ss_pred CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309 85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL 156 (259)
Q Consensus 85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L 156 (259)
+++|++|.|+|++|.+||+||++. ++.+||||+|++++.++.++.+.|++||.|.|+|+++|. +|+|+|
T Consensus 616 ~~~G~i~~G~V~~I~~~GafVei~--~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 616 PEVGKIYEGKVVRIMDFGAFVEIL--PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred cccCcEEEEEEEEEeCCEEEEEEC--CCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 348999999999999999999997 689999999999999999999999999999999999998 788765
No 70
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.20 E-value=3e-11 Score=120.50 Aligned_cols=79 Identities=32% Similarity=0.464 Sum_probs=72.5
Q ss_pred hhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 80 YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+...+. +|+++.|+|+++.+|||||+|. ++.+||+|+|++++.|+.+..+++++||.+.|||+.+|+ +|+++||++
T Consensus 613 i~~e~e-vg~iy~G~V~ri~~fGaFv~l~--~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~ 688 (692)
T COG1185 613 ITREVE-VGEVYEGTVVRIVDFGAFVELL--PGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIK 688 (692)
T ss_pred HHhhcc-cccEEEEEEEEEeecceEEEec--CCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceeh
Confidence 344444 9999999999999999999998 789999999999999999999999999999999999997 799999998
Q ss_pred ecc
Q 044309 160 RVS 162 (259)
Q Consensus 160 ~~~ 162 (259)
...
T Consensus 689 ~~~ 691 (692)
T COG1185 689 AVL 691 (692)
T ss_pred hcc
Confidence 753
No 71
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.19 E-value=3e-11 Score=117.93 Aligned_cols=81 Identities=25% Similarity=0.321 Sum_probs=73.7
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.+. .|.+++|+|+++.++|+||+|. ++.+||+|+|||+..++.+|.+.+.+||.|.|+.++.|+ ++.+.+|.|.+.
T Consensus 665 ~l~-~g~vy~~tIt~~rd~G~~V~l~--p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ralL 740 (760)
T KOG1067|consen 665 DLE-FGGVYTATITEIRDTGVMVELY--PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRALL 740 (760)
T ss_pred ceE-eeeEEEEEEeeecccceEEEec--CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhhhc
Confidence 344 7999999999999999999995 799999999999999999999999999999999999998 688888888888
Q ss_pred hhhHH
Q 044309 163 EEDIQ 167 (259)
Q Consensus 163 ~~~~~ 167 (259)
++|..
T Consensus 741 p~p~~ 745 (760)
T KOG1067|consen 741 PDPAT 745 (760)
T ss_pred CCccc
Confidence 87654
No 72
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.16 E-value=5.8e-11 Score=120.02 Aligned_cols=78 Identities=31% Similarity=0.454 Sum_probs=73.6
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.+. +|.++.|+|+++.+||+||+|+ -+.+|+||+|+++.+++.+|.+++++||.|+|+|+++|..+++|.||++.-.
T Consensus 655 dLk-~Gm~leg~Vrnv~~fgafVdIg--v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 655 DLK-PGMILEGTVRNVVDFGAFVDIG--VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred hcc-CCCEEEEEEEEeeeccceEEec--cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 455 8999999999999999999997 5899999999999999999999999999999999999999999999999765
Q ss_pred h
Q 044309 163 E 163 (259)
Q Consensus 163 ~ 163 (259)
.
T Consensus 732 ~ 732 (780)
T COG2183 732 E 732 (780)
T ss_pred C
Confidence 4
No 73
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=99.09 E-value=6.5e-10 Score=86.45 Aligned_cols=78 Identities=21% Similarity=0.335 Sum_probs=66.2
Q ss_pred cEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccC-----------ccccccCCCeEEEEEEEEeCCC-----C
Q 044309 89 MAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRS-----------VSSLIKVGRIEPVMVLRVDKEK-----G 152 (259)
Q Consensus 89 ~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~-----------~~~~~kvGd~V~vkVi~vD~~~-----g 152 (259)
+++.|+|+++.++|+||+|. +++|++|++++++++... ..+.|++||.+.|+|.++|.+. +
T Consensus 1 ~vv~g~V~~i~~~GifV~l~---~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~ 77 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG---PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRES 77 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc---CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence 47999999999999999995 599999999999866543 3477999999999999999763 5
Q ss_pred eEEEEEeecchhhHHHH
Q 044309 153 YIDLSKRRVSEEDIQAC 169 (259)
Q Consensus 153 kI~LSlK~~~~~~~~~~ 169 (259)
++.||+|+....+|.=.
T Consensus 78 ~i~ls~k~~~~g~~~~~ 94 (99)
T cd04460 78 KIGLTMRQPGLGKLEWI 94 (99)
T ss_pred eEEEEEecCCCCcHHHh
Confidence 89999999877666543
No 74
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.09 E-value=4.2e-10 Score=100.81 Aligned_cols=76 Identities=18% Similarity=0.211 Sum_probs=68.7
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----cCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
..|++||+|.|+|+++.++|+||+|. ++.+|+||++++++.++ .++++.|++||.|.|+|++++++ +.+.||+
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~--~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~LS~ 135 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDIN--SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVLTL 135 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeC--CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEEEE
Confidence 45679999999999999999999997 47999999999999887 78899999999999999999974 5699999
Q ss_pred eec
Q 044309 159 RRV 161 (259)
Q Consensus 159 K~~ 161 (259)
++.
T Consensus 136 k~~ 138 (235)
T PRK04163 136 KGK 138 (235)
T ss_pred cCC
Confidence 864
No 75
>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=99.04 E-value=1.6e-09 Score=78.54 Aligned_cols=63 Identities=24% Similarity=0.146 Sum_probs=55.4
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC--CeEEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK--GYIDLSK 158 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~--gkI~LSl 158 (259)
.|+++.|+|.++.+.|+||+++ +.+|+||.+|++. .+.+++||.++|.|++++.++ ++|.||+
T Consensus 3 ~g~iV~G~V~~~~~~~~~vdig---~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDLG---KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCEEEEEEEEEcCCCEEEEcC---CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 7999999999999999999995 5999999999973 467899999999999999643 5788874
No 76
>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=99.01 E-value=1.4e-09 Score=111.11 Aligned_cols=81 Identities=20% Similarity=0.340 Sum_probs=68.6
Q ss_pred chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEE
Q 044309 74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPV 142 (259)
Q Consensus 74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~v 142 (259)
...|+++... +|+++.|+|++|++||+||+|.+ .+++||+|+|++++++. ++..+.+++||.|.|
T Consensus 617 ~~~~~yl~~~---iG~~~~g~V~~v~~fGifV~L~~-~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~V 692 (709)
T TIGR02063 617 WKKAEYMSEK---IGEEFEGVISGVTSFGLFVELEN-NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKV 692 (709)
T ss_pred HHHHHhhhcc---CCcEEEEEEEEEEeCCEEEEecC-CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEE
Confidence 4466766654 79999999999999999999984 26999999999986543 334577999999999
Q ss_pred EEEEEeCCCCeEEEEE
Q 044309 143 MVLRVDKEKGYIDLSK 158 (259)
Q Consensus 143 kVi~vD~~~gkI~LSl 158 (259)
+|.++|..+++|++++
T Consensus 693 kv~~vd~~~~~I~~~l 708 (709)
T TIGR02063 693 RVVKADLDTGKIDFEL 708 (709)
T ss_pred EEEEEecccCeEEEEE
Confidence 9999999999999986
No 77
>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=98.92 E-value=5.3e-09 Score=106.03 Aligned_cols=81 Identities=22% Similarity=0.370 Sum_probs=69.2
Q ss_pred chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEE
Q 044309 74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPV 142 (259)
Q Consensus 74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~v 142 (259)
...|+++.+. +|+.+.|+|++|+++|+||+|++ .+++||+|++++.+++. ++....|++||.|+|
T Consensus 562 ~~~~~yl~~~---iG~~~~g~I~~v~~~GifV~L~~-~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~V 637 (654)
T TIGR00358 562 WLKCRYLLDK---VGTEFSGEISSVTRFGMFVRLDD-NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTV 637 (654)
T ss_pred HHHHHhhhhC---CCcEEEEEEEeEEcCcEEEEecC-CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEE
Confidence 3457776665 79999999999999999999986 47999999999997641 334577999999999
Q ss_pred EEEEEeCCCCeEEEEE
Q 044309 143 MVLRVDKEKGYIDLSK 158 (259)
Q Consensus 143 kVi~vD~~~gkI~LSl 158 (259)
+|.++|.++++|++++
T Consensus 638 ki~~vd~~~~~I~f~l 653 (654)
T TIGR00358 638 KLTEVNMETRSIIFEL 653 (654)
T ss_pred EEEEEecccCeEEEEE
Confidence 9999999999999985
No 78
>PRK11642 exoribonuclease R; Provisional
Probab=98.91 E-value=5.6e-09 Score=108.04 Aligned_cols=82 Identities=22% Similarity=0.294 Sum_probs=69.2
Q ss_pred hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEE
Q 044309 75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVM 143 (259)
Q Consensus 75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vk 143 (259)
+.|+++.+. +|+++.|+|++|++||+||+|++ .+++||||++++.+++. ++....|++||.|.|+
T Consensus 634 ~~~~~m~~~---iGe~f~G~Is~V~~fGifVeL~~-~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~Vk 709 (813)
T PRK11642 634 LKCDFMLDQ---VGNVFKGVISSVTGFGFFVRLDD-LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVR 709 (813)
T ss_pred HHHhhhhcc---CCcEEEEEEEEeecCceEEEECC-CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEE
Confidence 456666653 79999999999999999999974 35999999999987532 1235779999999999
Q ss_pred EEEEeCCCCeEEEEEee
Q 044309 144 VLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 144 Vi~vD~~~gkI~LSlK~ 160 (259)
|.++|.++++|+|++..
T Consensus 710 V~~vD~~~rkI~f~l~~ 726 (813)
T PRK11642 710 VEAVNMDERKIDFSLIS 726 (813)
T ss_pred EEEeecCCCeEEEEEec
Confidence 99999999999999853
No 79
>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=98.88 E-value=8.2e-09 Score=79.82 Aligned_cols=75 Identities=19% Similarity=0.213 Sum_probs=65.1
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEE--------ccCCCEEEEEEcccccccccc--CccccccCCCeEEEEEEEEeCCCCe
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSL--------LEYNNIEGMILFSELSRRRIR--SVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L--------~ey~~~eGllhisEls~~~v~--~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
.|++|++|.|+|++++...|.|++ . ....|++|++++...... ++.+.|++||.|.|+|++++. ...
T Consensus 3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~--~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~ 79 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLK--ESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASS 79 (92)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecC--CCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCC
Confidence 467999999999999999999999 5 368999999999876665 678999999999999999975 366
Q ss_pred EEEEEeec
Q 044309 154 IDLSKRRV 161 (259)
Q Consensus 154 I~LSlK~~ 161 (259)
+.||+++-
T Consensus 80 ~~Lst~~~ 87 (92)
T cd05791 80 YYLSTAEN 87 (92)
T ss_pred cEEEecCC
Confidence 88998753
No 80
>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=98.87 E-value=1.3e-08 Score=87.53 Aligned_cols=74 Identities=20% Similarity=0.267 Sum_probs=63.5
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEe-----CC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVD-----KE 150 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD-----~~ 150 (259)
+|+++.|+|++++++|+||+++ ..+|++|.+++.+.+.. +....++.||.|+++|.++| ++
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg---~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLG---PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeC---CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 7999999999999999999994 69999999999865431 23577999999999999998 55
Q ss_pred CCeEEEEEeecch
Q 044309 151 KGYIDLSKRRVSE 163 (259)
Q Consensus 151 ~gkI~LSlK~~~~ 163 (259)
..+|.||+|+...
T Consensus 158 ~~~I~lt~k~~~L 170 (179)
T TIGR00448 158 GSKIGLTMRQPLL 170 (179)
T ss_pred cceEEEEeccCcC
Confidence 6799999998644
No 81
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.71 E-value=9.1e-08 Score=93.62 Aligned_cols=67 Identities=22% Similarity=0.157 Sum_probs=61.2
Q ss_pred CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEEEeec
Q 044309 86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLSKRRV 161 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LSlK~~ 161 (259)
++|++|.|+|.++.++|+||+| ++++||||.++++ |++.|++||.++|.|++|+++++ +|.||++..
T Consensus 133 ~~GeIV~G~V~ri~~~giiVDL---ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 133 RVGEIITGVVKRVERGNIIVDL---GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred hcCCEEEEEEEEEecCCEEEEE---CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 3899999999999999999999 4899999999996 67889999999999999999766 899998854
No 82
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=98.69 E-value=1.3e-07 Score=100.12 Aligned_cols=110 Identities=20% Similarity=0.247 Sum_probs=97.1
Q ss_pred hhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 81 EARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 81 ~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+.+. .|+++.|.|.++.+.|+|+.|. .+++|++++|+++......+++.|.+|+.+.++|.+++...+++.||+|.
T Consensus 1157 ~eDlk-~g~iv~G~V~nv~~~glfi~ls--~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1157 IEDLK-IGDIVRGFVKNVETKGLFIALS--RKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred hhhcc-cCceeEEEEEEecCCcEEEEEc--cceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence 45666 8999999999999999999998 68999999999999999999999999999999999999999999999998
Q ss_pred cchhhH---HHHHHhccccceEEEEEEecccccCCch
Q 044309 161 VSEEDI---QACEERYNKSKLVHSIMRHVAETLGIDL 194 (259)
Q Consensus 161 ~~~~~~---~~~~~~~~~g~~v~g~V~~i~~~~G~fv 194 (259)
.....- .......++|+...|+|..+.+ +|.|+
T Consensus 1234 s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~-~G~fi 1269 (1710)
T KOG1070|consen 1234 SDIKDTVKLLKDSKDLKKGDREDGTVEVVDP-FGLFI 1269 (1710)
T ss_pred cccCCchhhhhhhhhhhccccccceEEEecC-CceEE
Confidence 654222 2234667899999999999965 99987
No 83
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.68 E-value=1.3e-07 Score=81.55 Aligned_cols=75 Identities=23% Similarity=0.421 Sum_probs=63.2
Q ss_pred CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccccc-----------CccccccCCCeEEEEEEEEeCCC--
Q 044309 85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIR-----------SVSSLIKVGRIEPVMVLRVDKEK-- 151 (259)
Q Consensus 85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~-----------~~~~~~kvGd~V~vkVi~vD~~~-- 151 (259)
|.+|+++.|+|++++++|+||+++ ..+|++|.+++.+++.. +....+++||.|+++|.+++.+.
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg---~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~ 155 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIG---PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR 155 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEe---CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence 347999999999999999999995 59999999999875432 34567999999999999999754
Q ss_pred ---CeEEEEEeecc
Q 044309 152 ---GYIDLSKRRVS 162 (259)
Q Consensus 152 ---gkI~LSlK~~~ 162 (259)
.+|.+|+++..
T Consensus 156 ~~~~~I~ls~~~~~ 169 (187)
T PRK08563 156 PRGSKIGLTMRQPG 169 (187)
T ss_pred CCCCEEEEEecCCC
Confidence 37899999754
No 84
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.66 E-value=9.2e-08 Score=82.40 Aligned_cols=81 Identities=20% Similarity=0.283 Sum_probs=65.7
Q ss_pred CCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc----------ccC-ccccccCCCeEEEEEEEEeCCC--
Q 044309 85 PEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR----------IRS-VSSLIKVGRIEPVMVLRVDKEK-- 151 (259)
Q Consensus 85 ~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~----------v~~-~~~~~kvGd~V~vkVi~vD~~~-- 151 (259)
|..|++|.|.|+++.+||+||.+. ..+||+|.|++.+.. +.+ -...+++||.|.+||+.++...
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~ig---p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIG---PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred eccccEEEEEEEEEeecceEEEec---cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence 447999999999999999999995 799999999999862 222 3447999999999999998654
Q ss_pred ---CeEEEEEeecch--hhHHH
Q 044309 152 ---GYIDLSKRRVSE--EDIQA 168 (259)
Q Consensus 152 ---gkI~LSlK~~~~--~~~~~ 168 (259)
.+|.+++|+.-. -+|-.
T Consensus 156 ~~~~~I~lTmrq~~LGklew~~ 177 (183)
T COG1095 156 PRESKIGLTMRQPGLGKLEWIE 177 (183)
T ss_pred cccceEEEEeccccCCcchhhh
Confidence 578999998653 34543
No 85
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=98.57 E-value=1.6e-07 Score=99.51 Aligned_cols=79 Identities=25% Similarity=0.301 Sum_probs=73.3
Q ss_pred hhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 80 YEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+.... +|.++.|+|.++.++||||.+. ++++||.|.|+++..++.++++.|.+||.+.|+|.++|.++.+|.||+|
T Consensus 594 ~~~~~--pg~~~~G~l~~~~~~g~~V~F~--g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r 669 (1710)
T KOG1070|consen 594 FEQAI--PGKITKGTLCAIKENGAFVTFT--GGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLR 669 (1710)
T ss_pred hhhcC--CCceEEEEEeeeccCCeEEEec--CccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhh
Confidence 44444 4999999999999999999996 7999999999999999999999999999999999999999999999999
Q ss_pred ecc
Q 044309 160 RVS 162 (259)
Q Consensus 160 ~~~ 162 (259)
...
T Consensus 670 ~s~ 672 (1710)
T KOG1070|consen 670 ASS 672 (1710)
T ss_pred hhh
Confidence 764
No 86
>PRK05054 exoribonuclease II; Provisional
Probab=98.48 E-value=6.6e-07 Score=90.79 Aligned_cols=83 Identities=24% Similarity=0.202 Sum_probs=65.5
Q ss_pred chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----cC-------ccccccCCCeEE
Q 044309 74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----RS-------VSSLIKVGRIEP 141 (259)
Q Consensus 74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----~~-------~~~~~kvGd~V~ 141 (259)
.+.|+++.+..- .|+.+.|.|++|+++|+||+|.+ .+++||||++.+...+. .+ -+..|++||.|.
T Consensus 549 ~~~~~y~~~~~G-~~~~f~g~I~~v~~~G~fV~l~~-~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~ 626 (644)
T PRK05054 549 WLYARYLKDKAG-TDTRFAAEIIDISRGGMRVRLLE-NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVID 626 (644)
T ss_pred HHHHHHHhhccC-CCeEEEEEEEeeecCcEEEEEeC-CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEE
Confidence 446666665521 24599999999999999999987 58999999999965311 01 125799999999
Q ss_pred EEEEEEeCCCCeEEEEE
Q 044309 142 VMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 142 vkVi~vD~~~gkI~LSl 158 (259)
|+|.++|..+++|++++
T Consensus 627 V~v~~vd~~~~~i~~~~ 643 (644)
T PRK05054 627 VTLAEVRMETRSIIARP 643 (644)
T ss_pred EEEEEEccccCeEEEEE
Confidence 99999999999999875
No 87
>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=98.41 E-value=2.3e-06 Score=80.77 Aligned_cols=67 Identities=24% Similarity=0.252 Sum_probs=58.7
Q ss_pred CCCcEEEEEEEEEeCce-EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCC--CCeEEEEEeec
Q 044309 86 EVDMAVMIQVKNIADMG-AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKE--KGYIDLSKRRV 161 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~G-afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~--~gkI~LSlK~~ 161 (259)
++|++++|+|.++.+.| +||++ ++.+|+||.+|+. +++.|++||.++|.|++++.. ..+|.||++..
T Consensus 130 k~GeiV~G~V~~v~~~g~v~Vdi---G~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVEL---GKTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEE---CCeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 38999999999999988 69999 4899999999988 456699999999999999954 35899998864
No 88
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.39 E-value=2.4e-06 Score=81.20 Aligned_cols=66 Identities=24% Similarity=0.190 Sum_probs=56.9
Q ss_pred CCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC--eEEEEEee
Q 044309 86 EVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG--YIDLSKRR 160 (259)
Q Consensus 86 ~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g--kI~LSlK~ 160 (259)
+.|++++|+|.++.+.|+||++ ++++|+||.+++. +++.|++||.++|.|++|+.+++ +|.||+..
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdl---g~vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNL---GKIEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEe---CCeEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 3899999999999999999999 4799999999886 36789999999999999996543 57777653
No 89
>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=98.35 E-value=5.7e-06 Score=79.98 Aligned_cols=58 Identities=21% Similarity=0.217 Sum_probs=51.3
Q ss_pred CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEccccccc------------cccCccccccCCCeEEEEEEE
Q 044309 87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSRR------------RIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~~------------~v~~~~~~~kvGd~V~vkVi~ 146 (259)
+|++|.|+|+++.+. ||||+|+ .+..||||++++.+. +..++.+.+++||.|.|.|.+
T Consensus 25 vGnIY~GrV~~i~p~l~aAFVdiG--~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 25 KGNIYKGRVTRILPSLQAAFVDIG--LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred CCCEEEEEEeeecCCCceEEEEcC--CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 899999999999999 9999998 579999999999752 244567789999999999997
No 90
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=98.30 E-value=3e-06 Score=75.86 Aligned_cols=77 Identities=21% Similarity=0.385 Sum_probs=67.6
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc----cCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI----RSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v----~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
..|++||+|.|+|..+...|+.|+|. +.+.|++|+|++.++.+ .+.+.+|++||.|.|+|..+|+ .+.+.|++
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~--sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~ 136 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIG--SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTL 136 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcC--CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEe
Confidence 45779999999999999999999997 56999999999976553 4578899999999999999998 68999999
Q ss_pred eecc
Q 044309 159 RRVS 162 (259)
Q Consensus 159 K~~~ 162 (259)
|...
T Consensus 137 k~~~ 140 (239)
T COG1097 137 KDEG 140 (239)
T ss_pred ecCC
Confidence 7643
No 91
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.29 E-value=5e-06 Score=63.72 Aligned_cols=74 Identities=14% Similarity=0.036 Sum_probs=62.4
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
.|++||.|.|+|+++...+.+|+|. +...|+||.+++... .+..+..+++||.|-|+|.++|+ .....||+...
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~--s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~~ 76 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIG--GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVDS 76 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcC--CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeCC
Confidence 4669999999999999999999997 468999999887533 34456789999999999999998 46788988763
No 92
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=98.23 E-value=8.1e-06 Score=70.59 Aligned_cols=94 Identities=16% Similarity=0.175 Sum_probs=78.9
Q ss_pred hcCCCCCcEEEEEEEEEeCceEEEEEcc-----C---CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309 82 ARYPEVDMAVMIQVKNIADMGAYVSLLE-----Y---NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 82 ~~~~~~G~iv~G~V~~I~~~GafV~L~e-----y---~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
..+|+.|++|.|.|+++....+.|++-. + +...|-+|+|+.+...+++.++.|++||.|.++|++.- ..
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~ 135 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP 135 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CC
Confidence 3577799999999999999999999851 0 02567899999999999999999999999999999974 46
Q ss_pred EEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCchH
Q 044309 154 IDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDLE 195 (259)
Q Consensus 154 I~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve 195 (259)
+.||.+.-. -|.|...|.++|.+|.
T Consensus 136 ~~Lst~~~d-----------------lGVI~A~CsrC~~~L~ 160 (188)
T COG1096 136 IQLSTKGND-----------------LGVIYARCSRCRAPLV 160 (188)
T ss_pred eEEEecCCc-----------------ceEEEEEccCCCcceE
Confidence 889888543 3999999999999773
No 93
>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=98.17 E-value=7e-06 Score=83.33 Aligned_cols=82 Identities=21% Similarity=0.236 Sum_probs=63.7
Q ss_pred chhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccc--ccc---c-C-----c-cccccCCCeEE
Q 044309 74 NLECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSR--RRI---R-S-----V-SSLIKVGRIEP 141 (259)
Q Consensus 74 ~~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~--~~v---~-~-----~-~~~~kvGd~V~ 141 (259)
.+.|+++.++.- .|+.+.|.|++++.+|+||+|.+ .+++||||++.+.. ... . . . ...|++||.|+
T Consensus 545 ~~~~~yl~~~~g-~~~~f~g~I~~v~~~g~~v~l~~-~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~ 622 (639)
T TIGR02062 545 WLYARFLADKAA-KNTRFAAEIVDISRGGMRVRLLE-NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVID 622 (639)
T ss_pred HHHHHHHhhccC-CCcEEEEEEEeeeCCcEEEEEec-CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEE
Confidence 345666666521 25599999999999999999986 68999999999965 111 0 1 1 23699999999
Q ss_pred EEEEEEeCCCCeEEEE
Q 044309 142 VMVLRVDKEKGYIDLS 157 (259)
Q Consensus 142 vkVi~vD~~~gkI~LS 157 (259)
|+|.++|.++++|++.
T Consensus 623 V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 623 VVLTEVRMETRSIIAR 638 (639)
T ss_pred EEEEEeccccCcEeee
Confidence 9999999999999874
No 94
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.09 E-value=1.2e-05 Score=82.52 Aligned_cols=81 Identities=23% Similarity=0.295 Sum_probs=67.5
Q ss_pred hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-----------ccCccccccCCCeEEEE
Q 044309 75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-----------IRSVSSLIKVGRIEPVM 143 (259)
Q Consensus 75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-----------v~~~~~~~kvGd~V~vk 143 (259)
+.|+++.+. +|+.+.|.|++++.+|+||.|.+ .+++|++|++.+...+ .......++.||.|+|+
T Consensus 613 ~~~~~m~~~---vg~~f~g~V~~v~~~g~~V~l~~-~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~ 688 (706)
T COG0557 613 LKAEYMKKR---VGEEFDGVVTGVTSFGFFVELPE-LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK 688 (706)
T ss_pred HHHHHHHHh---cCCEEEEEEEEEEeccEEEEecc-cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence 355666655 79999999999999999999986 4699999999999532 23345679999999999
Q ss_pred EEEEeCCCCeEEEEEe
Q 044309 144 VLRVDKEKGYIDLSKR 159 (259)
Q Consensus 144 Vi~vD~~~gkI~LSlK 159 (259)
|.+++...++|++++-
T Consensus 689 v~~v~~~~~~i~~~~v 704 (706)
T COG0557 689 VTSVDLDERKIDFELV 704 (706)
T ss_pred EEEEcccccceEEEec
Confidence 9999999999998864
No 95
>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=98.05 E-value=1.7e-05 Score=60.26 Aligned_cols=64 Identities=19% Similarity=0.269 Sum_probs=43.7
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccC----------------CCEEEEEEccccccccccC--ccccccCCCeEEEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEY----------------NNIEGMILFSELSRRRIRS--VSSLIKVGRIEPVMVL 145 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey----------------~~~eGllhisEls~~~v~~--~~~~~kvGd~V~vkVi 145 (259)
+|++|++|.|+|+++++.-|+++|.-- ....|+|+.+++....... +.+.|++||.|.|+|+
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 367999999999999999999998632 1467999999987644433 5788999999999999
Q ss_pred EE
Q 044309 146 RV 147 (259)
Q Consensus 146 ~v 147 (259)
+.
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 74
No 96
>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=98.04 E-value=4e-05 Score=58.80 Aligned_cols=63 Identities=10% Similarity=0.030 Sum_probs=50.5
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc-----------cCccccccCCCeEEEEEEEEeCCCC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI-----------RSVSSLIKVGRIEPVMVLRVDKEKG 152 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v-----------~~~~~~~kvGd~V~vkVi~vD~~~g 152 (259)
+|+++.|+|++++++|+||.++ .+++|+|.+.+..... .+-...++.|+.|++||+.+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G---pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG---PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc---CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 4899999999999999999994 7999999988864322 1124558999999999998876533
No 97
>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=98.00 E-value=3e-05 Score=57.53 Aligned_cols=68 Identities=24% Similarity=0.257 Sum_probs=57.6
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccC---ccccccCCCeE-EEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRS---VSSLIKVGRIE-PVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~---~~~~~kvGd~V-~vkVi~vD~~~gkI~LSlK 159 (259)
|++|.|+|..-++.+++|++.+ .++.|+||...+++ .+.+ .-..+++||++ .+.|+ +...+.|.||.|
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 GKLVDARVLKKTLNGLEVAILP-EEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecC-CCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 7899999999999999999996 58999999999998 4433 33558999999 89999 777788888865
No 98
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.92 E-value=7.2e-05 Score=64.46 Aligned_cols=72 Identities=11% Similarity=0.051 Sum_probs=56.3
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-----------cc-cCccccccCCCeEEEEEEEEeCCC--C
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-----------RI-RSVSSLIKVGRIEPVMVLRVDKEK--G 152 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-----------~v-~~~~~~~kvGd~V~vkVi~vD~~~--g 152 (259)
.|+++.|+|++++++|+||.++ -.++|||.+.+... |. ++-+..++.|+.|++||..+..+. .
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~G---p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~ 157 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAG---PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNL 157 (176)
T ss_pred CCCEEEEEEEEEecceEEEEee---CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCc
Confidence 7999999999999999999995 58899999999842 11 222456999999999998886543 3
Q ss_pred eEEEEEeec
Q 044309 153 YIDLSKRRV 161 (259)
Q Consensus 153 kI~LSlK~~ 161 (259)
++..|+|+.
T Consensus 158 ~~i~T~~~~ 166 (176)
T PTZ00162 158 FAIATINSD 166 (176)
T ss_pred EEEEEecCC
Confidence 455566654
No 99
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.88 E-value=9.4e-05 Score=70.50 Aligned_cols=68 Identities=19% Similarity=0.329 Sum_probs=57.6
Q ss_pred CCCCCcEEEEEEEEEeCc-eEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCC---eEEEEEe
Q 044309 84 YPEVDMAVMIQVKNIADM-GAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKG---YIDLSKR 159 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~-GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~g---kI~LSlK 159 (259)
..++|+++.|+|.++... ++||+| ++.+|+||.+|.. +++.|++||.+.|.|.+|+...+ +|.||+.
T Consensus 135 ~~~~Geiv~g~V~r~~~~~~i~vdl---g~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt 205 (374)
T PRK12328 135 KKKVGKIVFGTVVRVDNEENTFIEI---DEIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRT 205 (374)
T ss_pred HHhcCcEEEEEEEEEecCCCEEEEc---CCeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcC
Confidence 344899999999999864 599999 4899999999876 56889999999999999998654 7888876
Q ss_pred e
Q 044309 160 R 160 (259)
Q Consensus 160 ~ 160 (259)
.
T Consensus 206 ~ 206 (374)
T PRK12328 206 S 206 (374)
T ss_pred C
Confidence 4
No 100
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.82 E-value=0.00014 Score=51.94 Aligned_cols=61 Identities=21% Similarity=0.293 Sum_probs=35.8
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|++.+.+|++++++|+|++.+ .+.+-+||.+|+. ..+++||.+.|-| ..|. ++++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~--~~~~vlLp~~e~~--------~~~~~Gd~v~VFv-Y~D~-~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDG--EGKEVLLPKSEVP--------EPLKVGDEVEVFV-YLDK-EGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEET--T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECC--CCCEEEechHHcC--------CCCCCCCEEEEEE-EECC-CCCEEEecC
Confidence 4899999999999999999986 3699999999986 3488999999985 4566 568887764
No 101
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=97.77 E-value=2e-05 Score=63.31 Aligned_cols=44 Identities=39% Similarity=0.710 Sum_probs=37.3
Q ss_pred HHHHhhchhhHHhhcCHHHHHH-HHhcCcchhhccCCCccccCCC
Q 044309 196 ELYVNIGWPLYWKYGHAFEAFK-IIVTDPDSVLNSLTREVKEIGP 239 (259)
Q Consensus 196 ~~~~~~sw~l~~~~~~~~~~fk-~a~~~~~~~l~~l~~~~~~~~~ 239 (259)
++|.+++|||+++|||+|+||+ .++.+++++|.++++++....+
T Consensus 1 ely~~i~w~l~~~yg~~y~aFe~~~~~~~~~vl~~l~i~~~~~~~ 45 (114)
T PF07541_consen 1 ELYEKIGWPLYKKYGSLYDAFELSAADNGEEVLKKLGIPEEVKEA 45 (114)
T ss_dssp HHHHHTHHHHHHHCSSHHHHHHHHHHHHGGGGGBTTTBSCCHHHH
T ss_pred ChHHHHHHHHHHHhCcHHHHHHHHHcCCCcceeccCCCCHHHHHH
Confidence 4799999999999999999999 6667666899999988665443
No 102
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.66 E-value=6.6e-05 Score=74.57 Aligned_cols=101 Identities=21% Similarity=0.200 Sum_probs=76.9
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.+. .|..+.|+|+++..||+||+|. ..+.||+|-++++.. .-+.+|+.+.|.|..+.+.+|.|++....+.
T Consensus 119 Dve-~g~~Y~g~v~~v~~~GvFv~Ln--~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 119 DVE-AGKYYKGIVSRVEKYGVFVELN--SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hcc-cceeeeccccchhhhcceeecC--hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 444 8999999999999999999998 479999999999852 3478999999999999998899999887765
Q ss_pred hhhHHHHHHhc----------cccc--eEEEEEEecccccCC
Q 044309 163 EEDIQACEERY----------NKSK--LVHSIMRHVAETLGI 192 (259)
Q Consensus 163 ~~~~~~~~~~~----------~~g~--~v~g~V~~i~~~~G~ 192 (259)
...-.+..+++ ..|+ .+.|.|+.+..--|-
T Consensus 190 ~Y~~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GP 231 (715)
T COG1107 190 RYREVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGP 231 (715)
T ss_pred cchhhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCC
Confidence 32111111111 4455 567889888664443
No 103
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=97.65 E-value=0.00029 Score=64.34 Aligned_cols=97 Identities=22% Similarity=0.179 Sum_probs=76.9
Q ss_pred CCcEEEEEEEEEe-CceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecchhh
Q 044309 87 VDMAVMIQVKNIA-DMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSEED 165 (259)
Q Consensus 87 ~G~iv~G~V~~I~-~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~~~ 165 (259)
+|+.=.++|+.+. +.||||+.+ -..+-++|++++...+ .--+++||.+-|. +.+|. ++||.-.++ .+..
T Consensus 73 vg~~g~~~Vv~v~~~lGaFlD~G--l~KDl~vp~~elp~~~----~~wpq~Gd~l~v~-l~~Dk-k~Ri~g~~a--~~~~ 142 (287)
T COG2996 73 VGEYGWLKVVEVNKDLGAFLDWG--LPKDLLVPLDELPTLK----SLWPQKGDKLLVY-LYVDK-KGRIWGTLA--IEKI 142 (287)
T ss_pred ecceeEEEEEEEcCCcceEEecC--CCcceeeehhhccccc----ccCCCCCCEEEEE-EEEcc-CCcEEEEec--chhH
Confidence 8999999999998 999999997 3599999999998310 1127899999999 56887 578877665 3455
Q ss_pred HHHHHHhccc---cceEEEEEEecccccCCch
Q 044309 166 IQACEERYNK---SKLVHSIMRHVAETLGIDL 194 (259)
Q Consensus 166 ~~~~~~~~~~---g~~v~g~V~~i~~~~G~fv 194 (259)
.++....+.. ++.++|+|.++.+ .|.|+
T Consensus 143 l~~l~~~~~~~l~nq~v~~tVYr~~~-~G~fv 173 (287)
T COG2996 143 LENLATPAYNNLKNQEVDATVYRLLE-SGTFV 173 (287)
T ss_pred HHhcCCccchhhhcCeeeeEEEEEec-cceEE
Confidence 5566656655 9999999999966 89987
No 104
>PRK11712 ribonuclease G; Provisional
Probab=97.52 E-value=0.001 Score=65.71 Aligned_cols=126 Identities=20% Similarity=0.225 Sum_probs=79.4
Q ss_pred CCcEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccc------------cccCccccccCCCeEEEEEEEEe----
Q 044309 87 VDMAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRR------------RIRSVSSLIKVGRIEPVMVLRVD---- 148 (259)
Q Consensus 87 ~G~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~------------~v~~~~~~~kvGd~V~vkVi~vD---- 148 (259)
+|.+|.|+|.+|.+ .+|||+|+ .+..||+|++++... ...++.+.+++||.|-|.|.+--
T Consensus 38 vGnIY~G~V~~v~pg~~AAFVdIG--~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~K 115 (489)
T PRK11712 38 VGNIYKGRVSRVLPGMQAAFVDIG--LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK 115 (489)
T ss_pred cccEEEEEEeecCCCCceeEEeeC--CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCC
Confidence 79999999999964 37999998 589999999998320 12234667999999999998742
Q ss_pred ------------------CCCCeEEEEEeecchhhHHH---HHHhccccceEEEEEEecccccCCchHHHHHhhchhhHH
Q 044309 149 ------------------KEKGYIDLSKRRVSEEDIQA---CEERYNKSKLVHSIMRHVAETLGIDLEELYVNIGWPLYW 207 (259)
Q Consensus 149 ------------------~~~gkI~LSlK~~~~~~~~~---~~~~~~~g~~v~g~V~~i~~~~G~fve~~~~~~sw~l~~ 207 (259)
|...++.+|.|=..++.... ....+.... .|.+.+-+- -|+..+++..|+.. |.+
T Consensus 116 G~~lT~~Isl~GrylVl~P~~~~vgiSrKI~de~~R~rLk~i~~~~~~~~--~GvIiRT~A-~~a~~eel~~dl~~-L~~ 191 (489)
T PRK11712 116 GARLTTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQ--GGFIIRTAA-EGVGEEELAQDAAF-LKR 191 (489)
T ss_pred CCeEEEEEEeccceEEEECCCCCeeEecCCCChHHHHHHHHHHHhhCCCC--ceEEEEccC-CCCCHHHHHHHHHH-HHH
Confidence 22334455555333333332 233433333 477777644 57776666555543 444
Q ss_pred hhcCHHHHHHH
Q 044309 208 KYGHAFEAFKI 218 (259)
Q Consensus 208 ~~~~~~~~fk~ 218 (259)
.+....+.++.
T Consensus 192 ~w~~i~~~~~~ 202 (489)
T PRK11712 192 LWTKVMERKKR 202 (489)
T ss_pred HHHHHHHHHhc
Confidence 44444444443
No 105
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.49 E-value=0.00086 Score=65.21 Aligned_cols=70 Identities=10% Similarity=0.081 Sum_probs=57.8
Q ss_pred CCCCcEEEEEEEEEeCceEEEEEcc-CC--CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCC---CeEEEEE
Q 044309 85 PEVDMAVMIQVKNIADMGAYVSLLE-YN--NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEK---GYIDLSK 158 (259)
Q Consensus 85 ~~~G~iv~G~V~~I~~~GafV~L~e-y~--~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~---gkI~LSl 158 (259)
.++|+++.|+|.++...+++|+|.. ++ +++|+||.+|.. +++.|++||.++|.|.+|+... -+|.||+
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 3489999999999999999999941 12 399999999876 5688999999999999998752 3688887
Q ss_pred ee
Q 044309 159 RR 160 (259)
Q Consensus 159 K~ 160 (259)
..
T Consensus 224 t~ 225 (449)
T PRK12329 224 AN 225 (449)
T ss_pred CC
Confidence 64
No 106
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.35 E-value=0.002 Score=67.66 Aligned_cols=59 Identities=14% Similarity=0.201 Sum_probs=47.7
Q ss_pred CCcEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccccc---------cCccccccCCCeEEEEEEEE
Q 044309 87 VDMAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRRRI---------RSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 87 ~G~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~~v---------~~~~~~~kvGd~V~vkVi~v 147 (259)
+|.||.|+|.+|.+ .+|||+|+ .+..||||++++..... .++...+++||.|.|.|.+-
T Consensus 38 vGnIYkGkVenIvPGInAAFVDIG--~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 38 KANIYKGKITRIEPSLEAAFVDYG--AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred ccceEEEEEecccCCcceeEEEec--CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 79999999999953 47899998 58999999999963221 13456799999999999873
No 107
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=97.23 E-value=0.00037 Score=73.60 Aligned_cols=75 Identities=29% Similarity=0.409 Sum_probs=65.3
Q ss_pred CCCCCcEEEEEEEEEeCc-e--EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 84 YPEVDMAVMIQVKNIADM-G--AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~-G--afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
+- +|.+|.++|++|+.. | +=|.++ +|++|+||.+++|.+.+.+|...+++||.|.++|+++|.++=.+.||++.
T Consensus 983 ~~-~g~iV~~~V~~vt~rr~~Cv~v~ld--~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 983 FY-EGAIVPVTVTKVTHRRGICVRVRLD--CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred hc-cCceEEEeeeEEEecccceeEEEec--CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhh
Confidence 44 799999999999743 3 356676 79999999999999999999999999999999999999987788888876
Q ss_pred c
Q 044309 161 V 161 (259)
Q Consensus 161 ~ 161 (259)
.
T Consensus 1060 s 1060 (1299)
T KOG1856|consen 1060 S 1060 (1299)
T ss_pred H
Confidence 4
No 108
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.68 E-value=0.00012 Score=68.59 Aligned_cols=92 Identities=14% Similarity=0.166 Sum_probs=72.7
Q ss_pred cceeEEEeecCCccccchhhhhh----hhcccCccccCCCCchhhhhhhhcCCCCCcEEEEEEEEEe-CceEEEE-----
Q 044309 37 SGCLKTLILVPTPFEFSRENAKA----KKLSEQPIMASHSPNLECRMYEARYPEVDMAVMIQVKNIA-DMGAYVS----- 106 (259)
Q Consensus 37 ~g~~~~~~~~~~~~eid~e~~ri----K~l~~~pw~~~~~~~~~~R~~~~~~~~~G~iv~G~V~~I~-~~GafV~----- 106 (259)
.|..... .++++|++++++ |++.++||.. ..+.|+ .|+++.|+|..+. .+|+|++
T Consensus 66 vGd~v~v----kVl~VD~ekg~IdLS~K~v~~~pw~~----------~~e~~~-~g~~v~~~V~~ia~~~g~~~eely~~ 130 (319)
T PTZ00248 66 VGRHEVV----VVLRVDKEKGYIDLSKKRVSPEDIEA----------CEEKFS-KSKKVHSIMRHIAQKHGMSVEELYTK 130 (319)
T ss_pred CCCEEEE----EEEEEeCCCCEEEEEeeecccchHHH----------HHHhCc-CCCEEEEEEEEchhhcCCCHHHHHHH
Confidence 3544443 446889999994 8999999998 888999 9999999999994 6999998
Q ss_pred -EccCCCEEEEEEccccccccccCcccccc---CCCeEEEEEE
Q 044309 107 -LLEYNNIEGMILFSELSRRRIRSVSSLIK---VGRIEPVMVL 145 (259)
Q Consensus 107 -L~ey~~~eGllhisEls~~~v~~~~~~~k---vGd~V~vkVi 145 (259)
.. +..+++.|++++....+.++.+.|. +|+.+...++
T Consensus 131 i~~--pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~ 171 (319)
T PTZ00248 131 IIW--PLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLL 171 (319)
T ss_pred HHH--HHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHH
Confidence 22 5789999999998887888776766 6666555443
No 109
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=95.98 E-value=0.035 Score=47.81 Aligned_cols=97 Identities=18% Similarity=0.162 Sum_probs=67.2
Q ss_pred hhhcCCCCCcEEEEEEEEEeCceEEEEEcc-----C-CCEEEEEEccccccc--cccCccccccCCCeEEEEEEEEeCCC
Q 044309 80 YEARYPEVDMAVMIQVKNIADMGAYVSLLE-----Y-NNIEGMILFSELSRR--RIRSVSSLIKVGRIEPVMVLRVDKEK 151 (259)
Q Consensus 80 ~~~~~~~~G~iv~G~V~~I~~~GafV~L~e-----y-~~~eGllhisEls~~--~v~~~~~~~kvGd~V~vkVi~vD~~~ 151 (259)
+...+|.+|++|.++|.++..-=|=|+|.- | ....|+||..++..- .--.+-+.|++||.|.++|++... .
T Consensus 61 ~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~ 139 (193)
T KOG3409|consen 61 FNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-G 139 (193)
T ss_pred hhhcCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-C
Confidence 345688899999999999987777777641 1 257899998888641 112356779999999999999554 4
Q ss_pred CeEEEEEeecchhhHHHHHHhccccceEEEEEEecccccCCch
Q 044309 152 GYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAETLGIDL 194 (259)
Q Consensus 152 gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv 194 (259)
....||.-+-. -|.|..-+..+|..|
T Consensus 140 ~~y~LTtAene-----------------LGVV~a~as~~g~~M 165 (193)
T KOG3409|consen 140 SNYLLTTAENE-----------------LGVVFARASETGEPM 165 (193)
T ss_pred CcEEEEEeccc-----------------ceEEEEeccccCCce
Confidence 55666654211 266665554577755
No 110
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=95.19 E-value=0.072 Score=45.40 Aligned_cols=62 Identities=13% Similarity=0.031 Sum_probs=43.7
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccc----cccccC-------ccccccCCCeEEEEEEEEeCCC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELS----RRRIRS-------VSSLIKVGRIEPVMVLRVDKEK 151 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls----~~~v~~-------~~~~~kvGd~V~vkVi~vD~~~ 151 (259)
.|+++.|+|+.+...|+|++.+ .++.++.---+. ....+| -...++.|.+|+++|+...-+.
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~G---Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~ 153 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSG---PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE 153 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEecc---ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence 5999999999999999999995 566665322222 111222 1226889999999999876543
No 111
>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=94.81 E-value=0.21 Score=40.61 Aligned_cols=61 Identities=18% Similarity=-0.025 Sum_probs=44.7
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc---------c---c-cCccccccCCCeEEEEEEEEeC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR---------R---I-RSVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~---------~---v-~~~~~~~kvGd~V~vkVi~vD~ 149 (259)
+|+++.|+|++.+..|+.|.|+= =-+-+||.+.|... + . ..-.-++..|+.|++||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgF--FddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGF--FDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECC--EEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecc--cccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 69999999999999999999962 35788888888731 1 1 3334558999999999998865
No 112
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=94.42 E-value=0.06 Score=53.38 Aligned_cols=59 Identities=19% Similarity=0.244 Sum_probs=49.0
Q ss_pred CCcEEEEEEEEEeCc--eEEEEEccCCCEEEEEEccccccccccC-----ccccccCCCeEEEEEEEEe
Q 044309 87 VDMAVMIQVKNIADM--GAYVSLLEYNNIEGMILFSELSRRRIRS-----VSSLIKVGRIEPVMVLRVD 148 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~--GafV~L~ey~~~eGllhisEls~~~v~~-----~~~~~kvGd~V~vkVi~vD 148 (259)
+|.++.|+|++|.+. .|||+++ .+..||+|++++.+ +.+. +...++.||.+-|.|..-.
T Consensus 37 ~gniy~grv~~i~p~~~aafvdig--~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 37 VGNIYKGRVTRVLPSLEAAFVDIG--LERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred ecCceEEEecccCccchhheeecc--CCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 699999999999764 5899998 58999999999998 3332 3458999999999988753
No 113
>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=92.77 E-value=0.036 Score=40.80 Aligned_cols=31 Identities=13% Similarity=0.208 Sum_probs=25.8
Q ss_pred ccccceEEEEEEecccccCCch------HHH--HHhhchh
Q 044309 173 YNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWP 204 (259)
Q Consensus 173 ~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~ 204 (259)
+++|+++.|+|.++.+ +|+|+ +++ ++++||.
T Consensus 1 ~k~G~~V~g~V~~i~~-~G~fV~l~~~v~G~v~~~~ls~~ 39 (74)
T cd05705 1 IKEGQLLRGYVSSVTK-QGVFFRLSSSIVGRVLFQNVTKY 39 (74)
T ss_pred CCCCCEEEEEEEEEeC-CcEEEEeCCCCEEEEEHHHccCc
Confidence 4789999999999976 99997 334 8999995
No 114
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=92.49 E-value=0.88 Score=34.99 Aligned_cols=65 Identities=18% Similarity=0.132 Sum_probs=49.8
Q ss_pred EEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 90 AVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 90 iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+.|+|+.+-+.+.|. .|+ +|.+-+.|+|-= .+.-.-.+.+||.|.|.+--.|..+|+|..-.+.
T Consensus 8 e~~G~V~e~Lp~~~frV~Le--nG~~vla~isGK----mR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLE--NGVEVGAYASGR----MRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeC--CCCEEEEEeccc----eeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 5899999998888765 776 688888887732 1111122679999999999999999999987763
No 115
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=91.31 E-value=0.1 Score=42.73 Aligned_cols=55 Identities=11% Similarity=0.041 Sum_probs=38.0
Q ss_pred hccccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcCHHHHHHHHhcCcchh-hccCCCcc
Q 044309 172 RYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFKIIVTDPDSV-LNSLTREV 234 (259)
Q Consensus 172 ~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk~a~~~~~~~-l~~l~~~~ 234 (259)
.++.|++++|+|+.|.+ ||+||+ +| +++++....+.+ ...+..|+++ .+-|++++
T Consensus 2 ~~kvG~~l~GkItgI~~-yGAFV~l~~g~tGLVHISEIa~~fVkdI-------~d~L~vG~eV~vKVl~ide 65 (129)
T COG1098 2 SMKVGSKLKGKITGITP-YGAFVELEGGKTGLVHISEIADGFVKDI-------HDHLKVGQEVKVKVLDIDE 65 (129)
T ss_pred CccccceEEEEEEeeEe-cceEEEecCCCcceEEehHhhhhhHHhH-------HHHhcCCCEEEEEEEeecc
Confidence 46899999999999976 999993 34 777777533332 2344566666 55566555
No 116
>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=91.22 E-value=1.2 Score=32.68 Aligned_cols=60 Identities=22% Similarity=0.093 Sum_probs=45.6
Q ss_pred EEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEE
Q 044309 90 AVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYID 155 (259)
Q Consensus 90 iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~ 155 (259)
.+.|+|+..-+.|.|- .|+ +|.+-+.|+|-= .+.-+-.+.+||.|.|.+-..|..+|+|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~--ng~~vla~i~GK----mr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELE--NGHEVLAHISGK----IRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEEC--CCCEEEEEecCc----chhccEEECCCCEEEEEECcccCCcEeEE
Confidence 5889999998888765 776 688888887742 22112237799999999998888888875
No 117
>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=90.41 E-value=4.6 Score=28.44 Aligned_cols=50 Identities=20% Similarity=0.166 Sum_probs=36.1
Q ss_pred EEEEEEEEeC---ceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 91 VMIQVKNIAD---MGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 91 v~G~V~~I~~---~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
.+|+|+...+ || |+.-++ ++-+-|+|.|++.... -..++.|+.|.+.+..
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~-~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDD-GGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETT-SSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCce-EEEEcc-cceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 4799999864 55 555553 4569999999998643 2457899999999887
No 118
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=90.31 E-value=0.27 Score=44.92 Aligned_cols=76 Identities=22% Similarity=0.264 Sum_probs=61.6
Q ss_pred cCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc----cc------cCccccccCCCeEEEEEEEEeCCCC
Q 044309 83 RYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR----RI------RSVSSLIKVGRIEPVMVLRVDKEKG 152 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~----~v------~~~~~~~kvGd~V~vkVi~vD~~~g 152 (259)
..|++||+|.|+|..|...-+=|++. ...++.+.+|.+.-. |- ...+++|+.||.+.+.|-.+-. +|
T Consensus 81 Y~pEvGDvVVgRV~eVq~KRWkvd~n--sk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~-dG 157 (301)
T KOG3013|consen 81 YAPEVGDVVVGRVIEVQQKRWKVDLN--SKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH-DG 157 (301)
T ss_pred cCCccCCEEEEEeeeeecceeEEecc--cccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc-CC
Confidence 35779999999999999999999997 589999999977631 11 1368899999999999988865 68
Q ss_pred eEEEEEeec
Q 044309 153 YIDLSKRRV 161 (259)
Q Consensus 153 kI~LSlK~~ 161 (259)
-+.|-.|..
T Consensus 158 s~sLhTRS~ 166 (301)
T KOG3013|consen 158 SLSLHTRSL 166 (301)
T ss_pred eEEEEecch
Confidence 888876644
No 119
>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=89.58 E-value=0.12 Score=39.32 Aligned_cols=46 Identities=4% Similarity=-0.033 Sum_probs=33.9
Q ss_pred HhccccceEEEEEEecccc-cCCchH------HH--HHhhchhhHHhhcCHHHHH
Q 044309 171 ERYNKSKLVHSIMRHVAET-LGIDLE------EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 171 ~~~~~g~~v~g~V~~i~~~-~G~fve------~~--~~~~sw~l~~~~~~~~~~f 216 (259)
.++..|+++.|+|+.+.+. +|+|++ +| ++++||..+++..++.+.|
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~ 57 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL 57 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC
Confidence 3567999999999999873 399983 34 8999996545565665555
No 120
>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=89.12 E-value=2.3 Score=33.69 Aligned_cols=52 Identities=8% Similarity=0.046 Sum_probs=42.7
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
.|.+|.|+|..+.+.-+||+++ ....+.++..+... +.+..|.+|.+++...
T Consensus 23 ~gk~V~G~I~hvv~ddLYIDfG--~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 23 EGKIVIGKIFHVVDDDLYIDFG--GKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL 74 (104)
T ss_pred cCCEEEEEEEEEecCceEEEeC--CceeEEEecccccc-------cccccCCEEEEEECCH
Confidence 7999999999999889999997 67999998665542 4577899999887543
No 121
>PRK15463 cold shock-like protein CspF; Provisional
Probab=89.05 E-value=1.9 Score=31.60 Aligned_cols=51 Identities=14% Similarity=0.120 Sum_probs=38.8
Q ss_pred EEEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 91 VMIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 91 v~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
++|+|+...+ .|. |+.-+. ++-+.|+|+|.+..... ..+++||.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~-g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSD-GRKDVQVHISALNLRDA----EELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCC-CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence 4799998853 565 777764 56899999999975322 347899999998654
No 122
>PRK15464 cold shock-like protein CspH; Provisional
Probab=88.55 E-value=1.9 Score=31.63 Aligned_cols=51 Identities=14% Similarity=0.150 Sum_probs=38.9
Q ss_pred EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
++|+|+... +.|. |+.-++ ++-+.|+|+|.+.... ...+.+||.|.+.|..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~-g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSD-GRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCC-CCccEEEEehhehhcC----CCCCCCCCEEEEEEEE
Confidence 479999885 4566 787764 5689999999996432 2348899999998765
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=87.64 E-value=2 Score=31.53 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=38.5
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEE--------EEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDL--------SKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~L--------SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
.++||.|.++|++++.+.=.+++ ...++......+..+.++.|+.+.++|.++.+
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence 37899999999999764222322 22333333455566779999999999999855
No 124
>PRK10943 cold shock-like protein CspC; Provisional
Probab=87.24 E-value=3 Score=30.36 Aligned_cols=52 Identities=13% Similarity=0.208 Sum_probs=38.6
Q ss_pred EEEEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 90 AVMIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 90 iv~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
.++|+|+...+ .|. |+.-++ ++-+-|+|+|.+..... ..+.+||.|.+.+..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPAD-GSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCC-CCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 46799998853 555 777654 56899999999975322 447899999998765
No 125
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=86.65 E-value=3.4 Score=30.02 Aligned_cols=53 Identities=11% Similarity=0.160 Sum_probs=38.6
Q ss_pred EEEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 90 AVMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 90 iv~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
.++|+|+... +.|. |+.-++ ++-+-|+|+|.+..... ..+.+||.|.+.+..-
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPED-GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCC-CCeeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence 4679999885 3455 677764 56899999999974321 4478999999987653
No 126
>PRK09890 cold shock protein CspG; Provisional
Probab=85.81 E-value=4.2 Score=29.62 Aligned_cols=51 Identities=10% Similarity=0.164 Sum_probs=37.6
Q ss_pred EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
++|+|+... ..|. |+.-++ ++-+-|+|+|.+..... ..+++||.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDD-GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCC-CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 479999875 3454 777764 56899999999975422 347899999997654
No 127
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=85.53 E-value=3.8 Score=30.35 Aligned_cols=63 Identities=16% Similarity=0.053 Sum_probs=43.2
Q ss_pred EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
+|+|+-.. +.|. ||..++ ++.+.|+|+|.+...- ...+..||.|.+.+..- .+|+-...+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~-gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~~--~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQG--PKGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCC-CCccEEEEEeeccccC----CCCCCCCCEEEEEEEEC--CCCceeeEEEEC
Confidence 48888875 3565 777664 5799999999997432 24578999999997653 246544444443
No 128
>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=84.81 E-value=0.47 Score=34.42 Aligned_cols=41 Identities=15% Similarity=0.284 Sum_probs=30.2
Q ss_pred cccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcCHHHHHH
Q 044309 174 NKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAFK 217 (259)
Q Consensus 174 ~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~fk 217 (259)
+.|+++.|+|.++.+.+|+|++ ++ .++++|. ...++.+.|+
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~---~~~~~~~~~~ 50 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS---YTENPLEGFK 50 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc---ccCCHHHhCC
Confidence 5789999999998755899873 33 8888885 4556666663
No 129
>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=84.53 E-value=3.7 Score=29.17 Aligned_cols=53 Identities=23% Similarity=0.352 Sum_probs=35.4
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEE----------eecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSK----------RRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSl----------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+++|+.+.++|.++... .+.+.+ .++..+...+..+.|+.|+.+.++|..+..
T Consensus 1 ~~~G~iv~g~V~~v~~~--gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 1 LKVGDILPGRVTKVNDR--YVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CCCCCEEEEEEEEEeCC--eEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 36899999999999652 333333 222222223345679999999999999853
No 130
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=83.97 E-value=0.37 Score=47.49 Aligned_cols=76 Identities=22% Similarity=0.252 Sum_probs=58.4
Q ss_pred hhhhhhhhcCCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccc------------cCccccccCCCeEEE
Q 044309 75 LECRMYEARYPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRI------------RSVSSLIKVGRIEPV 142 (259)
Q Consensus 75 ~~~R~~~~~~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v------------~~~~~~~kvGd~V~v 142 (259)
+.||++.++-- ....+.+.|..|..-|.-|.|.+ +|..+|||-.-+-..+- -+-...+++||.+.|
T Consensus 550 LY~r~L~~k~~-~~~~F~AEI~Di~R~G~RvrLle-NGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V 627 (645)
T COG4776 550 LYARFLADKAG-TNTRFAAEIQDISRGGMRVRLLE-NGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDV 627 (645)
T ss_pred HHHHHhccccc-cCchhhhhhhhhccCceEEEecc-CCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEE
Confidence 46888877655 67789999999999999999998 89999999876654321 122455788888888
Q ss_pred EEEEEeCCCC
Q 044309 143 MVLRVDKEKG 152 (259)
Q Consensus 143 kVi~vD~~~g 152 (259)
++.+|..+++
T Consensus 628 ~l~eVr~etR 637 (645)
T COG4776 628 TLAEVRMETR 637 (645)
T ss_pred EeHHHHHhhh
Confidence 8888776544
No 131
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=82.81 E-value=5.9 Score=34.13 Aligned_cols=57 Identities=16% Similarity=0.296 Sum_probs=38.3
Q ss_pred cccccCCCeEEEEEEEEeCCCCeEEEEE------------------eecchhhHHHHHHhccccceEEEEEEecc
Q 044309 131 SSLIKVGRIEPVMVLRVDKEKGYIDLSK------------------RRVSEEDIQACEERYNKSKLVHSIMRHVA 187 (259)
Q Consensus 131 ~~~~kvGd~V~vkVi~vD~~~gkI~LSl------------------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~ 187 (259)
...+++||.|.++|.++....=.+++-- .++......+..+.|++|+.+..+|..+.
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 4557899999999999976433344421 11112222334577999999999999985
No 132
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=82.51 E-value=0.37 Score=47.69 Aligned_cols=75 Identities=17% Similarity=0.236 Sum_probs=52.4
Q ss_pred EEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEE-Eeecchh-----hHHHHHHhcc--ccceEEEEEE
Q 044309 113 IEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLS-KRRVSEE-----DIQACEERYN--KSKLVHSIMR 184 (259)
Q Consensus 113 ~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LS-lK~~~~~-----~~~~~~~~~~--~g~~v~g~V~ 184 (259)
-.+.|++++... ....+.+||.+.+.|...+. ||+.++ .|+.... .++...+.|+ .|+++.|+|.
T Consensus 71 ~~~eI~L~eAk~-----~~~~~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ 143 (470)
T PRK09202 71 PTKEISLEEARK-----IDPDAEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVK 143 (470)
T ss_pred CcceeeHHHHhh-----hCccccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEE
Confidence 456777776642 22347899999999988774 444433 3343333 3446778898 9999999999
Q ss_pred ecccccCCchH
Q 044309 185 HVAETLGIDLE 195 (259)
Q Consensus 185 ~i~~~~G~fve 195 (259)
++.+ +|++++
T Consensus 144 ri~~-~giiVD 153 (470)
T PRK09202 144 RVER-GNIIVD 153 (470)
T ss_pred EEec-CCEEEE
Confidence 9964 899875
No 133
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=82.04 E-value=6.5 Score=28.56 Aligned_cols=51 Identities=14% Similarity=0.173 Sum_probs=37.3
Q ss_pred EEEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 91 VMIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 91 v~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
..|+|+... +.|. |+.-++ ++-+-|+|+|.+.... ...+++||.|.+.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCC-CCccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence 379998874 3454 677654 5689999999997432 2457899999998665
No 134
>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=81.71 E-value=11 Score=26.40 Aligned_cols=51 Identities=14% Similarity=0.070 Sum_probs=37.1
Q ss_pred EEEEEEEeC-ceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 92 MIQVKNIAD-MGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 92 ~G~V~~I~~-~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
.|+|+...+ .|. |+..++ ++-+-|+|.+++...- ...+++|+.|.+.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~-~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDD-GGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCC-CCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 588888754 343 666653 4799999999998531 24578999999987654
No 135
>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=81.41 E-value=5.5 Score=28.77 Aligned_cols=50 Identities=14% Similarity=0.109 Sum_probs=36.9
Q ss_pred EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
+|+|+-.. +.|. |+.-++ ++-+.|+|+|.+.... ...++.||.|.+.+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEG-VDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCC-CCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEE
Confidence 58888874 4565 777764 5789999999997432 2457899999998654
No 136
>PRK14998 cold shock-like protein CspD; Provisional
Probab=81.20 E-value=6.9 Score=28.86 Aligned_cols=61 Identities=15% Similarity=0.041 Sum_probs=41.9
Q ss_pred EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
+|+|+-.. +.|. |+.-++ ++-+.|+|+|.+.... ...+..|+.|.+.+..-+ +|.-...+.
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~-g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~ 65 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGP--KGNHASVIV 65 (73)
T ss_pred CeEEEEEeCCCceEEEecCC-CCccEEEEeeeecccC----CCCCCCCCEEEEEEEECC--CCceeEEEE
Confidence 48888775 3565 777764 5789999999997432 245789999999976533 455444333
No 137
>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=81.18 E-value=2.6 Score=30.60 Aligned_cols=50 Identities=18% Similarity=0.272 Sum_probs=33.5
Q ss_pred CCeEEEEEEEEeCCCCeEEEEEe----------ecchhh--HHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSKR----------RVSEED--IQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~--~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.|.++|.++... -+.+++- ++..+. ..+..+.|+.|+.++++|..+..
T Consensus 1 G~~V~g~V~~i~~~--g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 1 GQEVTGFVNNVSKE--FVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDK 62 (73)
T ss_pred CCEEEEEEEEEeCC--EEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeC
Confidence 78899999998753 3333331 122111 33466889999999999999854
No 138
>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=80.89 E-value=0.45 Score=34.45 Aligned_cols=39 Identities=13% Similarity=0.107 Sum_probs=28.5
Q ss_pred cccceEEEEEEecccccCCchH-------HH--HHhhchhhHHhhcCHHHHH
Q 044309 174 NKSKLVHSIMRHVAETLGIDLE-------EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 174 ~~g~~v~g~V~~i~~~~G~fve-------~~--~~~~sw~l~~~~~~~~~~f 216 (259)
..|+++.|+|..+.+ ||+|++ ++ .++++|. ++.++.+.|
T Consensus 2 ~~g~~~~g~V~~i~~-fG~fv~l~~~~~eGlvh~sel~~~---~~~~~~~~~ 49 (73)
T cd05686 2 ALYQIFKGEVASVTE-YGAFVKIPGCRKQGLVHKSHMSSC---RVDDPSEVV 49 (73)
T ss_pred cCCCEEEEEEEEEEe-eeEEEEECCCCeEEEEEchhhCCC---cccCHhhEE
Confidence 478999999999976 999873 23 6788884 555555554
No 139
>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=80.63 E-value=1.4 Score=45.83 Aligned_cols=81 Identities=7% Similarity=0.088 Sum_probs=50.2
Q ss_pred EEEeCCCCeEEEEEeecchh--h---HHHHHH--hccccceEEEEEEecccccCCch------HHH--HHhhc---hhhH
Q 044309 145 LRVDKEKGYIDLSKRRVSEE--D---IQACEE--RYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIG---WPLY 206 (259)
Q Consensus 145 i~vD~~~gkI~LSlK~~~~~--~---~~~~~~--~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~s---w~l~ 206 (259)
+.++. +|++.++-.....- . .+.... ..+.|+++.|+|+++.+ ||+|+ ++| .+++| |.
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~d-fGaFVel~~G~eGLvHISeisdls~~-- 686 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTA-FGAFVSLLPGKDGLLHISQIRKLAGG-- 686 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEEC-ceEEEEecCCceEEEEhhhccccccc--
Confidence 45554 68888766543221 1 111223 36899999999999987 99998 344 67665 64
Q ss_pred HhhcCHHHHHHHHhcCcchh-hccCCCc
Q 044309 207 WKYGHAFEAFKIIVTDPDSV-LNSLTRE 233 (259)
Q Consensus 207 ~~~~~~~~~fk~a~~~~~~~-l~~l~~~ 233 (259)
++..++.+.| ..|+++ .+-++++
T Consensus 687 ~rv~~~~dv~----kvGd~V~VKVl~ID 710 (719)
T TIGR02696 687 KRVENVEDVL----SVGQKIQVEIADID 710 (719)
T ss_pred cCcCCHHHcC----CCCCEEEEEEEEEC
Confidence 5667776666 445544 4444444
No 140
>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=80.55 E-value=7.4 Score=28.03 Aligned_cols=65 Identities=15% Similarity=0.203 Sum_probs=40.0
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
|+..+-.|-.+++.|--+--. +.+.|+- +.-.|...-...+-+|+++++.|+.||.-+.++-+|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~--g~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSG--GQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEec--CCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 556666777765555333232 3456651 1122333334557899999999999998777776664
No 141
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=80.42 E-value=7.6 Score=34.72 Aligned_cols=63 Identities=13% Similarity=0.064 Sum_probs=46.2
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeC
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~ 149 (259)
.|.+||.|.|.|++-..-+.-|+|. +.-.|.|+.-.+... .+.=+-.+++||.|-++|...++
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDig--g~~~a~L~~laFe~A-tkrNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIG--GSEPASLSYLAFEGA-TKRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecC--CCCeeeeeeccccCc-cccCCCccccccEEEEEEEecCC
Confidence 5668999999999998888999996 346677665444321 11113448999999999998764
No 142
>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=78.09 E-value=4.5 Score=28.50 Aligned_cols=51 Identities=20% Similarity=0.247 Sum_probs=32.6
Q ss_pred CCeEEEEEEEEeCCCCeEEEEEe----------ecchhhHHHHHHhccccceEEEEEEecccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSKR----------RVSEEDIQACEERYNKSKLVHSIMRHVAET 189 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~ 189 (259)
|+.+.++|.+++.. .+.+.+- ++.........+.|+.|+.+..+|..+.++
T Consensus 1 G~iv~g~V~~i~~~--~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~ 61 (70)
T cd05687 1 GDIVKGTVVSVDDD--EVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDE 61 (70)
T ss_pred CCEEEEEEEEEeCC--EEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECC
Confidence 78889999999763 3333331 111111122345689999999999998643
No 143
>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=76.85 E-value=6.2 Score=28.01 Aligned_cols=50 Identities=12% Similarity=0.140 Sum_probs=32.4
Q ss_pred CCeEEEEEEEEeCCCCeEEEEE----------eecchh--hHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSK----------RRVSEE--DIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSl----------K~~~~~--~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.|.++|.+++.. .+.+.+ .++..+ ......+.|+.|+.+.++|..+..
T Consensus 1 G~iV~g~V~~i~~~--gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 1 GDLVKAKVKSVKPT--QLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CCEEEEEEEEEECC--cEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence 78889999998763 233333 222111 122345779999999999998843
No 144
>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=76.35 E-value=8.3 Score=28.35 Aligned_cols=55 Identities=18% Similarity=0.175 Sum_probs=36.3
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEE--------EEeecch----hhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDL--------SKRRVSE----EDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~L--------SlK~~~~----~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+++||.|.++|.++....-.+.+ ...++.. +...+..+.++.|+.+.++|..+.+
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 47999999999999764222322 1122221 1223455678999999999999854
No 145
>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=76.34 E-value=0.77 Score=32.26 Aligned_cols=28 Identities=21% Similarity=0.557 Sum_probs=22.0
Q ss_pred cceEEEEEEecccccCCchH------HH--HHhhchh
Q 044309 176 SKLVHSIMRHVAETLGIDLE------EL--YVNIGWP 204 (259)
Q Consensus 176 g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~ 204 (259)
|+++.|+|.++.+ +|+|++ ++ .++++|.
T Consensus 1 G~~~~g~V~~i~~-~G~fv~l~~~~~Glv~~~~l~~~ 36 (69)
T cd05690 1 GTVVSGKIKSITD-FGIFVGLDGGIDGLVHISDISWT 36 (69)
T ss_pred CCEEEEEEEEEEe-eeEEEEeCCCCEEEEEHHHCCCc
Confidence 6789999999976 999973 33 7777774
No 146
>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=76.00 E-value=7.3 Score=27.32 Aligned_cols=52 Identities=21% Similarity=0.333 Sum_probs=33.6
Q ss_pred CCeEEEEEEEEeCCCCeEEE--------EEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDL--------SKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~L--------SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.+.++|.++....-.+.| ...++..+......+.|+.|+.+..+|..+..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 67888888888753222222 22233333344456778999999999999854
No 147
>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=74.58 E-value=7.4 Score=27.37 Aligned_cols=50 Identities=10% Similarity=0.147 Sum_probs=34.0
Q ss_pred CCeEEEEEEEEeCCCCeEEEEEe----------ecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSKR----------RVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.+.++|.++... -+.+.+. .+..+++....+.|+.|+.+..+|..+..
T Consensus 1 G~~v~g~V~~v~~~--Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 1 GQVVKGTIRKLRPS--GIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred CCEEEEEEEEEecc--EEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 78888999888753 2333331 22334455566789999999999999854
No 148
>COG1278 CspC Cold shock proteins [Transcription]
Probab=74.53 E-value=7.2 Score=28.58 Aligned_cols=50 Identities=14% Similarity=0.175 Sum_probs=34.3
Q ss_pred EEEEEEEe-CceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 92 MIQVKNIA-DMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 92 ~G~V~~I~-~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
.|+|+=.. ..|. |+.=++ ++.+.|+|+|.+..... ..+..||+|.+.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~-G~~DvFVH~Sai~~~g~----~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPED-GGKDVFVHISAIQRAGF----RTLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCC-CCcCEEEEeeeeccCCC----cccCCCCEEEEEEec
Confidence 46666553 3344 665553 45899999999975433 347899999988764
No 149
>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=72.35 E-value=8.8 Score=29.09 Aligned_cols=50 Identities=20% Similarity=0.193 Sum_probs=27.6
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEEEeecch------------------------------hhHHHHHHhccccceEEEEEE
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLSKRRVSE------------------------------EDIQACEERYNKSKLVHSIMR 184 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LSlK~~~~------------------------------~~~~~~~~~~~~g~~v~g~V~ 184 (259)
++|+.|.++|+++.+ .+..+.+-.+.. .+.-+..+.|.+|+++.++|.
T Consensus 3 ~vGdiV~~rVtrv~~--~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 3 KVGDIVIARVTRVNP--RQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp -TT-EEEEEEEEE-S--SEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCEEEEEEEEEec--cEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 689999999999976 445544444411 112234577888888888876
Q ss_pred ec
Q 044309 185 HV 186 (259)
Q Consensus 185 ~i 186 (259)
++
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 53
No 150
>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=71.66 E-value=2.1 Score=30.39 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=19.4
Q ss_pred ccccceEEEEEEecccccCCchH
Q 044309 173 YNKSKLVHSIMRHVAETLGIDLE 195 (259)
Q Consensus 173 ~~~g~~v~g~V~~i~~~~G~fve 195 (259)
|+.|+.+.|+|..+.+ +|+|++
T Consensus 1 ~~~g~~~~g~V~~i~~-~G~fv~ 22 (72)
T cd05689 1 YPEGTRLFGKVTNLTD-YGCFVE 22 (72)
T ss_pred CcCCCEEEEEEEEEEe-eEEEEE
Confidence 6789999999999976 999984
No 151
>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=71.35 E-value=17 Score=25.07 Aligned_cols=48 Identities=15% Similarity=0.088 Sum_probs=30.5
Q ss_pred cEEEEEEEEEeCce----EEEEEccCCC-EEEEEEccccccccccCccccccCCCeEEEEE
Q 044309 89 MAVMIQVKNIADMG----AYVSLLEYNN-IEGMILFSELSRRRIRSVSSLIKVGRIEPVMV 144 (259)
Q Consensus 89 ~iv~G~V~~I~~~G----afV~L~ey~~-~eGllhisEls~~~v~~~~~~~kvGd~V~vkV 144 (259)
-.+.|+|..+.+-| +.+++.. +. +.+.++..... +-.+++||.|.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~-~~~l~a~it~~~~~-------~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGG-GETLTARITPESAE-------ELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETT-SEEEEEEEEHHHHH-------HCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECC-CCEEEEEEcHHHHH-------HcCCCCCCEEEEEE
Confidence 47899999999999 5555552 22 55666544432 12378999999875
No 152
>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=71.20 E-value=10 Score=28.90 Aligned_cols=53 Identities=17% Similarity=0.235 Sum_probs=35.6
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEEe------------ec------chh--hHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSKR------------RV------SEE--DIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSlK------------~~------~~~--~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
.++||.|.++|.++... +..+.+- .. ... +..+..+.|..|+.+.++|.++.+
T Consensus 4 P~~GDiVig~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~ 76 (92)
T cd05791 4 PKVGSIVIARVTRINPR--FAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD 76 (92)
T ss_pred CCCCCEEEEEEEEEcCC--EEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC
Confidence 37899999999999653 3433331 11 111 122466889999999999998854
No 153
>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=70.24 E-value=16 Score=26.76 Aligned_cols=55 Identities=18% Similarity=0.233 Sum_probs=36.8
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEE--------EEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDL--------SKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~L--------SlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+++|+.+.++|.++....-.+.| -..++..+......+.|+.|+.+..+|.++..
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 78999999999999763212222 11222223333456779999999999999854
No 154
>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=69.40 E-value=40 Score=26.01 Aligned_cols=54 Identities=17% Similarity=0.278 Sum_probs=33.2
Q ss_pred EEEEEEEEEeCce--EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEE
Q 044309 90 AVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVM 143 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vk 143 (259)
.+.|.|.++...| +|++|.+-. .+..++..++............++.|+.|.|.
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 4789999998666 899998511 25556654443222222222337899988764
No 155
>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=69.28 E-value=4.8 Score=28.56 Aligned_cols=54 Identities=20% Similarity=0.190 Sum_probs=37.5
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEEe----------ecchhhHHHHHHhccccceEEEEEEecccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSKR----------RVSEEDIQACEERYNKSKLVHSIMRHVAET 189 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~~~~~~~~~~~g~~v~g~V~~i~~~ 189 (259)
+++|+.+.++|.++++. -+.+.+- ++..+........|..|+.+...|..+...
T Consensus 2 ~~~G~iv~g~V~~v~~~--g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~ 65 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDF--GVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKE 65 (74)
T ss_dssp SSTTSEEEEEEEEEETT--EEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETT
T ss_pred CCCCCEEEEEEEEEECC--EEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECC
Confidence 57899999999999873 3333333 122121233567899999999999998654
No 156
>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=68.91 E-value=14 Score=25.77 Aligned_cols=50 Identities=14% Similarity=0.313 Sum_probs=33.4
Q ss_pred CCeEEEEEEEEeCCCCeEEEEE----------eecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSK----------RRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSl----------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.+.++|.++... | +.+.+ .++..+...+..+.|+.|+.+..+|.++..
T Consensus 1 G~~v~g~V~~v~~~-G-v~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 1 GDVVRGFVKNIANN-G-VFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred CCEEEEEEEEEECc-c-EEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence 67888888888753 2 33333 222223344456779999999999999855
No 157
>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=68.12 E-value=12 Score=26.35 Aligned_cols=54 Identities=19% Similarity=0.282 Sum_probs=34.1
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEE---E------eecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLS---K------RRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LS---l------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
++|+.+.++|.++.+..-.+.|. . .++..+......+.|+.|+.+..+|..+..
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeC
Confidence 46899999999997632233332 1 111112222234678999999999999854
No 158
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=68.03 E-value=53 Score=25.24 Aligned_cols=70 Identities=20% Similarity=0.255 Sum_probs=47.6
Q ss_pred CcEEEEEEEEEeC--ce-EEEEEccCCC--EEEEEEccccccccccCcc-ccccCCCeEEEEE-EEEeCCCCeEEEEEee
Q 044309 88 DMAVMIQVKNIAD--MG-AYVSLLEYNN--IEGMILFSELSRRRIRSVS-SLIKVGRIEPVMV-LRVDKEKGYIDLSKRR 160 (259)
Q Consensus 88 G~iv~G~V~~I~~--~G-afV~L~ey~~--~eGllhisEls~~~v~~~~-~~~kvGd~V~vkV-i~vD~~~gkI~LSlK~ 160 (259)
.-.|.|.|.+++. .| +|.+|-+ +. +.+.+--+.. ..+. ..++.|++|.|.. +++.+..|++.|...+
T Consensus 23 ~vwV~GEIs~~~~~~~gh~YftLkD-~~a~i~~~~~~~~~-----~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~ 96 (99)
T PF13742_consen 23 NVWVEGEISNLKRHSSGHVYFTLKD-EEASISCVIFRSRA-----RRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVED 96 (99)
T ss_pred CEEEEEEEeecEECCCceEEEEEEc-CCcEEEEEEEHHHH-----hhCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEE
Confidence 5679999999965 44 6999975 32 3344333332 2334 5689999998764 3566778999998887
Q ss_pred cch
Q 044309 161 VSE 163 (259)
Q Consensus 161 ~~~ 163 (259)
+.|
T Consensus 97 i~P 99 (99)
T PF13742_consen 97 IDP 99 (99)
T ss_pred eEC
Confidence 653
No 159
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=66.40 E-value=42 Score=26.34 Aligned_cols=67 Identities=16% Similarity=0.164 Sum_probs=47.9
Q ss_pred CCCCCcEEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
.| ....+.|+|+.....|.|- .+. +|..-++|++- +.+. +-.++.||.|.|.....|..+++|..-+
T Consensus 17 ~p-~e~e~~g~V~~~lG~~~~~V~~~--dG~~~la~i~G----K~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~ 84 (100)
T PRK04012 17 MP-EEGEVFGVVEQMLGANRVRVRCM--DGVERMGRIPG----KMKK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred CC-CCCEEEEEEEEEcCCCEEEEEeC--CCCEEEEEEch----hhcc-cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 45 3446899999998888765 665 68888887664 2222 3448899999999888887667766544
No 160
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=66.12 E-value=10 Score=25.69 Aligned_cols=52 Identities=17% Similarity=0.112 Sum_probs=33.1
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEEEe----------ecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLSKR----------RVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LSlK----------~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
++|+.+.++|.++... -+.+.+- ++...........|+.|+.+.+.|..+..
T Consensus 1 ~~G~~v~g~V~~v~~~--g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 1 EVGDVVEGTVTEITPF--GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CCCCEEEEEEEEEEcc--EEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 3699999999999863 2333222 11111111233569999999999999854
No 161
>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=65.33 E-value=16 Score=25.78 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=33.6
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEE----------EeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLS----------KRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LS----------lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+.|+.+.++|.++....-.+.|. ..++..+......+.|+.|+.+..+|..+..
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence 57999999999987532223331 1111222223345568999999999998854
No 162
>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=64.83 E-value=23 Score=27.45 Aligned_cols=53 Identities=15% Similarity=0.187 Sum_probs=35.3
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEEe----------ecchh--hH-----------------HHHHHhccccceEEEEEE
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSKR----------RVSEE--DI-----------------QACEERYNKSKLVHSIMR 184 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSlK----------~~~~~--~~-----------------~~~~~~~~~g~~v~g~V~ 184 (259)
+++|+.|.++|.++... -+.+++- ++..+ .| ....+.|++|+.+.++|.
T Consensus 1 L~~G~vV~G~V~~v~~~--gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi 78 (100)
T cd05693 1 LSEGMLVLGQVKEITKL--DLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVV 78 (100)
T ss_pred CCCCCEEEEEEEEEcCC--CEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEE
Confidence 47899999999999764 2333331 11111 11 014577999999999999
Q ss_pred eccc
Q 044309 185 HVAE 188 (259)
Q Consensus 185 ~i~~ 188 (259)
.+.+
T Consensus 79 ~~d~ 82 (100)
T cd05693 79 SLDK 82 (100)
T ss_pred EccC
Confidence 9965
No 163
>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=63.62 E-value=6.5 Score=40.76 Aligned_cols=67 Identities=12% Similarity=0.215 Sum_probs=44.8
Q ss_pred EEEeCCCCeEEEEEeecch-h----hHHHHHHhccccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcC
Q 044309 145 LRVDKEKGYIDLSKRRVSE-E----DIQACEERYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGH 211 (259)
Q Consensus 145 i~vD~~~gkI~LSlK~~~~-~----~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~ 211 (259)
+.|+. +|.+.++-..... + -........+.|+++.|+|+.+.+ ||+|++ ++ .++++|. ++.+
T Consensus 584 I~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~-~GafVei~~g~~GllHiSei~~~---~v~~ 658 (684)
T TIGR03591 584 IDIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD-FGAFVEILPGKDGLVHISEIANE---RVEK 658 (684)
T ss_pred EEEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeC-CEEEEEECCCcEEEEEHHHcCCC---cccC
Confidence 44554 6888877654322 1 111234556899999999999976 999983 34 8888884 5556
Q ss_pred HHHHH
Q 044309 212 AFEAF 216 (259)
Q Consensus 212 ~~~~f 216 (259)
..+.|
T Consensus 659 ~~~~~ 663 (684)
T TIGR03591 659 VEDVL 663 (684)
T ss_pred hhhcc
Confidence 66655
No 164
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=61.79 E-value=65 Score=24.09 Aligned_cols=66 Identities=23% Similarity=0.158 Sum_probs=47.3
Q ss_pred CcEEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 88 DMAVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 88 G~iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
.-.+.|+|..+-..|- .|.++ +|..-+-|++-=-.. -+--+.+||.|.|..-..|.++++|..-.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~e--dg~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELE--NGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEec--CCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 4468999999977664 57776 678888777642211 112377999999999999887888876444
No 165
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=61.43 E-value=55 Score=24.71 Aligned_cols=64 Identities=19% Similarity=0.128 Sum_probs=44.0
Q ss_pred CcEEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 88 DMAVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
...+.|+|+.....+.|- .+. +|..-+++++- +.+. +--++.||.|.|.....+..+|.|..-+
T Consensus 4 e~q~~g~V~~~lG~~~~~V~~~--dG~~~la~ipg----K~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r~ 68 (83)
T smart00652 4 DGQEIAQVVKMLGNGRLEVMCA--DGKERLARIPG----KMRK-KVWIRRGDIVLVDPWDFQDVKADIIYKY 68 (83)
T ss_pred CCcEEEEEEEEcCCCEEEEEEC--CCCEEEEEEch----hhcc-cEEEcCCCEEEEEecCCCCCEEEEEEEe
Confidence 345889999998877765 555 67888877654 2222 3348899999998877766566665433
No 166
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=59.82 E-value=22 Score=31.89 Aligned_cols=90 Identities=13% Similarity=0.074 Sum_probs=57.6
Q ss_pred cCCCCCcEEEEEEEEEe--CceEEEEEccC--CCEEEEEEccccccccccC----cccccc--CCCeEEEEEEEEeCCCC
Q 044309 83 RYPEVDMAVMIQVKNIA--DMGAYVSLLEY--NNIEGMILFSELSRRRIRS----VSSLIK--VGRIEPVMVLRVDKEKG 152 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~--~~GafV~L~ey--~~~eGllhisEls~~~v~~----~~~~~k--vGd~V~vkVi~vD~~~g 152 (259)
++. .|+++.|+..+.. .||+||+++-- ...++|+|.-+|....... +...|. .--.++|-|..+|...+
T Consensus 72 ~~~-~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~ 150 (247)
T COG4044 72 KVE-EGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQ 150 (247)
T ss_pred cCC-CCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhh
Confidence 455 8999999999985 67788888521 1478999999887644333 333333 34556777888887666
Q ss_pred eEEEEEeecchhhHHHHHHhccccc
Q 044309 153 YIDLSKRRVSEEDIQACEERYNKSK 177 (259)
Q Consensus 153 kI~LSlK~~~~~~~~~~~~~~~~g~ 177 (259)
.|..-+ .+.|.+....|..+.
T Consensus 151 EIea~l----td~qvd~l~gwt~d~ 171 (247)
T COG4044 151 EIEARL----TDKQVDKLKGWTSDS 171 (247)
T ss_pred hhhhhh----hHHHHHHHHhhhcCC
Confidence 554432 244555555555544
No 167
>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=59.62 E-value=20 Score=25.32 Aligned_cols=49 Identities=16% Similarity=0.201 Sum_probs=32.1
Q ss_pred CCeEEEEEEEEeCCCCeEEEEEee----cch-----hhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSKRR----VSE-----EDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSlK~----~~~-----~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.|.++|.++.. .| +.+.+-. ..+ +++.. .+.|+.|+.+..+|..+..
T Consensus 1 G~~V~g~V~~i~~-~G-~~v~l~~~v~g~v~~~~l~~~~~~-~~~~~~G~~i~~kVi~id~ 58 (66)
T cd05695 1 GMLVNARVKKVLS-NG-LILDFLSSFTGTVDFLHLDPEKSS-KSTYKEGQKVRARILYVDP 58 (66)
T ss_pred CCEEEEEEEEEeC-Cc-EEEEEcCCceEEEEHHHcCCccCc-ccCcCCCCEEEEEEEEEeC
Confidence 7889999999975 33 3333311 111 11222 5679999999999998854
No 168
>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=59.51 E-value=40 Score=25.05 Aligned_cols=61 Identities=16% Similarity=0.142 Sum_probs=43.1
Q ss_pred EEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 91 VMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 91 v~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
+.|+|+.....+.|- .++ +|..-+.|++- +.+. +--++.||.|.|.....|..+|+|.--+
T Consensus 2 ~~g~V~~~~g~~~~~V~~~--~g~~~la~i~g----K~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCF--DGKKRLCRIRG----KMRK-RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred EEEEEEEEcCCCEEEEEEC--CCCEEEEEEch----hhcc-cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 578999998877764 665 67787877654 2222 3448899999999887777666665433
No 169
>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=59.48 E-value=2.2 Score=40.50 Aligned_cols=64 Identities=13% Similarity=0.296 Sum_probs=43.3
Q ss_pred cCccccccCCCeEEEEEEEEeCCCCeEE-EEEeec-----chhhHHHHHHhcc--ccceEEEEEEecccccC-Cch
Q 044309 128 RSVSSLIKVGRIEPVMVLRVDKEKGYID-LSKRRV-----SEEDIQACEERYN--KSKLVHSIMRHVAETLG-IDL 194 (259)
Q Consensus 128 ~~~~~~~kvGd~V~vkVi~vD~~~gkI~-LSlK~~-----~~~~~~~~~~~~~--~g~~v~g~V~~i~~~~G-~fv 194 (259)
+.....+++||.+.+.+..-+. |++. -+.|++ ....++...+.|+ .|++++|+|.++.+ .| +++
T Consensus 78 ~~~d~~~~vGD~I~~~I~~~~f--gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~-~g~v~V 150 (341)
T TIGR01953 78 REIDPDVQIGDEVKKEIPPENF--GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNR-RGNLYV 150 (341)
T ss_pred HhhccccccCCEEEEEecccCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEec-CCcEEE
Confidence 3445668999999988854433 3433 334442 2456677788885 99999999999965 56 354
No 170
>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=56.33 E-value=40 Score=23.40 Aligned_cols=50 Identities=18% Similarity=0.140 Sum_probs=31.9
Q ss_pred CCeEEEEEEEEeCCCCeEEEEE----------eecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLSK----------RRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LSl----------K~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.+.++|.++.+. -+.+.+ .++..+......+.|+.|+.+..+|..+..
T Consensus 1 g~~~~g~V~~v~~~--G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 1 GLKTHGTIVKVKPN--GCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred CCEEEEEEEEEecC--cEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 78888999988753 233332 122222122344669999999999999855
No 171
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=54.82 E-value=1.1e+02 Score=26.77 Aligned_cols=58 Identities=17% Similarity=0.248 Sum_probs=39.0
Q ss_pred cccccCCCeEEEEEEEEeCCC------------------CeEEEEEeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 131 SSLIKVGRIEPVMVLRVDKEK------------------GYIDLSKRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 131 ~~~~kvGd~V~vkVi~vD~~~------------------gkI~LSlK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
....+.|+.|-++|++++... +...+.+-++.....+...+.|..|+++.+.|.+..+
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~~ 134 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTGD 134 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecCC
Confidence 356788888888888775421 2223333333444456677899999999999999753
No 172
>PRK08059 general stress protein 13; Validated
Probab=54.65 E-value=26 Score=28.06 Aligned_cols=55 Identities=13% Similarity=0.157 Sum_probs=35.7
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEE--------EeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLS--------KRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LS--------lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+++|+.+.++|.++.+..-.+.+. ..++..+........|+.|+.+..+|.++..
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~ 67 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDE 67 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEEC
Confidence 679999999999998732233332 1111112222234678999999999999843
No 173
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=53.71 E-value=18 Score=37.45 Aligned_cols=58 Identities=10% Similarity=0.271 Sum_probs=42.5
Q ss_pred EEEeCCCCeEEEEEeecch-----hhHHHHHHhccccceEEEEEEecccccCCch------HHH--HHhhchh
Q 044309 145 LRVDKEKGYIDLSKRRVSE-----EDIQACEERYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWP 204 (259)
Q Consensus 145 i~vD~~~gkI~LSlK~~~~-----~~~~~~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~ 204 (259)
+.++ ++|.+.++-..-.. .-.......+.+|+++.|+|+.+.+ ||+|+ +++ .++++|.
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~-fGaFv~l~~gkdgl~hiS~~~~~ 655 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVD-FGAFVELLPGKDGLVHISQLAKE 655 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEee-cceEEEecCCcceeEEehhhhhh
Confidence 3455 57888887765332 1233456888999999999999987 99998 344 7888885
No 174
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=53.04 E-value=1.2e+02 Score=30.18 Aligned_cols=71 Identities=14% Similarity=0.200 Sum_probs=42.8
Q ss_pred EEEEEEEEEeCce--EEEEEccC-CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 90 AVMIQVKNIADMG--AYVSLLEY-NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey-~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
.+.|.|.++...| +|++|.+- +.+..++..+++.........+ +..|+.|.|.=.=....+|.+.|....+
T Consensus 58 ~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v~G~v~~t~~ge~el~~~~~ 131 (491)
T PRK00484 58 SVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKK-LDLGDIIGVEGTLFKTKTGELSVKATEL 131 (491)
T ss_pred EEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhc-CCCCCEEEEEEEEEEcCCCcEEEEEeEE
Confidence 5889999998877 89999752 2367777655443221222223 7899998764222222356665554443
No 175
>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=52.37 E-value=30 Score=25.13 Aligned_cols=56 Identities=11% Similarity=0.150 Sum_probs=35.6
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEEeecch-hhHHHHH--HhccccceEEEEEEecccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSKRRVSE-EDIQACE--ERYNKSKLVHSIMRHVAET 189 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~-~~~~~~~--~~~~~g~~v~g~V~~i~~~ 189 (259)
++.|+.+.+.|.++....--+++....+.. =|..+.. +.+++|+.+..+|.++.+.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~ 60 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDD 60 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEECC
Confidence 578999999999997532235553222211 1111111 6689999999999988553
No 176
>PRK05807 hypothetical protein; Provisional
Probab=52.26 E-value=8.4 Score=31.67 Aligned_cols=32 Identities=9% Similarity=0.215 Sum_probs=25.4
Q ss_pred hccccceEEEEEEecccccCCchH-----HH--HHhhchh
Q 044309 172 RYNKSKLVHSIMRHVAETLGIDLE-----EL--YVNIGWP 204 (259)
Q Consensus 172 ~~~~g~~v~g~V~~i~~~~G~fve-----~~--~~~~sw~ 204 (259)
.+++|++++|+|+.+.+ +|+|++ ++ .++++|.
T Consensus 2 ~~~vG~vv~G~Vt~i~~-~GafV~L~~~~Glvhiseis~~ 40 (136)
T PRK05807 2 TLKAGSILEGTVVNITN-FGAFVEVEGKTGLVHISEVADT 40 (136)
T ss_pred CccCCCEEEEEEEEEEC-CeEEEEECCEEEEEEhhhcccc
Confidence 47789999999999976 999983 33 7777764
No 177
>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=51.95 E-value=23 Score=24.65 Aligned_cols=50 Identities=12% Similarity=0.079 Sum_probs=29.9
Q ss_pred cEEEEEEEEEeCceEEEEEcc-CC-C--EEEEEEccccccccccCccccccCCCeEEEEEE
Q 044309 89 MAVMIQVKNIADMGAYVSLLE-YN-N--IEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145 (259)
Q Consensus 89 ~iv~G~V~~I~~~GafV~L~e-y~-~--~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi 145 (259)
-.+.|+|.++...|.++++.= .+ + +.+.++.+.+. +-.+++|+.+.+.+.
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~-------~l~l~~G~~v~~~ik 60 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA-------ELGLKPGKEVYAVIK 60 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh-------hCCCCCCCEEEEEEE
Confidence 368899999987776655430 01 1 33333332221 233789999998864
No 178
>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=51.87 E-value=29 Score=25.14 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=34.0
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEEE--eecchhhHHHHHHhccccceEEEEEEecc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLSK--RRVSEEDIQACEERYNKSKLVHSIMRHVA 187 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LSl--K~~~~~~~~~~~~~~~~g~~v~g~V~~i~ 187 (259)
++.|+.+.++|.++.+-.-.+.+.- ..+ -+..+..+.|+.|+.+..++.++.
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l~~~~~Gl--v~~se~~~~~~iGd~v~v~I~~i~ 67 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGL--IHRSNLLRDYEVGDEVIVQVTDIP 67 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEECCCcEEE--EEchhccCcCCCCCEEEEEEEEEC
Confidence 6799999999999875322233321 011 012234567999999999999883
No 179
>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=51.44 E-value=28 Score=24.51 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=33.7
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEEEeecc-hhhHHHH--HHhccccceEEEEEEeccc
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLSKRRVS-EEDIQAC--EERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LSlK~~~-~~~~~~~--~~~~~~g~~v~g~V~~i~~ 188 (259)
+.|+.|.++|.+++.. + +.+.+-... -=|..+. .+.|+.|+.++..|..+.+
T Consensus 2 ~~g~iV~G~V~~~~~~-~-~~vdig~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 2 REGEIVTGIVKRVDRG-N-VIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CCCCEEEEEEEEEcCC-C-EEEEcCCeEEEeeHHHCCCCCcCCCCCEEEEEEEEEec
Confidence 4799999999999863 2 333332210 0122222 2468999999999999854
No 180
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=50.69 E-value=1e+02 Score=25.33 Aligned_cols=62 Identities=13% Similarity=0.110 Sum_probs=42.1
Q ss_pred cCCCCCcEEEEEEEEEeCce---------EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309 83 RYPEVDMAVMIQVKNIADMG---------AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 83 ~~~~~G~iv~G~V~~I~~~G---------afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
.++..|.+.+=+|..+.+.| |.|+|++ +-.++.|+..- + -+.+++|.+|++++.......+.
T Consensus 59 els~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~--~~~i~~~i~~~------~-p~~v~iGm~V~~v~~~~~~~~~~ 129 (140)
T COG1545 59 ELSGEGKVETYTVVYVKPPGFSLEEPYVIAIVELEE--GGRILGQLVDV------D-PDDVEIGMKVEAVFRKREEDGGR 129 (140)
T ss_pred EeCCCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCC--CCceEEEEEec------C-cccccCCCEEEEEEEEccccCCc
Confidence 35568999999999887766 5666653 33566565551 1 13578999999999877654433
No 181
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=50.55 E-value=3.2 Score=39.77 Aligned_cols=63 Identities=10% Similarity=0.157 Sum_probs=41.5
Q ss_pred cccccCCCeEEEEEEEEeCCCCeEEEEEeecc-----hhhHHHHHHhc--cccceEEEEEEecccccCCchH
Q 044309 131 SSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS-----EEDIQACEERY--NKSKLVHSIMRHVAETLGIDLE 195 (259)
Q Consensus 131 ~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~-----~~~~~~~~~~~--~~g~~v~g~V~~i~~~~G~fve 195 (259)
.....+||.+...+...+..+. ...+.|+.. .-..+...+.| +.|++++|+|.++.+ .|++++
T Consensus 84 ~~~~~vGD~i~~~I~~~~fgR~-aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~-~~~~Vd 153 (362)
T PRK12327 84 NPAYELGDVIEIEVTPKDFGRI-AAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDN-RFVYVN 153 (362)
T ss_pred CccccCCCEEEEecCcCCCChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeC-CcEEEE
Confidence 4558899999988765544221 111222221 23445567888 899999999999865 788774
No 182
>PF06196 DUF997: Protein of unknown function (DUF997); InterPro: IPR010398 This is a family of predicted bacterial membrane protein with unknown function.
Probab=48.71 E-value=10 Score=28.64 Aligned_cols=16 Identities=38% Similarity=0.899 Sum_probs=13.2
Q ss_pred CCcccccchhhHHHHH
Q 044309 1 YNYLCTLPLSIIYTYL 16 (259)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (259)
|.|.+|+|+|.++.-+
T Consensus 36 y~~i~GlPlWF~~SCi 51 (80)
T PF06196_consen 36 YKYIFGLPLWFFYSCI 51 (80)
T ss_pred cccccCCcHHHHHHHH
Confidence 6799999999877654
No 183
>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=48.68 E-value=31 Score=25.23 Aligned_cols=59 Identities=17% Similarity=-0.023 Sum_probs=36.9
Q ss_pred EEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCC
Q 044309 91 VMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKE 150 (259)
Q Consensus 91 v~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~ 150 (259)
..++|--+...=|.|.|.+ .+--..+|.+.=-+.-.+.-.+.+++|+.+.|.+...+..
T Consensus 4 htA~VQh~~kdfAvvSL~~-t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~~ 62 (69)
T cd05701 4 HTAIVQHADKDFAIVSLAT-TGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCL 62 (69)
T ss_pred cchhhhhhhhceEEEEeec-cccEEEEEchhhccccccccceeeeccceEEEEEecCccC
Confidence 4555666654457778865 3444555554333333444457799999999998876553
No 184
>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=48.48 E-value=41 Score=22.80 Aligned_cols=51 Identities=14% Similarity=0.048 Sum_probs=30.7
Q ss_pred CCCeEEEEEEEEeCCCCeEEEEEe---------ecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 136 VGRIEPVMVLRVDKEKGYIDLSKR---------RVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 136 vGd~V~vkVi~vD~~~gkI~LSlK---------~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+|+.+.++|.+++.. | +.+.+- ++.........+.|+.|+.+...|..+..
T Consensus 1 ~g~~~~g~V~~v~~~-g-~~v~l~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 1 EGDVVEGTVKSITDF-G-AFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred CCCEEEEEEEEEEee-e-EEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEEC
Confidence 478888888888753 2 222221 11111111233568999999999998843
No 185
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=46.45 E-value=90 Score=26.55 Aligned_cols=67 Identities=16% Similarity=0.185 Sum_probs=45.4
Q ss_pred CCCCCcEEEEEEEEEeCceEE-EEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAY-VSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSK 158 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~Gaf-V~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSl 158 (259)
+|+.|+ +.|+|+.....|.| |.+. +|..-++|++-=-.+ .--+.+||.|.|..-..+..+++|..-+
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~--dG~~rLa~I~GKmRK-----~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCF--DGVKRLCHIRGKMRK-----RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEEC--CCCEEEEEeecccee-----eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 554665 67999999877765 4565 688888887642222 2337899999998766666566665533
No 186
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=46.18 E-value=33 Score=23.94 Aligned_cols=32 Identities=25% Similarity=0.326 Sum_probs=25.8
Q ss_pred ccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309 130 VSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE 163 (259)
Q Consensus 130 ~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~ 163 (259)
+++.+.+|+.+.++|++++ .+++.|.+.+...
T Consensus 8 ~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~~ 39 (54)
T PF02599_consen 8 VGESIVIGDDIEITVLEIS--GGQVKLGIDAPKE 39 (54)
T ss_dssp TT-EEEETTTEEEEEEEEE--TTEEEEEEEECTT
T ss_pred CCCEEEECCCEEEEEEEEc--CCEEEEEEECCCC
Confidence 4567789999999999998 5889999887654
No 187
>PRK08582 hypothetical protein; Provisional
Probab=45.57 E-value=55 Score=26.96 Aligned_cols=55 Identities=15% Similarity=0.222 Sum_probs=35.9
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEE--------EeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLS--------KRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LS--------lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
+++|+.+.++|.+|..-.-.+.|. +.++..+......+.|+.|+.+..+|..+..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~ 65 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED 65 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC
Confidence 678999999999987632122221 1222222233334679999999999999964
No 188
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=45.21 E-value=8.7 Score=39.88 Aligned_cols=62 Identities=10% Similarity=0.165 Sum_probs=40.6
Q ss_pred CCeEEEEEeecchh-----hHHHHHHhccccceEEEEEEecccccCCchH------HH--HHhhchhhHHhhcCHHHHH
Q 044309 151 KGYIDLSKRRVSEE-----DIQACEERYNKSKLVHSIMRHVAETLGIDLE------EL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 151 ~gkI~LSlK~~~~~-----~~~~~~~~~~~g~~v~g~V~~i~~~~G~fve------~~--~~~~sw~l~~~~~~~~~~f 216 (259)
+|.+.++-.....- -........++|+++.|+|+++.+ ||+|++ ++ +++++|. ++.++.+.|
T Consensus 592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~-fGafVei~~~~~GllhiSels~~---~v~~~~~v~ 666 (693)
T PRK11824 592 DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVD-FGAFVEILPGKDGLVHISEIADE---RVEKVEDVL 666 (693)
T ss_pred CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEEC-CeEEEEECCCCEEEEEeeeccCc---cccCcccee
Confidence 57777766543321 111223557899999999999976 999984 34 7888884 455554444
No 189
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=43.36 E-value=70 Score=26.97 Aligned_cols=52 Identities=10% Similarity=0.124 Sum_probs=41.8
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
.|.+|.|+|-.+...-+|++++ ....+.+..-++. .+.++.|-.|..+++..
T Consensus 82 ~gklV~GkIfhiV~~DlYIDFG--~KFhcVC~rP~~n-------~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 82 KGKLVIGKIFHIVEEDLYIDFG--GKFHCVCKRPALN-------GEAYQKGARVRLRLIDL 133 (173)
T ss_pred CCcEEEeeeeeeeccceEEecC--CeEEEEEcCcCcC-------HHHhhcCceEEEEEcCh
Confidence 6999999999999999999997 5788888766655 24567888888887644
No 190
>CHL00010 infA translation initiation factor 1
Probab=43.34 E-value=1.3e+02 Score=22.17 Aligned_cols=65 Identities=26% Similarity=0.110 Sum_probs=38.8
Q ss_pred EEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 91 VMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 91 v~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
+.|.|+++...|. +|.+. +|..-.++++- ..+.-.-.+.+||.|.+.+-..+..+|.|..-.+..
T Consensus 9 ~~G~Vik~lg~~~y~V~~~--~g~~~~c~~rG----klr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLD--NGCQVLGYISG----KIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEcCCCEEEEEeC--CCCEEEEEecc----ceecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 6799998875554 44554 35444444332 222112236789999998766666667777655543
No 191
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=42.19 E-value=10 Score=40.48 Aligned_cols=42 Identities=14% Similarity=0.133 Sum_probs=32.5
Q ss_pred HhccccceEE-EEEEecccccCCch------HHH--HHhhchhhHHhhcCHHHHH
Q 044309 171 ERYNKSKLVH-SIMRHVAETLGIDL------EEL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 171 ~~~~~g~~v~-g~V~~i~~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~f 216 (259)
...+.|+++. |+|+++.+ ||+|| ++| +++++|. ++.+..+.|
T Consensus 749 ~~~~vG~iy~~g~V~~I~~-FGaFVeL~~g~EGLVHISeLs~~---rv~~~~dv~ 799 (891)
T PLN00207 749 MVPTVGDIYRNCEIKSIAP-YGAFVEIAPGREGLCHISELSSN---WLAKPEDAF 799 (891)
T ss_pred cCcCCCcEEECcEEEEEec-cEEEEEeCCCCEEEEEhhhcCCc---cccCHHHhc
Confidence 3457999995 69999977 99998 345 8999994 566676655
No 192
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=40.60 E-value=54 Score=30.02 Aligned_cols=58 Identities=12% Similarity=0.031 Sum_probs=38.3
Q ss_pred ccccCCCeEEEEEEEEeCCCCeEEEEEee------------cchhhHHHHHHhccccceEEEEEEecccccC
Q 044309 132 SLIKVGRIEPVMVLRVDKEKGYIDLSKRR------------VSEEDIQACEERYNKSKLVHSIMRHVAETLG 191 (259)
Q Consensus 132 ~~~kvGd~V~vkVi~vD~~~gkI~LSlK~------------~~~~~~~~~~~~~~~g~~v~g~V~~i~~~~G 191 (259)
+..++|+.+.++|.++... -+.+++-. +..+......+.++.|+.+..+|.++...-|
T Consensus 4 ~~P~~GdiV~G~V~~I~~~--G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~ 73 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDF--GAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG 73 (262)
T ss_pred CCCCCCCEEEEEEEEEECC--EEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccC
Confidence 5568999999999999763 23333321 1112222345678999999999999965333
No 193
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=40.54 E-value=1.4e+02 Score=21.58 Aligned_cols=61 Identities=23% Similarity=0.103 Sum_probs=35.9
Q ss_pred EEEEEEEEEeCceE-EEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309 90 AVMIQVKNIADMGA-YVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL 156 (259)
Q Consensus 90 iv~G~V~~I~~~Ga-fV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L 156 (259)
.+.|.|++....|. +|.+. +|..-.++++- ..+.-.....+||.|.+.+-..+..+|.|..
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~--~g~~~~c~~~G----klr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELE--NGHEVLAHISG----KMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeC--CCCEEEEEEcc----ceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 46799998876544 44453 45444444332 1111122267999999987666665666654
No 194
>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=40.40 E-value=1.5e+02 Score=22.00 Aligned_cols=62 Identities=15% Similarity=0.094 Sum_probs=41.9
Q ss_pred EEEEEEEEeCceEE-EEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE-eCCCCeEEEEEe
Q 044309 91 VMIQVKNIADMGAY-VSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV-DKEKGYIDLSKR 159 (259)
Q Consensus 91 v~G~V~~I~~~Gaf-V~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v-D~~~gkI~LSlK 159 (259)
..|+|+.....+.| |++. +|..-++|++-=-. ++ --++.||.|.|..... |..++.|..-+.
T Consensus 2 ~i~~V~~~lG~~~~~V~~~--dg~~~l~~i~gK~R---k~--iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~ 65 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECA--DGQRRLVSIPGKLR---KN--IWIKRGDFLIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred eEEEEEEECCCCEEEEEEC--CCCEEEEEEchhhc---cC--EEEcCCCEEEEEecccCCCceEEEEEEeC
Confidence 46889998877765 4665 67888887664221 11 3378999999988777 565666655433
No 195
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=40.29 E-value=1.2e+02 Score=27.04 Aligned_cols=55 Identities=15% Similarity=0.099 Sum_probs=36.7
Q ss_pred ccCCCeEEEEEEEEeCCCCeEEEE--Eee------cchh----hHHHHHHhccccceEEEEEEeccc
Q 044309 134 IKVGRIEPVMVLRVDKEKGYIDLS--KRR------VSEE----DIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 134 ~kvGd~V~vkVi~vD~~~gkI~LS--lK~------~~~~----~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
.++||.|.++|.++....-.+++. ... +... +..+..+.|+.|+.+.++|.++.+
T Consensus 61 P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~ 127 (235)
T PRK04163 61 PKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR 127 (235)
T ss_pred CCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence 489999999999998754344432 111 1111 114455678999999999998854
No 196
>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=40.16 E-value=80 Score=21.16 Aligned_cols=52 Identities=12% Similarity=0.199 Sum_probs=29.2
Q ss_pred CCeEEEEEEEEeCCCCeEEEE--------EeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 137 GRIEPVMVLRVDKEKGYIDLS--------KRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 137 Gd~V~vkVi~vD~~~gkI~LS--------lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
|+.+.++|.++.+..-.+.+. ...+..+.+....+.|+.|+.+..+|..+..
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEEC
Confidence 566677777765422122221 1112222222334568999999999998854
No 197
>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=40.00 E-value=67 Score=22.79 Aligned_cols=58 Identities=26% Similarity=0.229 Sum_probs=35.0
Q ss_pred EEEEEEEEEeCceEE-EEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeE
Q 044309 90 AVMIQVKNIADMGAY-VSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYI 154 (259)
Q Consensus 90 iv~G~V~~I~~~Gaf-V~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI 154 (259)
.+.|+|+.....+.| |.+. +|.+-+++++-=..++ -.++.||.|.|.+-..|..+|+|
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 EVIGRVTEMLGNNLFEVECE--DGEERLARIPGKFRKR-----IWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp EEEEEEEEEESSSEEEEEET--TSEEEEEEE-HHHHTC-----C---TTEEEEEEESTTCTTEEEE
T ss_pred EEEEEEEEECCCCEEEEEeC--CCCEEEEEeccceeee-----EecCCCCEEEEEecccCCCeEEE
Confidence 578899998877765 5565 6777777765422111 23789999988875445444544
No 198
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=39.86 E-value=84 Score=27.62 Aligned_cols=61 Identities=16% Similarity=0.006 Sum_probs=44.2
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccc-----------cc---c---CccccccCCCeEEEEEEEEeC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRR-----------RI---R---SVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~-----------~v---~---~~~~~~kvGd~V~vkVi~vD~ 149 (259)
+|+++.|+|.+....|+-|.|.= =-+-+||.+-|... |. + ...-++.+|..|++||.+...
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~F--FdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f 158 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGF--FDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESF 158 (202)
T ss_pred cceEEEEEeecCCccceEEEEEe--eeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecc
Confidence 79999999999999999999962 23566666655531 11 1 123358999999999987643
No 199
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=39.38 E-value=1.1e+02 Score=20.11 Aligned_cols=66 Identities=17% Similarity=0.228 Sum_probs=36.3
Q ss_pred EEEEEEEEeCc-----eEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 91 VMIQVKNIADM-----GAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 91 v~G~V~~I~~~-----GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
+.|.|.++... -+++.|.++. .|-+.+.=... ........++.|+.+.+. -.++..+++..|.+.+
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~--~~~i~~~~~~~-~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~~ 72 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGT--GGTIRVTLFGE-LAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVES 72 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCC--CCEEEEEEEch-HHHHHHhhccCCCEEEEE-EEEEecCCeEEEEeee
Confidence 46777777533 3677776422 13333322221 111224568899988887 6666555666666543
No 200
>PRK01712 carbon storage regulator; Provisional
Probab=39.21 E-value=60 Score=23.57 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=26.6
Q ss_pred CccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309 129 SVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE 163 (259)
Q Consensus 129 ~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~ 163 (259)
.+++.+.+|+.+.++|+.+. .+++.|.+.+...
T Consensus 7 k~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~~ 39 (64)
T PRK01712 7 KVGESLMIGDDIEVTVLGVK--GNQVRIGINAPKE 39 (64)
T ss_pred cCCCEEEeCCCEEEEEEEEe--CCEEEEEEECCCC
Confidence 34577889999999999997 4789998887644
No 201
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=38.59 E-value=1.5e+02 Score=21.47 Aligned_cols=66 Identities=17% Similarity=0.209 Sum_probs=37.7
Q ss_pred EEEEEEEEEe-Cce-EEEEEccCCCEEEEEEcccccccc-ccCccccccCCCeEEEEEEEEeCCCCeEEEEEeec
Q 044309 90 AVMIQVKNIA-DMG-AYVSLLEYNNIEGMILFSELSRRR-IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRV 161 (259)
Q Consensus 90 iv~G~V~~I~-~~G-afV~L~ey~~~eGllhisEls~~~-v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~ 161 (259)
.++|.|.+.. ..| +|+.|.+ .+ +-|+. ..|+. ..+....++.||.|.+. =+++..+|++.|...++
T Consensus 2 ~v~GeVs~~~~~~GHvyfsLkD-~~--a~i~c--v~f~~~~~~~~~~l~~Gd~V~v~-G~v~~~~G~~ql~v~~i 70 (73)
T cd04487 2 HIEGEVVQIKQTSGPTIFTLRD-ET--GTVWA--AAFEEAGVRAYPEVEVGDIVRVT-GEVEPRDGQLQIEVESL 70 (73)
T ss_pred EEEEEEeccccCCCCEEEEEEc-CC--EEEEE--EEEchhccCCcCCCCCCCEEEEE-EEEecCCeEEEEEEeeE
Confidence 4678887653 445 8999963 22 22221 22221 12244558999998864 23444577787766554
No 202
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=38.58 E-value=60 Score=30.04 Aligned_cols=49 Identities=14% Similarity=0.028 Sum_probs=38.5
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
-+.+|++-.|.|.+....|.+|+++ ...++.+++ -+.+|..|.+++.+.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG----~~~~~~l~~-----------~~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIG----KDKLAKLSS-----------PAPPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEec----CCcceeccC-----------CCCCCceEEEEEEec
Confidence 3558999999999999999999994 344433332 167999999999987
No 203
>COG5009 MrcA Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]
Probab=38.49 E-value=1.1e+02 Score=32.38 Aligned_cols=58 Identities=19% Similarity=0.223 Sum_probs=44.2
Q ss_pred CCCCCcEEEEEEEEEeCceEEEEEccCCCEEEEEEcccccccc-----ccCccccccCCCeEEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRR-----IRSVSSLIKVGRIEPVM 143 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~-----v~~~~~~~kvGd~V~vk 143 (259)
+...|+..-+.|.++.+.|+.+-+. ++...=++...|.|-+ -+++.+.++.||.|.|+
T Consensus 342 l~~~~~~~~AvV~~~~~~~a~i~~~--~~~~~~~~~~~m~wa~~~~~~~~~~~~~l~~G~~i~V~ 404 (797)
T COG5009 342 LSDVGELLPAVVLSVAKSGAKIGLA--DGSKVTLSMEAMRWARRLLSDNKSPEDVLKPGDVIYVR 404 (797)
T ss_pred hcccccceEEEEEEeccCCCeEEee--ccccccccHHhhhhhhhhcccccccccccCCCCEEEEE
Confidence 3347999999999999999988887 3555545666677732 23578899999999988
No 204
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=37.93 E-value=59 Score=28.45 Aligned_cols=43 Identities=30% Similarity=0.359 Sum_probs=34.2
Q ss_pred EEEEEEccccccccccCccccccCCCeEEEEEEEEeCC-CCeEEEEEeec
Q 044309 113 IEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKE-KGYIDLSKRRV 161 (259)
Q Consensus 113 ~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~-~gkI~LSlK~~ 161 (259)
++|++|..+.. +.+.+++|+++.+.+.++... +|++.+|+...
T Consensus 2 ~~~~l~~~~~~------~~e~~~~g~ri~~~~~~v~~~~~g~~~~srt~~ 45 (190)
T COG0195 2 VEAILPKREQI------PGENFKVGDRIRALLYEVQKEAKGQIELSRTIP 45 (190)
T ss_pred ceeEcchhhcC------CCcccccCcEEEEEEeeeeecCcccEEEEeccH
Confidence 57888888876 568899999999999999863 45677776654
No 205
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=37.84 E-value=32 Score=36.24 Aligned_cols=44 Identities=11% Similarity=0.117 Sum_probs=32.1
Q ss_pred HHHhccccceEEEEEEecccccCCch------HHH--HHhhchhhHHhhcCHHHHH
Q 044309 169 CEERYNKSKLVHSIMRHVAETLGIDL------EEL--YVNIGWPLYWKYGHAFEAF 216 (259)
Q Consensus 169 ~~~~~~~g~~v~g~V~~i~~~~G~fv------e~~--~~~~sw~l~~~~~~~~~~f 216 (259)
..+..+.|.+++|+|+++.+ ||+|| +++ .+.+|. +-+.++.+..
T Consensus 652 ~i~dLk~Gm~leg~Vrnv~~-fgafVdIgv~qDglvHis~ls~---~fv~~P~~vv 703 (780)
T COG2183 652 SITDLKPGMILEGTVRNVVD-FGAFVDIGVHQDGLVHISQLSD---KFVKDPNEVV 703 (780)
T ss_pred hHhhccCCCEEEEEEEEeee-ccceEEeccccceeeeHHHhhh---hhcCChHHhc
Confidence 34688999999999999987 99998 344 666666 3444454444
No 206
>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=36.98 E-value=1.9e+02 Score=28.94 Aligned_cols=71 Identities=14% Similarity=0.200 Sum_probs=42.2
Q ss_pred EEEEEEEEEeCce--EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 90 AVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+.|.|.++...| +|++|.+-. .+..++..++++..........+..||.|.|.=.=.....|.+.|....
T Consensus 57 ~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~ 130 (496)
T TIGR00499 57 SIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTE 130 (496)
T ss_pred EEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeE
Confidence 4789999998776 899998522 3777776655442211111234789998876422122335655554443
No 207
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=36.85 E-value=1.5e+02 Score=20.83 Aligned_cols=67 Identities=18% Similarity=0.154 Sum_probs=38.6
Q ss_pred EEEEEEEEEe--Cce-EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEE-eCCCCeEEEEEeec
Q 044309 90 AVMIQVKNIA--DMG-AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV-DKEKGYIDLSKRRV 161 (259)
Q Consensus 90 iv~G~V~~I~--~~G-afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v-D~~~gkI~LSlK~~ 161 (259)
.+.|.|+++. ..| +|+.|.+.. .+++.+--+.+ ......++.|+.|.+...-- +..++++.|...++
T Consensus 3 ~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~-----~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i 74 (78)
T cd04489 3 WVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNA-----RRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEI 74 (78)
T ss_pred EEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchh-----hhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEE
Confidence 3566666663 456 789997522 24555543322 23456789999987664322 33246677766654
No 208
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=36.42 E-value=1.4e+02 Score=20.42 Aligned_cols=67 Identities=19% Similarity=0.211 Sum_probs=36.9
Q ss_pred EEEEEEEEE-e--CceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe-EEEEEeec
Q 044309 90 AVMIQVKNI-A--DMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY-IDLSKRRV 161 (259)
Q Consensus 90 iv~G~V~~I-~--~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk-I~LSlK~~ 161 (259)
.+.|.|+++ . ..-+|+.|.+.. |.+.+.=.. .......+.+++|+.|.+. =.+...++. +.|.....
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~t---g~i~~~~~~-~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l~~~~i 72 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGT---GSIQVVFFN-EEYERFREKLKEGDIVRVR-GKVKRYNGGELELIVPKI 72 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETT---EEEEEEEET-HHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEEEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECC---ccEEEEEcc-HHhhHHhhcCCCCeEEEEE-EEEEEECCccEEEEECEE
Confidence 367888888 3 333688887421 333322222 1222345668899999876 444444454 77765543
No 209
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=33.79 E-value=3.1e+02 Score=30.34 Aligned_cols=95 Identities=15% Similarity=0.183 Sum_probs=50.7
Q ss_pred hcccCccccCCCCchhhhhhhhcCCCCCc--EEEEEEEEEeCce--EEEEEccCC-CEEEEEEccccccccccCcccccc
Q 044309 61 KLSEQPIMASHSPNLECRMYEARYPEVDM--AVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIK 135 (259)
Q Consensus 61 ~l~~~pw~~~~~~~~~~R~~~~~~~~~G~--iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~v~~~~~~~k 135 (259)
....+|+...-.....|.-+.+.. .|+ .+.|.|.++.+.| +|++|.+-. .++.++..+++...........+.
T Consensus 626 ~~g~~pyp~~~~~~~~~~~~~~~~--~~~~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~ 703 (1094)
T PRK02983 626 AAGVDPYPVGVPPTHTVAEALDAP--TGEEVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVD 703 (1094)
T ss_pred HcCCCCCCCCCcCccCHHHHHHhc--CCCEEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCC
Confidence 334467653212222233333332 455 5789999998887 899998521 366666655543221222223477
Q ss_pred CCCeEEEEEEEEeCCCCeEEEE
Q 044309 136 VGRIEPVMVLRVDKEKGYIDLS 157 (259)
Q Consensus 136 vGd~V~vkVi~vD~~~gkI~LS 157 (259)
.||.|.|.=.=....+|.+.+.
T Consensus 704 ~gd~V~v~G~v~~t~~ge~ei~ 725 (1094)
T PRK02983 704 LGDLVEVTGTMGTSRNGTLSLL 725 (1094)
T ss_pred CCCEEEEEEEEEEcCCCCEEEE
Confidence 8998876422122234555443
No 210
>PRK07252 hypothetical protein; Provisional
Probab=33.67 E-value=1e+02 Score=24.70 Aligned_cols=54 Identities=11% Similarity=0.095 Sum_probs=33.9
Q ss_pred cCCCeEEEEEEEEeCCCCeEEEE--------EeecchhhHHHHHHhccccceEEEEEEeccc
Q 044309 135 KVGRIEPVMVLRVDKEKGYIDLS--------KRRVSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 135 kvGd~V~vkVi~vD~~~gkI~LS--------lK~~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
++|+.+.++|.++....-.+.+. ..++..+......+.|..|+.+..+|.++..
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence 57999999999997632122221 1111122222334668999999999999854
No 211
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=33.27 E-value=1.4e+02 Score=21.42 Aligned_cols=50 Identities=20% Similarity=0.086 Sum_probs=34.2
Q ss_pred cEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEe
Q 044309 89 MAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVD 148 (259)
Q Consensus 89 ~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD 148 (259)
+.++|+|++|.+...-+.|+. |..=-+| .+.. -+.+++|.+|.+..-.++
T Consensus 3 ~~veG~I~~id~~~~titLdD--Gksy~lp-~ef~-------~~~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDD--GKSYKLP-EEFD-------FDGLKPGMKVVVFYDEVD 52 (61)
T ss_pred ccceEEEEEEcCCceEEEecC--CCEEECC-Cccc-------ccccCCCCEEEEEEEccC
Confidence 358999999999999999984 4322222 2322 245889999887765544
No 212
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=32.98 E-value=1.6e+02 Score=29.56 Aligned_cols=72 Identities=17% Similarity=0.234 Sum_probs=51.2
Q ss_pred cEEEEEEEEEeCce--EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 89 MAVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 89 ~iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
=.+-|+|..+..+| +|..|.+-+ .++-++...++.........+.+..||.|.|+-.=....+|.+++....
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~ 138 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEE 138 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEE
Confidence 34788999998888 899987422 4888888887666555556677889999987654444446777766554
No 213
>PRK00568 carbon storage regulator; Provisional
Probab=31.62 E-value=81 Score=23.67 Aligned_cols=33 Identities=18% Similarity=0.244 Sum_probs=26.2
Q ss_pred CccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309 129 SVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE 163 (259)
Q Consensus 129 ~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~ 163 (259)
..++.+.+||.+.++|+++. .+++.|.+.+...
T Consensus 7 K~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (76)
T PRK00568 7 KVNEGIVIDDNIHIKVISID--RGSVRLGFEAPES 39 (76)
T ss_pred eCCCeEEeCCCeEEEEEEEc--CCEEEEEEECCCC
Confidence 34567889999999999996 5789998877643
No 214
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=31.45 E-value=1.3e+02 Score=22.22 Aligned_cols=47 Identities=19% Similarity=0.311 Sum_probs=32.9
Q ss_pred cccCCCeEEEEEE----------E---EeCCCCeEEEEEeecchhhHHHHHHhccccceE
Q 044309 133 LIKVGRIEPVMVL----------R---VDKEKGYIDLSKRRVSEEDIQACEERYNKSKLV 179 (259)
Q Consensus 133 ~~kvGd~V~vkVi----------~---vD~~~gkI~LSlK~~~~~~~~~~~~~~~~g~~v 179 (259)
.+.+||-+.+++- + .+.+++.+.+.+|..............+.|+.+
T Consensus 29 ~~~pGQ~v~v~~~~~~~~~~R~yS~~s~~~~~~~~~~~ik~~~~G~~S~~L~~l~~Gd~v 88 (99)
T PF00970_consen 29 DFKPGQFVSVRVPINGKQVSRPYSPASSPDDKGYLEFAIKRYPNGRVSRYLHQLKPGDEV 88 (99)
T ss_dssp SSTTT-EEEEEEEETTEEEEEEEEBCSSTTSSSEEEEEEEECTTSHHHHHHHTSCTTSEE
T ss_pred ccCcceEEEEEEccCCcceecceeEeeecCCCCcEEEEEEeccCCHHHHHHHhCCCCCEE
Confidence 4678888888776 1 122356899999988666666666778999987
No 215
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=31.39 E-value=37 Score=30.73 Aligned_cols=57 Identities=14% Similarity=0.178 Sum_probs=42.1
Q ss_pred CCCCCcEEEEEEEEEeC--ceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeC
Q 044309 84 YPEVDMAVMIQVKNIAD--MGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~--~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~ 149 (259)
-|++|++..|.|--+.. .|+.|. +-..+-||..+++-+|. .+.+||+.++.|.+.|.
T Consensus 104 ~Pk~Gd~LeG~Vn~vS~sHIglLIh----g~FNASIpk~nip~dw~-----fI~md~eee~~v~ntD~ 162 (253)
T KOG4134|consen 104 RPKAGDILEGVVNHVSRSHIGLLIH----GVFNASIPKTNIPADWE-----FIAMDQEEEIRVKNTDI 162 (253)
T ss_pred CCCCCCeeeeeeeecchhhhceeeh----hhhhccCCCCCCcccee-----eecCCchhhhceeeccc
Confidence 46699999999988864 355432 34566777777665544 57899999999999885
No 216
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=30.60 E-value=97 Score=27.03 Aligned_cols=57 Identities=18% Similarity=0.207 Sum_probs=39.6
Q ss_pred ccccCCCeEEEEEEEEeCCCCeEEEEEe-e-----------------cchhhHHHHHHhccccceEEEEEEeccc
Q 044309 132 SLIKVGRIEPVMVLRVDKEKGYIDLSKR-R-----------------VSEEDIQACEERYNKSKLVHSIMRHVAE 188 (259)
Q Consensus 132 ~~~kvGd~V~vkVi~vD~~~gkI~LSlK-~-----------------~~~~~~~~~~~~~~~g~~v~g~V~~i~~ 188 (259)
-.-..|+.|.+||.+++..--++.+.-- + ..+.+.-+..+.|.+|+++-.+|.+...
T Consensus 64 ~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~ 138 (193)
T KOG3409|consen 64 LLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD 138 (193)
T ss_pred cCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC
Confidence 3456899999999999876555543321 1 1223344567889999999999998543
No 217
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=30.48 E-value=1.2e+02 Score=19.40 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=25.9
Q ss_pred CCcEEEEEEEEEe-CceEEEEEccCCCEEEEEEcccc
Q 044309 87 VDMAVMIQVKNIA-DMGAYVSLLEYNNIEGMILFSEL 122 (259)
Q Consensus 87 ~G~iv~G~V~~I~-~~GafV~L~ey~~~eGllhisEl 122 (259)
-|..+.|+|.++. +..+.|.+.+|+ ....++.++|
T Consensus 11 d~~wyra~V~~~~~~~~~~V~f~DyG-~~~~v~~~~l 46 (48)
T cd04508 11 DGKWYRAKITSILSDGKVEVFFVDYG-NTEVVPLSDL 46 (48)
T ss_pred CCeEEEEEEEEECCCCcEEEEEEcCC-CcEEEeHHHc
Confidence 4889999999998 555778877764 4455776655
No 218
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=29.97 E-value=2.8e+02 Score=27.85 Aligned_cols=71 Identities=14% Similarity=0.121 Sum_probs=41.8
Q ss_pred EEEEEEEEEeCce--EEEEEccC-CCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 90 AVMIQVKNIADMG--AYVSLLEY-NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey-~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+.|.|.++...| +|++|.+- +.+..++..+++........-..+..||.|.|.=.=....+|.+.|....
T Consensus 69 ~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~ 142 (505)
T PRK12445 69 SVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTE 142 (505)
T ss_pred EEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeE
Confidence 5799999998777 89999752 24677776555432111111134779998876422122235666655443
No 219
>PLN00208 translation initiation factor (eIF); Provisional
Probab=29.15 E-value=2.5e+02 Score=23.64 Aligned_cols=65 Identities=17% Similarity=0.143 Sum_probs=44.2
Q ss_pred CCCCCcEEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEE
Q 044309 84 YPEVDMAVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDL 156 (259)
Q Consensus 84 ~~~~G~iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~L 156 (259)
+|+.|+ +.|+|+.....|.|- .+. +|..-++|++-=-.+ +--+++||.|.|.+-..+..++.|..
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c~--dG~~rLa~IpGKmRK-----rIWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALCI--DGTKRLCHIRGKMRK-----KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEEC--CCCEEEEEEecccee-----eEEecCCCEEEEEccCCCCCEEEEEE
Confidence 564565 778999988777654 555 688888887642222 23378999999997766665555554
No 220
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=28.79 E-value=1.1e+02 Score=22.61 Aligned_cols=33 Identities=27% Similarity=0.288 Sum_probs=26.2
Q ss_pred CccccccCCCeEEEEEEEEeCCCCeEEEEEeecch
Q 044309 129 SVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVSE 163 (259)
Q Consensus 129 ~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~~ 163 (259)
.+++.+.+|+.+.++|+++. .+++.|.+.+...
T Consensus 7 k~gE~I~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (69)
T TIGR00202 7 KVNESIQIGDDIEVKVLSVK--GDQVKLGIEAPKE 39 (69)
T ss_pred cCCCEEEeCCCEEEEEEEEc--CCeEEEEEECCCC
Confidence 35577889999999999996 5788888876543
No 221
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.65 E-value=3.8e+02 Score=23.23 Aligned_cols=55 Identities=7% Similarity=-0.044 Sum_probs=37.9
Q ss_pred EEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309 90 AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 90 iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
.+.|+|..+.+..+.++... -|++-+++.+.+. ..-+.|+.+.+-+--+-.++..
T Consensus 4 ~l~G~v~~~~~~~vvi~~~G-vGY~v~~s~~~~~--------~l~~~g~~~~l~t~~~vrEd~~ 58 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSG-VGFRCYMPATSPA--------LIGGLGQRVRVFTHLHVREDAL 58 (194)
T ss_pred eEEEEEEEecCCEEEEEECC-EEEEEEeCHHHHH--------hcccCCCeEEEEEEEEEecCCc
Confidence 57899999998888888852 2577777665554 2224689888877666555443
No 222
>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=28.62 E-value=3.8e+02 Score=23.17 Aligned_cols=54 Identities=9% Similarity=0.014 Sum_probs=37.8
Q ss_pred EEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309 90 AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 90 iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
.+.|+|..+.+..+.++... -|++-++|.+.+. .++.|+.+.+.+--+-.++..
T Consensus 4 ~l~G~v~~~~~~~vvi~v~G-vGY~v~v~~~~~~---------~l~~g~~v~l~t~~~vred~~ 57 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNG-VGYELQVPMTCAY---------ELNLEQKAQVFTHLVVREDAE 57 (191)
T ss_pred eEEEEEEEEcCCEEEEEECC-EEEEEEecHHHHH---------hcCCCCeEEEEEEEEEecCCc
Confidence 57899999999999999852 1566666655554 134588888877665554443
No 223
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=27.86 E-value=1.6e+02 Score=19.51 Aligned_cols=36 Identities=14% Similarity=0.072 Sum_probs=27.5
Q ss_pred CCcEEEEEEEEEeC-ceEEEEEccCCCEEEEEEccccc
Q 044309 87 VDMAVMIQVKNIAD-MGAYVSLLEYNNIEGMILFSELS 123 (259)
Q Consensus 87 ~G~iv~G~V~~I~~-~GafV~L~ey~~~eGllhisEls 123 (259)
-|..+.|+|.++.+ ..+.|.+.+|+ ...-++.++|.
T Consensus 15 d~~wyra~I~~~~~~~~~~V~f~D~G-~~~~v~~~~l~ 51 (57)
T smart00333 15 DGEWYRARIIKVDGEQLYEVFFIDYG-NEEVVPPSDLR 51 (57)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCC-ccEEEeHHHee
Confidence 68999999999987 67788887654 45566666654
No 224
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=27.70 E-value=2.1e+02 Score=19.66 Aligned_cols=58 Identities=22% Similarity=0.346 Sum_probs=31.2
Q ss_pred Cce---EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 100 DMG---AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 100 ~~G---afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
..| +++.+.+ ..|-+...=.... .....+.+++|+.+.+. -.++...+...|...++.
T Consensus 15 k~g~~~~~~~l~D---~tg~~~~~~f~~~-~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~~i~ 75 (84)
T cd04485 15 KKGKRMAFVTLED---LTGSIEVVVFPET-YEKYRDLLKEDALLLVE-GKVERRDGGLRLIAERIE 75 (84)
T ss_pred CCCCEEEEEEEEe---CCCeEEEEECHHH-HHHHHHHhcCCCEEEEE-EEEEecCCceEEEeeccc
Confidence 456 7777764 2333332222211 11234568889888765 345544566777766554
No 225
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=27.49 E-value=3.3e+02 Score=26.27 Aligned_cols=71 Identities=15% Similarity=0.137 Sum_probs=47.5
Q ss_pred CcEEEEEEEEEeC--ce-EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEEE-EEEeCCCCeEEEEEeecc
Q 044309 88 DMAVMIQVKNIAD--MG-AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVMV-LRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 88 G~iv~G~V~~I~~--~G-afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vkV-i~vD~~~gkI~LSlK~~~ 162 (259)
.=.|.|.|++++. .| +|.+|-+-. .+.+.+-.+.. ....-.++.|+.|.|.. +++.+..|++.|...++.
T Consensus 25 ~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~-----~~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~~i~ 99 (438)
T PRK00286 25 QVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSA-----RRLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVEEIE 99 (438)
T ss_pred cEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChh-----hcCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEee
Confidence 5679999999864 46 899997411 24444433322 23344588999998754 455677898999888876
Q ss_pred h
Q 044309 163 E 163 (259)
Q Consensus 163 ~ 163 (259)
+
T Consensus 100 ~ 100 (438)
T PRK00286 100 P 100 (438)
T ss_pred e
Confidence 4
No 226
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=27.33 E-value=2e+02 Score=25.58 Aligned_cols=25 Identities=8% Similarity=0.029 Sum_probs=21.4
Q ss_pred CcEEEEEEEEEeCceEEEEEccCCC
Q 044309 88 DMAVMIQVKNIADMGAYVSLLEYNN 112 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV~L~ey~~ 112 (259)
-+.+.|+|..+.+.-++++..+|++
T Consensus 39 ~~tiEGrVvEV~~~~i~iesk~yn~ 63 (213)
T PRK06763 39 FSTIEGRVVEVDNGVIVIKSKQYEE 63 (213)
T ss_pred cceeeeEEEEEeCCEEEEEeccCCC
Confidence 4589999999999889999988754
No 227
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=26.19 E-value=3.2e+02 Score=21.32 Aligned_cols=51 Identities=10% Similarity=0.141 Sum_probs=35.5
Q ss_pred CcEEEEEEEEEeCceEEE-EEccCCCEEEEEEccccccccccCccccccCCCeEEEEEE
Q 044309 88 DMAVMIQVKNIADMGAYV-SLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVL 145 (259)
Q Consensus 88 G~iv~G~V~~I~~~GafV-~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi 145 (259)
-..+.|+|+.....+.|- .+. +|..-++|++- +.+. .--++.||.|.|...
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~--dG~~~la~i~G----K~Rk-~iwI~~GD~VlVsp~ 69 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCL--DGKTRLGRIPG----KLKK-RIWIREGDVVIVKPW 69 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeC--CCCEEEEEEch----hhcc-cEEecCCCEEEEEEc
Confidence 346899999998877764 565 67888877664 2222 334889999998543
No 228
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=26.17 E-value=98 Score=23.01 Aligned_cols=31 Identities=16% Similarity=0.222 Sum_probs=24.6
Q ss_pred ccccccCCCeEEEEEEEEeCCCCeEEEEEeecc
Q 044309 130 VSSLIKVGRIEPVMVLRVDKEKGYIDLSKRRVS 162 (259)
Q Consensus 130 ~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~~~ 162 (259)
.++.+.+||.+.++|++++. +++.+.+.+..
T Consensus 8 ~~Esi~IgddI~itVl~i~g--nqVkiGi~APk 38 (73)
T COG1551 8 VGESIMIGDDIEITVLSIKG--NQVKIGINAPK 38 (73)
T ss_pred cCceEEecCCeEEEEEEEcC--CeEEEeecCCh
Confidence 35668899999999999974 67888777654
No 229
>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=26.10 E-value=3e+02 Score=26.85 Aligned_cols=53 Identities=19% Similarity=0.211 Sum_probs=33.7
Q ss_pred EEEEEEEEEeCce--EEEEEccC-CCEEEEEEccccccccccCccccccCCCeEEEE
Q 044309 90 AVMIQVKNIADMG--AYVSLLEY-NNIEGMILFSELSRRRIRSVSSLIKVGRIEPVM 143 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey-~~~eGllhisEls~~~v~~~~~~~kvGd~V~vk 143 (259)
.+.|.|.++...| +|++|.+- +.+.+++..++.+....... ..+..|+.|.|.
T Consensus 16 ~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v~ 71 (428)
T TIGR00458 16 TFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWA-KKLNLESVVAVR 71 (428)
T ss_pred EEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHH-hCCCCCcEEEEE
Confidence 4679999998887 89999751 13666666554332211111 347889888763
No 230
>PLN02502 lysyl-tRNA synthetase
Probab=25.98 E-value=3.7e+02 Score=27.35 Aligned_cols=71 Identities=18% Similarity=0.171 Sum_probs=40.5
Q ss_pred EEEEEEEEEeCce--EEEEEccCC-CEEEEEEcccccccc--ccCccccccCCCeEEEEEEEEeCCCCeEEEEEee
Q 044309 90 AVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRR--IRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKRR 160 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~--v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK~ 160 (259)
.+.|.|.++...| +|++|.+-+ .+..++..+.+.... .......+..||.|.|.=.=....+|.+.|..+.
T Consensus 112 ~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~~ 187 (553)
T PLN02502 112 SVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPTS 187 (553)
T ss_pred EEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEeE
Confidence 4689999998777 799997521 356666544432211 1122234789998876422222234555554443
No 231
>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=25.92 E-value=2.2e+02 Score=19.48 Aligned_cols=43 Identities=16% Similarity=0.025 Sum_probs=27.5
Q ss_pred EEEEEEeCce-EEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 93 IQVKNIADMG-AYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 93 G~V~~I~~~G-afV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
|++.. ++.| .||..++ .+.+-|||-.++.. .--||+|.|+++.
T Consensus 1 G~~~~-~~~GfGFv~~~~-~~~DifIp~~~l~~---------A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKI-HPKGFGFVIPDD-GGEDIFIPPRNLNG---------AMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE--SSS-EEEEECT--TEEEEE-HHHHTT---------S-TT-EEEEEEEE
T ss_pred CEEEE-EcCCCEEEEECC-CCCCEEECHHHHCC---------CCCCCEEEEEEec
Confidence 44543 3333 5777764 47899999888863 3479999999988
No 232
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.18 E-value=4.3e+02 Score=23.03 Aligned_cols=60 Identities=12% Similarity=-0.097 Sum_probs=39.1
Q ss_pred EEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCeEEEEEe
Q 044309 90 AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGYIDLSKR 159 (259)
Q Consensus 90 iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gkI~LSlK 159 (259)
.+.|+|..+.+..+.++... -|++-++|.+.+. .++.|+.+.+.+--+-.++...-.-..
T Consensus 4 ~l~G~i~~~~~~~vvi~~~G-vGY~V~vs~~~~~---------~l~~g~~v~l~t~~~vrEd~~~LyGF~ 63 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGG-VGLEVQCPAPTLA---------RLVEGQEAELHTRLVVREDALSLYGFP 63 (197)
T ss_pred eEEEEEEEecCCEEEEEECC-EEEEEEcCHHHHH---------HcCCCCeEEEEEEEEEccCCceeeCcC
Confidence 57899999998888888852 1466666544433 235799998877666555544333333
No 233
>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=25.15 E-value=2.3e+02 Score=21.50 Aligned_cols=52 Identities=13% Similarity=0.155 Sum_probs=28.8
Q ss_pred EEEEEEEEEeCce--EEEEEccCC-CEEEEEEccccccccccCccccccCCCeEEEE
Q 044309 90 AVMIQVKNIADMG--AYVSLLEYN-NIEGMILFSELSRRRIRSVSSLIKVGRIEPVM 143 (259)
Q Consensus 90 iv~G~V~~I~~~G--afV~L~ey~-~~eGllhisEls~~~v~~~~~~~kvGd~V~vk 143 (259)
.+.|.|.++...| +|++|.+.. .+..++..+ .+....... ..+..|+.|.+.
T Consensus 3 ~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~-~~~~~~~~~-~~l~~~s~v~V~ 57 (103)
T cd04319 3 TLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKD-LNEEAYREA-KKVGIESSVIVE 57 (103)
T ss_pred EEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCC-CCHHHHHHH-hCCCCCCEEEEE
Confidence 4789999987665 899997411 244444322 211111111 236788887653
No 234
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.35 E-value=4.7e+02 Score=22.62 Aligned_cols=47 Identities=11% Similarity=-0.006 Sum_probs=33.6
Q ss_pred EEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 90 AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 90 iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
.+.|+|..+.+..+.++... -|++-.+|.+.+. . ++.|+.+.+.+..
T Consensus 4 ~l~G~v~~~~~~~~ii~~~G-vGY~v~v~~~~~~--------~-l~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGN-VGYIVYLSAKVLS--------T-CKIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCCEEEEEECC-EEEEEEecHHHHH--------h-hCCCCeEEEEEEE
Confidence 57899999999889999852 1466666654443 2 4689998887654
No 235
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=24.20 E-value=2.7e+02 Score=19.77 Aligned_cols=22 Identities=9% Similarity=-0.007 Sum_probs=20.1
Q ss_pred CCcEEEEEEEEEeCceEEEEEc
Q 044309 87 VDMAVMIQVKNIADMGAYVSLL 108 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ 108 (259)
.|..+.|++.++...|+.+.+.
T Consensus 21 ~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 21 GGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp TTEEEEEEEEEETTSEEEEEEC
T ss_pred CCcEEEEEEEEECccceEEEEC
Confidence 6888999999999999999995
No 236
>PF14444 S1-like: S1-like
Probab=24.09 E-value=2.7e+02 Score=19.82 Aligned_cols=43 Identities=16% Similarity=0.078 Sum_probs=25.3
Q ss_pred EEEEEEEEE-eCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEE
Q 044309 90 AVMIQVKNI-ADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLR 146 (259)
Q Consensus 90 iv~G~V~~I-~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~ 146 (259)
.+.|.||++ .+||+. + -+-|-+.+-+. ....++||+|.|.-+.
T Consensus 3 ~~~GvVTkl~~~yG~I---D----e~vFF~~~vv~-------G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 3 VFTGVVTKLCDDYGFI---D----EDVFFQTDVVK-------GNVPKVGDRVLVEAIY 46 (58)
T ss_pred eEEEEEEEEeCCcceE---c----ccEEEEcccEe-------cCCCccCCEEEEEEEe
Confidence 578999998 466752 1 12222222222 2345799999987654
No 237
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=24.02 E-value=1.2e+02 Score=20.01 Aligned_cols=22 Identities=23% Similarity=0.084 Sum_probs=17.9
Q ss_pred CCcEEEEEEEEEeCceEEEE-Ec
Q 044309 87 VDMAVMIQVKNIADMGAYVS-LL 108 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~-L~ 108 (259)
.++.+.|++..|.+.|+.+- .+
T Consensus 11 ~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCeEEEEEEEEECCCCEEEEEEC
Confidence 47889999999999998554 43
No 238
>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=23.62 E-value=2.2e+02 Score=18.68 Aligned_cols=48 Identities=13% Similarity=0.106 Sum_probs=29.0
Q ss_pred EEEEEEe-CceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEE
Q 044309 93 IQVKNIA-DMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRV 147 (259)
Q Consensus 93 G~V~~I~-~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~v 147 (259)
|+|.... .+| |+.-++ .+.+-++|.+.+.. . ...+..||.|.+++..-
T Consensus 2 G~i~~~~~g~g-fv~~~~-~~~~i~v~~~~~~~-~----~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFG-FIRPDD-GGKDVFVHPSQIQG-G----LKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCee-EEecCC-CCccEEEEhHHhhc-C----CCcCCCCCEEEEEEEEc
Confidence 5555443 345 444442 22588888876532 1 13367899999998764
No 239
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=21.89 E-value=1.4e+02 Score=22.14 Aligned_cols=31 Identities=6% Similarity=0.133 Sum_probs=20.9
Q ss_pred cccccCCCeEEEEEEEEeCC-------CCeEEEEEeec
Q 044309 131 SSLIKVGRIEPVMVLRVDKE-------KGYIDLSKRRV 161 (259)
Q Consensus 131 ~~~~kvGd~V~vkVi~vD~~-------~gkI~LSlK~~ 161 (259)
+..+++||.|.++++-.+.. ...+.+.++..
T Consensus 8 r~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp 45 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDP 45 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEET
T ss_pred ccCcCCCCEEEEEEEEeccccccccccCCceEEEEECC
Confidence 46689999999999955443 23566776654
No 240
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.76 E-value=5.4e+02 Score=22.38 Aligned_cols=55 Identities=11% Similarity=-0.017 Sum_probs=37.3
Q ss_pred EEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeCCCCe
Q 044309 90 AVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDKEKGY 153 (259)
Q Consensus 90 iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~~~gk 153 (259)
.+.|+|..+.+..+.++... -|++-++|.+.+. +.-++|+.+.+.+.-+-.++..
T Consensus 4 ~i~G~i~~~~~~~viie~~G-vGY~v~vs~~~~~--------~l~~~g~~v~l~t~~~vrEd~~ 58 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGG-VGLLIYAPRSVLA--------AIGAIGDEVFLYTHLIVREDAL 58 (195)
T ss_pred eEEEEEEEEcCCEEEEEECC-EEEEEEeCHHHHH--------HhccCCCeEEEEEEEEEecCCc
Confidence 57899999998888888852 1566666655543 2225799998877665554443
No 241
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=21.63 E-value=2.4e+02 Score=21.26 Aligned_cols=54 Identities=20% Similarity=0.190 Sum_probs=31.8
Q ss_pred EEEEEEEEEe---Cce-EEEEEccCCCEEEEEEcccccccc---ccCccccccCCCeEEEEEEEEeC
Q 044309 90 AVMIQVKNIA---DMG-AYVSLLEYNNIEGMILFSELSRRR---IRSVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 90 iv~G~V~~I~---~~G-afV~L~ey~~~eGllhisEls~~~---v~~~~~~~kvGd~V~vkVi~vD~ 149 (259)
.+.|+|+++. .-| +|+.|.+ .+ +-++. ..|+. .+.....++.||.|.+. =+++.
T Consensus 2 ~v~GeVs~~~~~~~sGH~yFtlkD-~~--~~i~c--v~f~~~g~~~~~~~~l~~Gd~V~v~-G~v~~ 62 (91)
T cd04482 2 RVTGKVVEEPRTIEGGHVFFKISD-GT--GEIDC--AAYEPTKEFRDVVRLLIPGDEVTVY-GSVRP 62 (91)
T ss_pred EEEEEEeCCeecCCCCCEEEEEEC-CC--cEEEE--EEECcccccccccCCCCCCCEEEEE-EEEec
Confidence 4789998875 345 8999963 22 22221 22221 23455668999999875 33443
No 242
>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=21.52 E-value=2.7e+02 Score=18.88 Aligned_cols=50 Identities=16% Similarity=0.216 Sum_probs=31.2
Q ss_pred CCcEEEEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCccccccCCCeEEEEEEEEeC
Q 044309 87 VDMAVMIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVSSLIKVGRIEPVMVLRVDK 149 (259)
Q Consensus 87 ~G~iv~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~~~~kvGd~V~vkVi~vD~ 149 (259)
+|+.+...|.+..+.|-++--.+ ++..-+++-. ... +|+.+.|+|.+..+
T Consensus 4 ~G~~~~VlVe~~~~~g~~~gr~~-~~~~V~v~~~-----------~~~-iG~~v~v~I~~~~~ 53 (61)
T PF01938_consen 4 VGKTLEVLVEELGDEGQGIGRTD-NGKVVFVPGG-----------LPL-IGEFVKVRITKAKK 53 (61)
T ss_dssp TTEEEEEEEEEE-TTSEEEEEET--TEEEEETT-------------T---TEEEEEEEEEE-S
T ss_pred CCcEEEEEEEEecCCCEEEEEeC-CCeEEEECCC-----------CCC-CCCEEEEEEEEeeC
Confidence 69999999999887676654432 2444444322 112 69999999999865
No 243
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=20.99 E-value=2.4e+02 Score=26.01 Aligned_cols=49 Identities=10% Similarity=-0.043 Sum_probs=35.5
Q ss_pred hhhcCCCCCcEE-----EEEEEEEeCceEEEEEccCCCEEEEEEccccccccccCcc
Q 044309 80 YEARYPEVDMAV-----MIQVKNIADMGAYVSLLEYNNIEGMILFSELSRRRIRSVS 131 (259)
Q Consensus 80 ~~~~~~~~G~iv-----~G~V~~I~~~GafV~L~ey~~~eGllhisEls~~~v~~~~ 131 (259)
+.+.|. +||.+ .|+|.+|.-+---+.-. +|..-.+|.+.+....+.|..
T Consensus 126 ~~rpf~-vGD~I~i~~~~G~V~~I~~r~T~i~t~--d~~~v~IPNs~~~~~~i~N~s 179 (286)
T PRK10334 126 MFRPFR-AGEYVDLGGVAGTVLSVQIFSTTMRTA--DGKIIVIPNGKIIAGNIINFS 179 (286)
T ss_pred hcCCCC-CCCEEEECCEEEEEEEEEeEEEEEEcC--CCCEEEEcchHhcCCeeEEcC
Confidence 345566 88884 68888886655555543 588999999999987776654
No 244
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=20.72 E-value=2.7e+02 Score=22.58 Aligned_cols=56 Identities=14% Similarity=0.030 Sum_probs=33.2
Q ss_pred EEEEEEEEeCce--EEEEEccCCCEEEEEEcccccccc-ccCccccccCCCeEEE--EEEEEe
Q 044309 91 VMIQVKNIADMG--AYVSLLEYNNIEGMILFSELSRRR-IRSVSSLIKVGRIEPV--MVLRVD 148 (259)
Q Consensus 91 v~G~V~~I~~~G--afV~L~ey~~~eGllhisEls~~~-v~~~~~~~kvGd~V~v--kVi~vD 148 (259)
+.|+|+.+.+.| +-+... +|.+-|+|+.==+..- .+--...++.||.|++ .++++|
T Consensus 42 ~~G~v~~i~~T~HA~~i~~~--~G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~D 102 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIESD--SGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFD 102 (124)
T ss_pred CCeEEEEEccCCCEEEEEeC--CCcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 679999996654 335554 5899999987543221 1112233566776654 344554
Done!