Query psy9900
Match_columns 191
No_of_seqs 228 out of 1917
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 22:33:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9900hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1278 CspC Cold shock protei 99.9 2.1E-24 4.6E-29 142.6 7.6 66 8-77 1-66 (67)
2 COG1278 CspC Cold shock protei 99.9 2E-24 4.4E-29 142.7 7.1 66 110-179 2-67 (67)
3 PRK15464 cold shock-like prote 99.9 1.7E-23 3.8E-28 140.9 8.5 67 7-77 3-69 (70)
4 PRK10943 cold shock-like prote 99.9 3E-23 6.5E-28 139.7 8.4 67 7-77 2-68 (69)
5 PRK15463 cold shock-like prote 99.9 4.9E-23 1.1E-27 138.8 8.5 68 6-77 2-69 (70)
6 PRK10354 RNA chaperone/anti-te 99.9 7.1E-23 1.5E-27 138.3 9.2 68 6-77 2-69 (70)
7 PRK09890 cold shock protein Cs 99.9 8.5E-23 1.8E-27 137.8 9.1 67 7-77 3-69 (70)
8 PRK09507 cspE cold shock prote 99.9 8.2E-23 1.8E-27 137.5 8.7 68 6-77 1-68 (69)
9 PRK09937 stationary phase/star 99.9 1.5E-22 3.2E-27 137.9 9.7 66 9-78 2-67 (74)
10 PRK15464 cold shock-like prote 99.9 8.9E-23 1.9E-27 137.4 8.4 66 109-178 4-69 (70)
11 PRK10943 cold shock-like prote 99.9 9.5E-23 2.1E-27 137.2 8.3 68 108-179 2-69 (69)
12 PRK14998 cold shock-like prote 99.9 1.6E-22 3.4E-27 137.4 9.3 67 9-79 2-68 (73)
13 PRK15463 cold shock-like prote 99.9 1.8E-22 3.9E-27 136.1 8.5 66 109-178 4-69 (70)
14 TIGR02381 cspD cold shock doma 99.9 1.6E-22 3.4E-27 135.8 8.1 65 9-77 2-66 (68)
15 PRK09890 cold shock protein Cs 99.9 3.7E-22 8.1E-27 134.7 8.7 67 109-179 4-70 (70)
16 PRK10354 RNA chaperone/anti-te 99.9 4.2E-22 9.2E-27 134.5 8.8 67 109-179 4-70 (70)
17 PRK09507 cspE cold shock prote 99.9 4.8E-22 1E-26 133.8 8.2 66 109-178 3-68 (69)
18 PRK09937 stationary phase/star 99.9 6.9E-22 1.5E-26 134.5 8.8 66 111-180 3-68 (74)
19 TIGR02381 cspD cold shock doma 99.9 9.4E-22 2E-26 132.1 7.9 65 111-179 3-67 (68)
20 PRK14998 cold shock-like prote 99.9 1.4E-21 3.1E-26 132.7 8.5 68 110-181 2-69 (73)
21 PF00313 CSD: 'Cold-shock' DNA 99.8 7E-20 1.5E-24 122.1 8.9 65 9-77 1-65 (66)
22 PF00313 CSD: 'Cold-shock' DNA 99.8 8.2E-20 1.8E-24 121.8 9.0 65 110-178 1-65 (66)
23 cd04458 CSP_CDS Cold-Shock Pro 99.8 1.6E-19 3.5E-24 120.0 8.5 64 9-76 1-64 (65)
24 cd04458 CSP_CDS Cold-Shock Pro 99.8 3E-19 6.5E-24 118.7 8.3 65 110-178 1-65 (65)
25 KOG3070|consensus 99.6 8.2E-15 1.8E-19 120.0 7.1 88 103-190 50-137 (235)
26 KOG3070|consensus 99.5 3.9E-14 8.4E-19 116.0 6.3 89 3-91 51-139 (235)
27 smart00357 CSP Cold shock prot 99.0 2.7E-09 5.9E-14 69.4 7.9 62 111-179 1-64 (64)
28 smart00357 CSP Cold shock prot 98.9 5.4E-09 1.2E-13 68.0 7.7 61 10-77 1-63 (64)
29 PRK11642 exoribonuclease R; Pr 98.7 1.9E-07 4.1E-12 88.9 13.2 125 9-181 85-216 (813)
30 TIGR00358 3_prime_RNase VacB a 98.5 2.1E-06 4.6E-11 80.3 13.6 127 8-181 16-150 (654)
31 PRK05054 exoribonuclease II; P 98.4 3.9E-06 8.6E-11 78.3 13.6 128 7-181 20-153 (644)
32 PF08206 OB_RNB: Ribonuclease 98.4 1.2E-06 2.5E-11 56.8 5.7 45 18-71 6-50 (58)
33 TIGR02062 RNase_B exoribonucle 98.3 1.9E-05 4.2E-10 73.6 13.6 129 6-181 16-150 (639)
34 TIGR02063 RNase_R ribonuclease 98.2 2.4E-05 5.2E-10 73.9 13.4 126 8-181 68-202 (709)
35 PF08206 OB_RNB: Ribonuclease 98.1 8.7E-06 1.9E-10 52.6 6.2 49 120-177 7-57 (58)
36 PF14444 S1-like: S1-like 97.4 0.00087 1.9E-08 43.1 5.9 48 108-169 2-49 (58)
37 PF14444 S1-like: S1-like 97.3 0.00096 2.1E-08 42.9 5.9 47 8-68 3-49 (58)
38 COG2996 Predicted RNA-bindinin 97.0 0.038 8.2E-07 46.3 13.4 127 1-170 1-131 (287)
39 PRK13806 rpsA 30S ribosomal pr 96.8 0.032 6.9E-07 50.8 12.9 142 7-168 294-438 (491)
40 PF07497 Rho_RNA_bind: Rho ter 96.7 0.0044 9.6E-08 42.4 4.9 62 10-80 4-73 (78)
41 COG0557 VacB Exoribonuclease R 96.6 0.031 6.8E-07 53.0 11.8 124 10-181 71-204 (706)
42 PRK07899 rpsA 30S ribosomal pr 96.6 0.063 1.4E-06 48.8 13.1 150 7-177 210-363 (486)
43 PF07497 Rho_RNA_bind: Rho ter 96.4 0.012 2.5E-07 40.4 5.9 64 111-183 4-75 (78)
44 PRK13806 rpsA 30S ribosomal pr 96.2 0.15 3.3E-06 46.4 13.4 153 7-179 204-365 (491)
45 PRK12269 bifunctional cytidyla 95.9 0.23 5E-06 48.3 13.9 152 8-180 496-652 (863)
46 PRK11642 exoribonuclease R; Pr 95.8 0.027 5.8E-07 54.3 7.0 63 109-182 84-148 (813)
47 PRK12269 bifunctional cytidyla 95.7 0.22 4.7E-06 48.4 12.7 143 7-169 580-726 (863)
48 cd04459 Rho_CSD Rho_CSD: Rho p 95.7 0.025 5.4E-07 37.7 4.6 41 19-66 9-54 (68)
49 PRK07400 30S ribosomal protein 95.6 0.52 1.1E-05 40.6 13.7 148 7-183 120-271 (318)
50 COG0539 RpsA Ribosomal protein 95.6 0.18 4E-06 46.3 11.2 140 8-168 195-336 (541)
51 cd04459 Rho_CSD Rho_CSD: Rho p 95.4 0.049 1.1E-06 36.3 5.2 48 112-168 3-55 (68)
52 PRK06676 rpsA 30S ribosomal pr 95.4 0.96 2.1E-05 39.7 14.8 156 7-183 194-353 (390)
53 PRK00087 4-hydroxy-3-methylbut 95.3 0.64 1.4E-05 43.8 14.2 154 7-181 479-636 (647)
54 TIGR00358 3_prime_RNase VacB a 95.3 0.069 1.5E-06 50.3 7.6 63 109-182 16-81 (654)
55 TIGR02062 RNase_B exoribonucle 95.1 0.092 2E-06 49.4 7.9 62 108-181 17-78 (639)
56 PRK05054 exoribonuclease II; P 95.1 0.084 1.8E-06 49.6 7.6 62 108-181 20-81 (644)
57 TIGR00717 rpsA ribosomal prote 95.0 1.3 2.8E-05 40.3 15.0 142 7-168 361-505 (516)
58 PRK06299 rpsA 30S ribosomal pr 94.8 1.4 3E-05 40.7 14.7 140 8-168 204-346 (565)
59 COG0539 RpsA Ribosomal protein 94.8 0.47 1E-05 43.7 11.2 144 6-169 278-423 (541)
60 PRK06299 rpsA 30S ribosomal pr 94.5 1.2 2.6E-05 41.1 13.6 150 7-177 375-530 (565)
61 PF13509 S1_2: S1 domain; PDB: 94.2 0.15 3.2E-06 33.0 5.0 52 112-174 7-59 (61)
62 TIGR02063 RNase_R ribonuclease 93.8 0.19 4.2E-06 47.7 7.0 63 109-182 68-134 (709)
63 TIGR00717 rpsA ribosomal prote 93.5 2.2 4.7E-05 38.9 13.1 142 7-168 274-419 (516)
64 PRK09376 rho transcription ter 93.3 0.22 4.7E-06 44.3 6.1 70 109-187 50-127 (416)
65 cd04453 S1_RNase_E S1_RNase_E: 93.1 0.82 1.8E-05 31.7 7.6 62 106-168 7-71 (88)
66 cd05698 S1_Rrp5_repeat_hs6_sc5 92.6 1 2.2E-05 29.2 7.2 59 109-170 3-61 (70)
67 cd04461 S1_Rrp5_repeat_hs8_sc7 92.5 1.1 2.4E-05 30.3 7.5 60 107-169 15-74 (83)
68 PRK07899 rpsA 30S ribosomal pr 92.5 2.8 6E-05 38.3 12.1 140 8-168 125-266 (486)
69 PRK06676 rpsA 30S ribosomal pr 92.4 2.7 5.9E-05 36.9 11.7 141 7-168 19-161 (390)
70 COG1158 Rho Transcription term 92.3 0.29 6.2E-06 42.7 5.2 72 110-190 54-133 (422)
71 PF00575 S1: S1 RNA binding do 92.2 1.2 2.7E-05 29.1 7.3 60 108-170 6-65 (74)
72 cd00164 S1_like S1_like: Ribos 92.0 0.65 1.4E-05 28.8 5.5 55 10-67 2-56 (65)
73 PRK07400 30S ribosomal protein 91.9 2.7 5.8E-05 36.2 10.8 137 8-168 34-172 (318)
74 cd05696 S1_Rrp5_repeat_hs4 S1_ 91.5 2 4.3E-05 28.3 7.6 56 112-169 7-62 (71)
75 PF00575 S1: S1 RNA binding do 91.4 0.62 1.3E-05 30.6 5.1 59 7-68 6-64 (74)
76 PRK12608 transcription termina 90.6 0.67 1.5E-05 40.9 5.9 68 6-83 16-89 (380)
77 cd05704 S1_Rrp5_repeat_hs13 S1 90.4 2.4 5.2E-05 28.0 7.3 61 108-170 5-65 (72)
78 COG4776 Rnb Exoribonuclease II 90.4 0.33 7.1E-06 43.8 3.8 51 6-68 19-69 (645)
79 cd04461 S1_Rrp5_repeat_hs8_sc7 90.3 1 2.2E-05 30.5 5.5 58 8-68 17-74 (83)
80 PRK08582 hypothetical protein; 90.2 4.5 9.7E-05 30.6 9.4 74 107-183 6-80 (139)
81 cd05697 S1_Rrp5_repeat_hs5 S1_ 90.1 2.7 5.9E-05 27.1 7.3 59 109-170 3-61 (69)
82 cd00164 S1_like S1_like: Ribos 90.1 1.8 4E-05 26.7 6.3 56 111-169 2-57 (65)
83 PRK08582 hypothetical protein; 90.0 3.9 8.5E-05 30.9 9.0 73 1-76 1-74 (139)
84 PRK12608 transcription termina 89.6 1 2.3E-05 39.7 6.3 65 109-183 18-88 (380)
85 cd04472 S1_PNPase S1_PNPase: P 89.6 3.1 6.7E-05 26.4 7.2 58 109-169 3-60 (68)
86 cd04453 S1_RNase_E S1_RNase_E: 89.2 2 4.2E-05 29.8 6.3 61 7-68 9-72 (88)
87 cd05696 S1_Rrp5_repeat_hs4 S1_ 89.2 1.8 3.8E-05 28.5 5.8 53 11-65 7-59 (71)
88 cd05698 S1_Rrp5_repeat_hs6_sc5 89.2 2.2 4.7E-05 27.6 6.2 58 8-68 3-60 (70)
89 smart00316 S1 Ribosomal protei 89.1 3.2 7E-05 26.0 7.0 59 108-169 4-62 (72)
90 cd05692 S1_RPS1_repeat_hs4 S1_ 89.1 3.7 8E-05 25.9 7.3 58 109-169 3-60 (69)
91 PRK09376 rho transcription ter 88.9 1.4 3.1E-05 39.3 6.6 64 9-81 51-122 (416)
92 cd05692 S1_RPS1_repeat_hs4 S1_ 88.9 2 4.2E-05 27.2 5.8 57 8-67 3-59 (69)
93 cd04472 S1_PNPase S1_PNPase: P 88.7 2.2 4.9E-05 27.0 6.0 57 8-67 3-59 (68)
94 cd05706 S1_Rrp5_repeat_sc10 S1 88.6 5 0.00011 26.1 8.1 59 108-169 5-63 (73)
95 PF13509 S1_2: S1 domain; PDB: 88.4 1.3 2.7E-05 28.6 4.5 52 10-72 6-58 (61)
96 PRK12678 transcription termina 88.2 1.2 2.6E-05 41.7 5.8 70 110-189 296-377 (672)
97 cd05691 S1_RPS1_repeat_ec6 S1_ 88.1 4.3 9.2E-05 26.2 7.1 59 109-170 3-61 (73)
98 smart00316 S1 Ribosomal protei 87.9 1.8 3.8E-05 27.3 5.1 59 7-68 4-62 (72)
99 cd05697 S1_Rrp5_repeat_hs5 S1_ 86.9 2.4 5.2E-05 27.4 5.4 58 8-68 3-60 (69)
100 cd05694 S1_Rrp5_repeat_hs2_sc2 86.9 5.1 0.00011 26.7 7.0 54 108-170 6-60 (74)
101 COG1158 Rho Transcription term 86.8 0.91 2E-05 39.6 4.0 63 11-82 56-126 (422)
102 cd05703 S1_Rrp5_repeat_hs12_sc 86.6 5.9 0.00013 26.2 7.2 59 109-170 3-63 (73)
103 cd05689 S1_RPS1_repeat_ec4 S1_ 86.6 6.7 0.00014 25.4 7.8 59 108-169 5-64 (72)
104 cd05706 S1_Rrp5_repeat_sc10 S1 86.2 4.3 9.4E-05 26.4 6.4 57 8-67 6-62 (73)
105 cd05691 S1_RPS1_repeat_ec6 S1_ 85.1 4.6 0.0001 26.0 6.1 57 9-68 4-60 (73)
106 PRK07252 hypothetical protein; 84.9 12 0.00027 27.4 8.8 59 108-169 5-63 (120)
107 cd04473 S1_RecJ_like S1_RecJ_l 84.8 9.2 0.0002 25.4 7.8 50 107-167 17-66 (77)
108 PRK00087 4-hydroxy-3-methylbut 84.8 25 0.00054 33.2 12.9 136 7-166 304-443 (647)
109 TIGR00767 rho transcription te 84.6 1.8 3.9E-05 38.6 4.9 51 109-168 50-105 (415)
110 cd05687 S1_RPS1_repeat_ec1_hs1 84.4 4.4 9.6E-05 26.1 5.7 56 8-66 3-58 (70)
111 PRK07252 hypothetical protein; 84.2 9.3 0.0002 28.1 7.9 59 7-68 5-63 (120)
112 cd05704 S1_Rrp5_repeat_hs13 S1 83.9 7.8 0.00017 25.4 6.8 60 8-69 6-65 (72)
113 cd05690 S1_RPS1_repeat_ec5 S1_ 83.9 7.6 0.00016 24.7 6.7 57 109-168 3-60 (69)
114 PRK05807 hypothetical protein; 83.8 4.7 0.0001 30.3 6.3 72 1-76 1-73 (136)
115 cd05705 S1_Rrp5_repeat_hs14 S1 83.7 7.4 0.00016 25.8 6.6 59 108-169 5-66 (74)
116 PF11604 CusF_Ec: Copper bindi 83.7 2 4.3E-05 28.5 3.8 28 151-178 40-68 (70)
117 cd05707 S1_Rrp5_repeat_sc11 S1 82.8 7.2 0.00016 25.0 6.2 58 109-169 3-60 (68)
118 TIGR00757 RNaseEG ribonuclease 82.6 7 0.00015 35.0 7.9 74 107-181 26-115 (414)
119 PRK08059 general stress protei 82.6 11 0.00023 27.7 7.7 71 108-181 9-81 (123)
120 COG2996 Predicted RNA-bindinin 82.6 29 0.00062 29.4 12.1 117 21-166 87-204 (287)
121 TIGR00767 rho transcription te 82.5 1.4 3E-05 39.4 3.3 50 9-67 51-105 (415)
122 cd05686 S1_pNO40 S1_pNO40: pNO 82.3 6.8 0.00015 25.7 6.0 58 7-67 5-63 (73)
123 cd05689 S1_RPS1_repeat_ec4 S1_ 82.2 11 0.00024 24.3 7.1 57 8-67 6-63 (72)
124 cd05690 S1_RPS1_repeat_ec5 S1_ 81.9 6.2 0.00013 25.2 5.6 55 9-66 4-59 (69)
125 cd05686 S1_pNO40 S1_pNO40: pNO 81.3 8.9 0.00019 25.1 6.3 59 108-169 5-64 (73)
126 cd05684 S1_DHX8_helicase S1_DH 81.3 13 0.00028 24.6 7.7 68 109-179 3-74 (79)
127 cd05687 S1_RPS1_repeat_ec1_hs1 81.0 11 0.00023 24.2 6.5 57 109-168 3-59 (70)
128 PRK05807 hypothetical protein; 81.0 19 0.00041 27.0 8.7 70 107-180 6-76 (136)
129 cd04452 S1_IF2_alpha S1_IF2_al 80.4 13 0.00029 24.1 7.1 59 108-169 5-65 (76)
130 cd04473 S1_RecJ_like S1_RecJ_l 80.4 9.3 0.0002 25.4 6.2 49 7-66 18-66 (77)
131 cd04455 S1_NusA S1_NusA: N-uti 80.3 11 0.00024 24.3 6.4 51 108-168 5-55 (67)
132 cd05707 S1_Rrp5_repeat_sc11 S1 79.9 7.6 0.00016 24.9 5.5 57 8-67 3-59 (68)
133 PF05606 DUF777: Borrelia burg 79.2 3.4 7.3E-05 32.3 4.0 48 9-62 36-83 (181)
134 cd05702 S1_Rrp5_repeat_hs11_sc 78.6 14 0.0003 23.9 6.5 58 109-169 3-62 (70)
135 cd05705 S1_Rrp5_repeat_hs14 S1 78.4 7.3 0.00016 25.9 5.1 58 7-67 5-65 (74)
136 cd05685 S1_Tex S1_Tex: The C-t 77.7 14 0.00031 23.0 6.6 58 109-169 3-60 (68)
137 cd04455 S1_NusA S1_NusA: N-uti 76.0 12 0.00025 24.2 5.5 51 7-67 5-55 (67)
138 cd04452 S1_IF2_alpha S1_IF2_al 76.0 16 0.00035 23.6 6.3 57 8-67 6-64 (76)
139 cd05703 S1_Rrp5_repeat_hs12_sc 75.8 8.8 0.00019 25.3 5.0 55 8-66 3-60 (73)
140 cd05685 S1_Tex S1_Tex: The C-t 75.7 10 0.00022 23.7 5.2 56 9-67 4-59 (68)
141 cd04471 S1_RNase_R S1_RNase_R: 75.6 20 0.00043 23.5 7.2 58 109-169 4-73 (83)
142 PRK09838 periplasmic copper-bi 74.1 6.2 0.00013 28.9 4.1 65 108-178 43-113 (115)
143 PRK08059 general stress protei 74.0 21 0.00045 26.1 7.0 58 7-67 9-66 (123)
144 cd05684 S1_DHX8_helicase S1_DH 73.6 23 0.0005 23.3 7.2 58 9-69 4-65 (79)
145 cd04465 S1_RPS1_repeat_ec2_hs2 73.5 8.4 0.00018 24.6 4.3 53 8-68 3-57 (67)
146 PRK12678 transcription termina 72.0 13 0.00028 35.0 6.6 48 9-66 296-346 (672)
147 cd05702 S1_Rrp5_repeat_hs11_sc 71.5 20 0.00043 23.1 5.8 56 8-66 3-60 (70)
148 cd05688 S1_RPS1_repeat_ec3 S1_ 71.0 14 0.00031 23.1 5.0 56 8-67 4-59 (68)
149 PF11604 CusF_Ec: Copper bindi 70.7 8.1 0.00018 25.5 3.8 27 50-76 40-67 (70)
150 PRK11712 ribonuclease G; Provi 70.0 24 0.00052 32.3 7.8 73 108-181 40-128 (489)
151 cd05708 S1_Rrp5_repeat_sc12 S1 69.4 16 0.00034 23.6 5.1 57 8-67 5-62 (77)
152 cd04465 S1_RPS1_repeat_ec2_hs2 69.4 18 0.00039 23.0 5.2 55 109-169 3-57 (67)
153 cd05688 S1_RPS1_repeat_ec3 S1_ 68.5 26 0.00056 21.8 6.1 57 109-169 4-60 (68)
154 PTZ00248 eukaryotic translatio 67.8 27 0.00059 30.2 7.3 75 106-183 17-95 (319)
155 cd05694 S1_Rrp5_repeat_hs2_sc2 66.8 34 0.00074 22.6 6.6 52 8-68 7-59 (74)
156 cd04471 S1_RNase_R S1_RNase_R: 65.9 35 0.00075 22.3 6.5 57 8-67 4-72 (83)
157 COG4776 Rnb Exoribonuclease II 65.8 10 0.00022 34.5 4.4 51 107-169 19-69 (645)
158 COG1098 VacB Predicted RNA bin 62.1 17 0.00036 27.2 4.2 71 9-83 9-81 (129)
159 COG1098 VacB Predicted RNA bin 61.2 16 0.00035 27.2 4.1 73 108-183 7-80 (129)
160 cd05695 S1_Rrp5_repeat_hs3 S1_ 60.8 41 0.0009 21.5 6.3 55 109-168 3-57 (66)
161 KOG3209|consensus 59.9 33 0.00071 33.0 6.7 51 12-64 652-704 (984)
162 cd05708 S1_Rrp5_repeat_sc12 S1 59.3 45 0.00097 21.4 6.8 58 109-169 5-63 (77)
163 COG0557 VacB Exoribonuclease R 57.8 24 0.00052 33.7 5.7 61 110-181 70-135 (706)
164 PLN00207 polyribonucleotide nu 57.7 23 0.00049 34.9 5.5 55 10-67 759-813 (891)
165 TIGR02696 pppGpp_PNP guanosine 57.6 34 0.00073 32.9 6.5 60 106-168 647-710 (719)
166 TIGR01451 B_ant_repeat conserv 57.2 18 0.00038 22.5 3.3 30 152-181 6-36 (53)
167 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 57.1 55 0.0012 21.8 7.0 59 108-169 8-70 (86)
168 PLN00207 polyribonucleotide nu 56.5 49 0.0011 32.6 7.6 67 109-178 756-824 (891)
169 PRK11824 polynucleotide phosph 55.8 61 0.0013 31.0 8.0 60 107-169 622-681 (693)
170 PF03100 CcmE: CcmE; InterPro 55.8 60 0.0013 24.1 6.5 61 112-180 62-123 (131)
171 cd04454 S1_Rrp4_like S1_Rrp4_l 55.5 58 0.0013 21.5 7.0 59 109-170 9-67 (82)
172 PRK11824 polynucleotide phosph 53.9 46 0.001 31.8 6.9 58 7-67 623-680 (693)
173 PRK09202 nusA transcription el 53.2 48 0.001 30.2 6.6 117 32-169 71-187 (470)
174 TIGR03591 polynuc_phos polyrib 53.0 46 0.001 31.8 6.7 60 107-169 619-678 (684)
175 cd04454 S1_Rrp4_like S1_Rrp4_l 52.2 62 0.0013 21.4 5.6 59 8-69 9-67 (82)
176 PHA02945 interferon resistance 52.0 80 0.0017 22.1 6.5 63 108-176 13-79 (88)
177 PRK03987 translation initiatio 50.2 71 0.0015 26.7 6.8 67 108-177 10-80 (262)
178 cd04460 S1_RpoE S1_RpoE: RpoE, 49.9 73 0.0016 22.0 5.9 55 9-67 3-68 (99)
179 PRK10676 DNA-binding transcrip 49.6 1.5E+02 0.0033 24.6 11.2 128 4-167 125-255 (263)
180 PRK10811 rne ribonuclease E; R 49.3 73 0.0016 31.9 7.4 72 108-180 40-124 (1068)
181 TIGR00757 RNaseEG ribonuclease 48.4 58 0.0012 29.2 6.2 62 6-68 26-99 (414)
182 KOG0109|consensus 48.3 29 0.00063 29.8 4.1 21 10-30 26-46 (346)
183 TIGR00638 Mop molybdenum-pteri 48.2 68 0.0015 20.2 5.5 61 1-66 1-62 (69)
184 PRK13168 rumA 23S rRNA m(5)U19 47.5 1.9E+02 0.0041 25.9 9.5 60 107-183 13-73 (443)
185 TIGR03591 polynuc_phos polyrib 47.4 52 0.0011 31.4 6.1 58 7-67 620-677 (684)
186 TIGR02696 pppGpp_PNP guanosine 47.3 50 0.0011 31.8 5.9 57 7-66 649-709 (719)
187 PRK09838 periplasmic copper-bi 47.3 33 0.00072 25.1 3.8 27 50-76 86-112 (115)
188 PTZ00248 eukaryotic translatio 45.7 88 0.0019 27.1 6.7 68 7-77 19-90 (319)
189 PRK09202 nusA transcription el 43.4 53 0.0012 29.9 5.3 52 6-67 135-186 (470)
190 PF01345 DUF11: Domain of unkn 43.1 39 0.00084 22.1 3.4 30 152-181 35-65 (76)
191 COG5569 Uncharacterized conser 42.2 31 0.00067 24.7 2.8 27 151-177 81-107 (108)
192 PF06523 DUF1106: Protein of u 41.3 92 0.002 21.0 4.8 58 103-165 26-88 (91)
193 PF11948 DUF3465: Protein of u 40.7 54 0.0012 24.6 4.1 56 110-170 41-104 (131)
194 PF11948 DUF3465: Protein of u 39.6 69 0.0015 24.1 4.5 58 8-69 40-104 (131)
195 PF05606 DUF777: Borrelia burg 39.1 54 0.0012 25.7 4.0 48 110-163 36-83 (181)
196 COG2183 Tex Transcriptional ac 38.5 1.4E+02 0.0031 29.0 7.5 74 106-182 658-733 (780)
197 PF01551 Peptidase_M23: Peptid 38.2 63 0.0014 22.0 4.0 36 6-41 17-55 (96)
198 CHL00010 infA translation init 36.9 1.3E+02 0.0028 20.2 6.6 59 1-65 1-59 (78)
199 PF01336 tRNA_anti-codon: OB-f 35.4 89 0.0019 19.6 4.2 49 110-163 3-54 (75)
200 cd05693 S1_Rrp5_repeat_hs1_sc1 35.0 1.6E+02 0.0034 20.6 5.8 59 108-169 5-82 (100)
201 TIGR00448 rpoE DNA-directed RN 34.9 1.2E+02 0.0026 23.6 5.5 58 4-65 80-148 (179)
202 cd05701 S1_Rrp5_repeat_hs10 S1 34.7 1.1E+02 0.0024 20.2 4.3 49 120-168 12-60 (69)
203 PRK03987 translation initiatio 34.5 90 0.002 26.1 5.0 58 8-68 11-70 (262)
204 TIGR01953 NusA transcription t 33.9 1.3E+02 0.0029 26.2 6.1 53 6-67 132-184 (341)
205 COG2183 Tex Transcriptional ac 33.7 55 0.0012 31.7 3.9 69 9-80 662-732 (780)
206 PF03459 TOBE: TOBE domain; I 32.4 1.3E+02 0.0027 18.7 4.8 55 108-167 5-60 (64)
207 cd04489 ExoVII_LU_OBF ExoVII_L 31.7 1.4E+02 0.0031 19.1 5.0 52 110-167 4-59 (78)
208 PRK10811 rne ribonuclease E; R 30.9 1.5E+02 0.0033 29.8 6.4 60 9-69 42-110 (1068)
209 PRK12327 nusA transcription el 30.0 1.7E+02 0.0037 25.7 6.2 52 107-168 135-186 (362)
210 PF05753 TRAP_beta: Translocon 29.1 1.1E+02 0.0025 24.0 4.5 47 127-181 15-62 (181)
211 COG1095 RPB7 DNA-directed RNA 27.9 1.1E+02 0.0023 24.4 4.1 68 108-179 83-164 (183)
212 PRK00276 infA translation init 27.6 1.8E+02 0.0039 19.0 6.7 59 1-65 1-59 (72)
213 PRK12327 nusA transcription el 27.5 1.3E+02 0.0027 26.6 4.9 52 6-67 135-186 (362)
214 PRK12442 translation initiatio 26.8 2.2E+02 0.0049 19.8 8.8 59 1-65 1-59 (87)
215 PRK11637 AmiB activator; Provi 26.2 72 0.0016 28.4 3.2 19 8-26 345-363 (428)
216 cd04470 S1_EF-P_repeat_1 S1_EF 26.1 1.6E+02 0.0035 18.6 4.1 53 117-179 9-61 (61)
217 KOG0125|consensus 26.0 39 0.00084 29.4 1.4 15 16-30 130-146 (376)
218 cd04451 S1_IF1 S1_IF1: Transla 24.1 1.9E+02 0.0042 18.2 5.8 51 110-166 3-53 (64)
219 TIGR01953 NusA transcription t 23.2 2.5E+02 0.0053 24.5 5.9 53 107-168 132-184 (341)
220 PF04225 OapA: Opacity-associa 22.3 61 0.0013 22.2 1.6 27 150-177 39-65 (85)
221 PRK11712 ribonuclease G; Provi 21.8 3.1E+02 0.0066 25.3 6.4 63 6-69 39-113 (489)
222 PF01796 DUF35: DUF35 OB-fold 21.6 2.3E+02 0.005 18.1 5.1 37 22-63 31-67 (68)
223 COG1185 Pnp Polyribonucleotide 21.6 2.4E+02 0.0053 27.1 5.8 60 108-170 621-681 (692)
224 COG1093 SUI2 Translation initi 21.6 2E+02 0.0044 24.2 4.8 67 108-177 13-81 (269)
225 PF14326 DUF4384: Domain of un 21.4 2E+02 0.0044 19.1 4.1 19 153-171 2-20 (83)
226 cd04486 YhcR_OBF_like YhcR_OBF 20.9 2.7E+02 0.0058 18.5 6.1 50 110-168 2-59 (78)
227 PRK08563 DNA-directed RNA poly 20.8 2.4E+02 0.0053 21.8 5.0 57 6-66 82-149 (187)
228 PF11061 DUF2862: Protein of u 20.3 1.8E+02 0.0039 19.1 3.4 33 110-142 28-62 (64)
229 PF11213 DUF3006: Protein of u 20.2 2.6E+02 0.0057 18.2 5.0 41 112-162 2-42 (71)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.91 E-value=2.1e-24 Score=142.62 Aligned_cols=66 Identities=39% Similarity=0.693 Sum_probs=62.8
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
+.+|+|||||..||||||.++++++|||||+|+++.. |++.|.+|++|+|++.++++|++|.+|..
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~----g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~ 66 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA----GFRTLREGQKVEFEVEQGRKGPSAANVRA 66 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC----CCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence 4689999999999999999999999999999999987 79999999999999999999999999974
No 2
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.91 E-value=2e-24 Score=142.70 Aligned_cols=66 Identities=39% Similarity=0.684 Sum_probs=62.3
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
.+|+|||||..||||||+|+++++|||||+|++... |+++|.+||+|+|++.+++||++|+||+.+
T Consensus 2 ~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~----g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~~ 67 (67)
T COG1278 2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA----GFRTLREGQKVEFEVEQGRKGPSAANVRAL 67 (67)
T ss_pred CcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC----CCcccCCCCEEEEEEecCCCCCceeEEEeC
Confidence 579999999999999999999999999999999974 699999999999999999999999999863
No 3
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.90 E-value=1.7e-23 Score=140.87 Aligned_cols=67 Identities=33% Similarity=0.357 Sum_probs=62.4
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
.+++|+|||||..||||||.++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|..
T Consensus 3 ~~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~~kG~~A~~v~~ 69 (70)
T PRK15464 3 RKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNGLRGPTAANVYL 69 (70)
T ss_pred ccceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 45689999999999999999999999999999999876 67899999999999999999999999874
No 4
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.89 E-value=3e-23 Score=139.67 Aligned_cols=67 Identities=42% Similarity=0.708 Sum_probs=63.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
.+++|+|||||..||||||.++++++|||||+|+|... +++.|.+|++|+|++.++++|++|.+|+.
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~ 68 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTA 68 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 47899999999999999999999899999999999976 68999999999999999999999999975
No 5
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.89 E-value=4.9e-23 Score=138.84 Aligned_cols=68 Identities=34% Similarity=0.359 Sum_probs=62.8
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
+.+++|+|||||..||||||.++++++|||||+++|... |++.|.+|++|+|++.++++|++|.+|..
T Consensus 2 ~~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~----g~~~l~~G~~V~f~v~~~~~G~~A~~V~~ 69 (70)
T PRK15463 2 SRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR----DAEELTTGLRVEFCRINGLRGPTAANVYL 69 (70)
T ss_pred CccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 345689999999999999999999999999999999876 68999999999999999999999999864
No 6
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.89 E-value=7.1e-23 Score=138.26 Aligned_cols=68 Identities=43% Similarity=0.638 Sum_probs=62.8
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
+.+++|+|||||..||||||.++++++|||||+|+|... +++.|.+|++|+|++.++++|++|.+|..
T Consensus 2 ~~~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK10354 2 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS 69 (70)
T ss_pred CccceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 344589999999999999999999999999999999976 68999999999999999999999999975
No 7
>PRK09890 cold shock protein CspG; Provisional
Probab=99.89 E-value=8.5e-23 Score=137.83 Aligned_cols=67 Identities=36% Similarity=0.659 Sum_probs=62.5
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
.+++|+|||||..||||||.++++++|||||+|+|... +++.|.+|++|+|++.++++|++|.+|..
T Consensus 3 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK09890 3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT 69 (70)
T ss_pred ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 34699999999999999999999889999999999976 68999999999999999999999999975
No 8
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.89 E-value=8.2e-23 Score=137.53 Aligned_cols=68 Identities=40% Similarity=0.669 Sum_probs=63.1
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
|.+.+|+|||||..||||||.++++++|||||+|+|... +++.|.+|++|+|++.++++|++|.+|..
T Consensus 1 ~~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 68 (69)
T PRK09507 1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA 68 (69)
T ss_pred CCccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence 346889999999999999999999999999999999976 68999999999999999999999999874
No 9
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.89 E-value=1.5e-22 Score=137.85 Aligned_cols=66 Identities=33% Similarity=0.550 Sum_probs=62.6
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 78 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~ 78 (191)
.+|+|||||..||||||.++++++|||||+|+|... |++.|.+|++|+|++.++++|++|.+|...
T Consensus 2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (74)
T PRK09937 2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67 (74)
T ss_pred CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence 479999999999999999999999999999999976 689999999999999999999999999875
No 10
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.88 E-value=8.9e-23 Score=137.42 Aligned_cols=66 Identities=33% Similarity=0.359 Sum_probs=61.6
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
+++|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.+++||++|++|..
T Consensus 4 ~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~~kG~~A~~v~~ 69 (70)
T PRK15464 4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 4689999999999999999999999999999999864 47899999999999999999999999974
No 11
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.88 E-value=9.5e-23 Score=137.21 Aligned_cols=68 Identities=41% Similarity=0.685 Sum_probs=63.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
++++|+|+|||..||||||+++++++|||||+|+|... +++.|.+|++|+|++.++++|++|++|+.+
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~~ 69 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEcC
Confidence 36789999999999999999999889999999999974 578999999999999999999999999864
No 12
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.88 E-value=1.6e-22 Score=137.44 Aligned_cols=67 Identities=33% Similarity=0.522 Sum_probs=62.7
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN 79 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~ 79 (191)
.+|+|||||..||||||.++++++|||||+|+|... |++.|.+|++|+|++.++++|++|.+|....
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~ 68 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIE 68 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEECc
Confidence 479999999999999999999999999999999876 6899999999999999999999999998643
No 13
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.88 E-value=1.8e-22 Score=136.13 Aligned_cols=66 Identities=35% Similarity=0.376 Sum_probs=61.7
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
+++|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|++|++
T Consensus 4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~----g~~~l~~G~~V~f~v~~~~~G~~A~~V~~ 69 (70)
T PRK15463 4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR----DAEELTTGLRVEFCRINGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 4689999999999999999999999999999999864 47899999999999999999999999974
No 14
>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=99.88 E-value=1.6e-22 Score=135.83 Aligned_cols=65 Identities=34% Similarity=0.564 Sum_probs=61.4
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
.+|+|||||.+||||||.++++++|||||+|+|... |++.|.+|++|+|++..+++|++|.+|..
T Consensus 2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 66 (68)
T TIGR02381 2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVP 66 (68)
T ss_pred CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence 479999999999999999999999999999999876 68999999999999999999999999975
No 15
>PRK09890 cold shock protein CspG; Provisional
Probab=99.87 E-value=3.7e-22 Score=134.68 Aligned_cols=67 Identities=36% Similarity=0.642 Sum_probs=62.4
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
+++|+|+|||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|..+
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 70 (70)
T PRK09890 4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVTL 70 (70)
T ss_pred cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEeC
Confidence 4689999999999999999999889999999999975 478999999999999999999999999864
No 16
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.87 E-value=4.2e-22 Score=134.47 Aligned_cols=67 Identities=43% Similarity=0.652 Sum_probs=62.2
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
+++|+|+|||..||||||+++++++|||||+++|... +++.|.+|+.|+|++.++++|++|.+|+.+
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 70 (70)
T PRK10354 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70 (70)
T ss_pred cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEeC
Confidence 3589999999999999999999889999999999874 578999999999999999999999999863
No 17
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.87 E-value=4.8e-22 Score=133.77 Aligned_cols=66 Identities=41% Similarity=0.678 Sum_probs=61.8
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
+.+|+|+|||..||||||+++++++|||||+++|... +++.|.+|+.|+|++.++++|++|++|+.
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 68 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA 68 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence 4789999999999999999999899999999999864 57899999999999999999999999975
No 18
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.87 E-value=6.9e-22 Score=134.54 Aligned_cols=66 Identities=33% Similarity=0.564 Sum_probs=62.5
Q ss_pred eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCC
Q psy9900 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPN 180 (191)
Q Consensus 111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~ 180 (191)
+|+|+|||..||||||+++++++|||||+++|... +++.|.+|+.|+|++.++++|++|++|..++
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~ 68 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPVE 68 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEECC
Confidence 69999999999999999999999999999999864 5899999999999999999999999999884
No 19
>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=99.86 E-value=9.4e-22 Score=132.06 Aligned_cols=65 Identities=34% Similarity=0.550 Sum_probs=61.1
Q ss_pred eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
+|+|||||..||||||+++++++|||||+|+|... +++.|.+|++|+|++.++++|++|.+|+.+
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVPI 67 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEEC
Confidence 69999999999999999999899999999999864 578999999999999999999999999864
No 20
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.86 E-value=1.4e-21 Score=132.71 Aligned_cols=68 Identities=32% Similarity=0.517 Sum_probs=63.0
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~ 181 (191)
.+|+|+|||..||||||+++++++|||||+|+|... +++.|.+|++|+|++.++++|++|++|..++.
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~ 69 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIEA 69 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEECcc
Confidence 369999999999999999999999999999999864 57899999999999999999999999988753
No 21
>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=99.82 E-value=7e-20 Score=122.11 Aligned_cols=65 Identities=43% Similarity=0.710 Sum_probs=59.0
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeec
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 77 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~ 77 (191)
++|+|+|||..||||||.++++++|||||++++... +++.|..|++|+|++..+++|++|.+|..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~ 65 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRK 65 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence 589999999999999999999989999999999986 57899999999999999999999999974
No 22
>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=99.82 E-value=8.2e-20 Score=121.77 Aligned_cols=65 Identities=43% Similarity=0.710 Sum_probs=59.2
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
++|+|+||+..+|||||+++++++|||||++++... +++.|+.|+.|+|.+..+++|++|++|+.
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~ 65 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRK 65 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence 589999999999999999999889999999999985 36899999999999999999999999985
No 23
>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=99.81 E-value=1.6e-19 Score=120.01 Aligned_cols=64 Identities=45% Similarity=0.735 Sum_probs=60.2
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEee
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVT 76 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~ 76 (191)
++|+|||||..||||||.++++++|||||+++|... ++..|.+|++|+|++..+++|++|.+|.
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~ 64 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVR 64 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeE
Confidence 479999999999999999999999999999999976 5799999999999999999999999986
No 24
>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=99.80 E-value=3e-19 Score=118.70 Aligned_cols=65 Identities=45% Similarity=0.701 Sum_probs=60.4
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
++|+|+||+..+|||||+++++++|||||++++... ++..|++|+.|+|++..+++|++|++|+.
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~~ 65 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVRL 65 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeEC
Confidence 369999999999999999999999999999999974 36899999999999999999999999973
No 25
>KOG3070|consensus
Probab=99.55 E-value=8.2e-15 Score=119.99 Aligned_cols=88 Identities=47% Similarity=0.761 Sum_probs=80.2
Q ss_pred ccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCCC
Q psy9900 103 FFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGI 182 (191)
Q Consensus 103 ~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~~ 182 (191)
...+....+|+|||||..+|||||+++|+++|||||+++|....+..++++|.+++.|.|.++.+.+|.+|++|+.+++.
T Consensus 50 ~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g~ 129 (235)
T KOG3070|consen 50 KKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDGV 129 (235)
T ss_pred cccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCCc
Confidence 34556678999999999999999999999999999999999966777899999999999999999999999999999999
Q ss_pred CCCCCCCC
Q psy9900 183 PVQGAPKV 190 (191)
Q Consensus 183 ~~~~~~~~ 190 (191)
++..+++.
T Consensus 130 ~~~~s~~~ 137 (235)
T KOG3070|consen 130 PVRGSKGA 137 (235)
T ss_pred cccccccc
Confidence 99877653
No 26
>KOG3070|consensus
Probab=99.49 E-value=3.9e-14 Score=116.01 Aligned_cols=89 Identities=47% Similarity=0.799 Sum_probs=79.3
Q ss_pred eeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCC
Q psy9900 3 KFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIP 82 (191)
Q Consensus 3 ~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~ 82 (191)
+.+....+|+|||||..+|||||.++++.+|||||+++|....+.+++++|.+++.|.|.++...+|..|++|+.+++.+
T Consensus 51 ~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g~~ 130 (235)
T KOG3070|consen 51 KVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDGVP 130 (235)
T ss_pred ccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCCcc
Confidence 35677889999999999999999999999999999999998656669999999999999999999999999999999988
Q ss_pred ccCCCCCCC
Q psy9900 83 VQGAPKSSS 91 (191)
Q Consensus 83 ~~~~~~~~~ 91 (191)
+..+.....
T Consensus 131 ~~~s~~~~~ 139 (235)
T KOG3070|consen 131 VRGSKGAVK 139 (235)
T ss_pred ccccccccc
Confidence 866554443
No 27
>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=99.00 E-value=2.7e-09 Score=69.41 Aligned_cols=62 Identities=40% Similarity=0.643 Sum_probs=50.8
Q ss_pred eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE--cCCCceeEEeecC
Q psy9900 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTGP 179 (191)
Q Consensus 111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~--~~kg~~A~~V~~~ 179 (191)
+|+|.|++ +|||||.+++...++|||.+++... ...+..||.|.|.+.. ..++++|..|+.+
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~~-----~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~~ 64 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPRGGGKPEAENVVKL 64 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhcC-----CCcCCCCCEEEEEEEEccCCCCcEEEEEEeC
Confidence 48999996 7999999987657999999987541 4678899999999987 5566899988753
No 28
>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=98.94 E-value=5.4e-09 Score=67.99 Aligned_cols=61 Identities=41% Similarity=0.657 Sum_probs=48.4
Q ss_pred ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE--cCCCceeeEeec
Q psy9900 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTG 77 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~--~~~g~~A~~v~~ 77 (191)
+|+|+||+ +|||||.+++...|+|||.+++.. +...+..||.|.|.+.. ..++++|..+..
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-----~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-----GLKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-----CCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 58999997 899999998765799999998764 24667899999999987 344567776643
No 29
>PRK11642 exoribonuclease R; Provisional
Probab=98.72 E-value=1.9e-07 Score=88.91 Aligned_cols=125 Identities=22% Similarity=0.252 Sum_probs=91.8
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CCC-ceeeEeecCCCCCccCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KKD-IEAINVTGPNGIPVQGA 86 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~g-~~A~~v~~~~~~~~~~~ 86 (191)
..|+|+. ..+||||+.++++++|||++...+..++ .||+|.+.+... .++ +.+.-+
T Consensus 85 ~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~A~---------~GD~V~v~i~~~~~~~r~eg~Vv----------- 142 (813)
T PRK11642 85 LKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKTCI---------HGDQVLAQPLGADRKGRREARIV----------- 142 (813)
T ss_pred EEEEEEE--CCCccEEEEECCCCCCEEEChHHHccCC---------CCCEEEEEEccCCCCCCcEEEEE-----------
Confidence 5688884 4899999999876789999999999886 899999997642 223 333333
Q ss_pred CCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 87 PKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
.++++..+-.|..|...++++|+.|+|.. .+||+...+.. .++.|+.|.++|
T Consensus 143 -----------------~IleR~~~~~vG~~~~~~~~~~v~P~d~r~~~~i~i~~~~~~---------~~~~gd~V~v~I 196 (813)
T PRK11642 143 -----------------RVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEQIM---------GARMGFVVVVEL 196 (813)
T ss_pred -----------------EEEecCCCEEEEEEEEeCCeEEEEECCCCCCCcEEecccccc---------CCCCCCEEEEEE
Confidence 34455556667777778899999999864 67888654443 557899999999
Q ss_pred EEcCC---CceeEEeecCCC
Q psy9900 165 GVGKK---DIEAINVTGPNG 181 (191)
Q Consensus 165 ~~~~k---g~~A~~V~~~~~ 181 (191)
..-+. -+.+.-|+.++.
T Consensus 197 ~~~p~~~~~~~g~iv~vLG~ 216 (813)
T PRK11642 197 TQRPTRRTKAVGKIVEVLGD 216 (813)
T ss_pred ecCCCcCCCCCEEEEEEecC
Confidence 97432 266777776664
No 30
>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=98.51 E-value=2.1e-06 Score=80.25 Aligned_cols=127 Identities=24% Similarity=0.311 Sum_probs=90.1
Q ss_pred ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CCC-ceeeEeecCCCCCcc
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KKD-IEAINVTGPNGIPVQ 84 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~g-~~A~~v~~~~~~~~~ 84 (191)
..+|+|+. ..|||||+.+++ +++|||+.-..+..++ .||+|.+.+... .++ +.|.-+
T Consensus 16 ~~~G~i~~--~~~gfgFv~~~~~~~~difI~~~~~~~a~---------~GD~V~v~i~~~~~~~~~~g~v~--------- 75 (654)
T TIGR00358 16 LVKGVVKA--HNKGFGFLRPDDDDKKDYFIPPPQMKKVM---------HGDLVEACPLSQPQRGRFEAEVE--------- 75 (654)
T ss_pred eEEEEEEE--CCCccEEEEeCCCCCCcEEEchHHhCcCC---------CCCEEEEEEeecCCCCCceEEEE---------
Confidence 46799995 489999999986 3689999999999886 899999997543 233 234333
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 162 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f 162 (191)
.++++..+-.|+.|...++++|+.|++.. .+||+...+.. ..++.||.|..
T Consensus 76 -------------------~il~r~~~~~vG~~~~~~~~~~v~p~~~~~~~~i~i~~~~~~--------~~~~~g~~V~v 128 (654)
T TIGR00358 76 -------------------RILEPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVK--------NELAEGDKVVV 128 (654)
T ss_pred -------------------EEeccCCCEEEEEEEEeCCeEEEEECCCCCCCcEEEcCCccc--------cCCCCCCEEEE
Confidence 23444455566667677889999998864 67888544222 25678999999
Q ss_pred EEEEcC--CC-ceeEEeecCCC
Q psy9900 163 NIGVGK--KD-IEAINVTGPNG 181 (191)
Q Consensus 163 ~i~~~~--kg-~~A~~V~~~~~ 181 (191)
+|..=+ .+ +.+.-++.++.
T Consensus 129 ~i~~~p~~~~~~~g~i~~~lG~ 150 (654)
T TIGR00358 129 ELTEYPLRRNLFYGEITQILGN 150 (654)
T ss_pred EEccCCCCCCCceEEEEEEEcC
Confidence 998733 22 66666666654
No 31
>PRK05054 exoribonuclease II; Provisional
Probab=98.45 E-value=3.9e-06 Score=78.29 Aligned_cols=128 Identities=16% Similarity=0.078 Sum_probs=86.4
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGA 86 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~~ 86 (191)
....|+|+. ..|||||+.+++ .+||||+...+..++ .||+|.+.+....++.+|.-+.+
T Consensus 20 ~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a~---------~GD~V~v~i~~~~~r~~g~v~~i--------- 78 (644)
T PRK05054 20 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDRIIAVIHTEKDREIAEPEEL--------- 78 (644)
T ss_pred CeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCC---------CCCEEEEEEecCCCCcEEEEEEE---------
Confidence 356799984 489999998855 469999999999886 89999999764322333333222
Q ss_pred CCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 87 PKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
+.+...-.|+.|...++++|+.|++.. .+||+....-. ...++.||.|.++|
T Consensus 79 -------------------l~r~~~~~vG~~~~~~~~~~~~p~d~~~~~~i~i~~~~~~-------~~~~~~gd~V~v~i 132 (644)
T PRK05054 79 -------------------IEPFLTRFVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGL-------NHEFKEGDWVVAEL 132 (644)
T ss_pred -------------------EecCCCEEEEEEEEeCceEEEEECCCCCCccEEecccccc-------ccCCCCCCEEEEEE
Confidence 222333445556667789999999864 67888532111 12467899999999
Q ss_pred EEcC----CCceeEEeecCCC
Q psy9900 165 GVGK----KDIEAINVTGPNG 181 (191)
Q Consensus 165 ~~~~----kg~~A~~V~~~~~ 181 (191)
..-+ +.+++.-++.++.
T Consensus 133 ~~~p~~~~~~~~g~i~~~lG~ 153 (644)
T PRK05054 133 RRHPLKGDRGFYAEITQFITD 153 (644)
T ss_pred ecCCCCCCCCceEEEEEEECC
Confidence 8642 2266777776664
No 32
>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=98.37 E-value=1.2e-06 Score=56.80 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=34.2
Q ss_pred CCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCce
Q psy9900 18 SKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIE 71 (191)
Q Consensus 18 ~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~ 71 (191)
+.+||||+.+++.++|||++..++..++ .||+|.+.+....++..
T Consensus 6 ~~~GfGFv~~~~~~~DifIp~~~l~~A~---------~gD~V~v~i~~~~~~~~ 50 (58)
T PF08206_consen 6 HPKGFGFVIPDDGGEDIFIPPRNLNGAM---------DGDKVLVRITPPSRGKR 50 (58)
T ss_dssp -SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSEEE
T ss_pred EcCCCEEEEECCCCCCEEECHHHHCCCC---------CCCEEEEEEecCCCCCC
Confidence 4899999999998899999999999986 99999999998444433
No 33
>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=98.27 E-value=1.9e-05 Score=73.63 Aligned_cols=129 Identities=16% Similarity=0.076 Sum_probs=85.1
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQG 85 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~ 85 (191)
.....|+|+. ..|||||+..++ .+|||++...+..++ .||+|.+.+....+..+|.-+.
T Consensus 16 ~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A~---------~GD~V~v~i~~~~~r~~~~v~~--------- 74 (639)
T TIGR02062 16 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDKIIAVIHSEKERESAEPEE--------- 74 (639)
T ss_pred CceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccCC---------CCCEEEEEEecCCCCcEEEEEE---------
Confidence 3456799985 489999997655 569999999999886 8999999876533323332222
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
++++..+-.|..|...++++|+.|+|.. .+|++ ..-... ...++.||.|.++
T Consensus 75 -------------------iver~~~~~vG~~~~~~~~~~v~p~d~~~~~~i~~--~~~~~~-----~~~~~~gd~V~v~ 128 (639)
T TIGR02062 75 -------------------LIEPFLTRFVGKVQGKDDKLAIVPDHPLLKDAIPC--RAAKGL-----NHEFQEGDWAVAE 128 (639)
T ss_pred -------------------EEccCCCEEEEEEEEeCCeEEEEECCCCCCccEEe--cCcccc-----ccCCCCCCEEEEE
Confidence 2233444556666677889999999853 33333 111110 0245789999999
Q ss_pred EEEcC-CC---ceeEEeecCCC
Q psy9900 164 IGVGK-KD---IEAINVTGPNG 181 (191)
Q Consensus 164 i~~~~-kg---~~A~~V~~~~~ 181 (191)
|.+-+ ++ +++.-++.++.
T Consensus 129 I~~~p~~~~~~~~~~I~~vLG~ 150 (639)
T TIGR02062 129 LRRHPLKGDRSFYAELTQYITF 150 (639)
T ss_pred EeccCCCCCCCceEEEEEEeCC
Confidence 98632 22 67777777664
No 34
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.22 E-value=2.4e-05 Score=73.86 Aligned_cols=126 Identities=24% Similarity=0.265 Sum_probs=87.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC--C-CceeeEeecCCCCCc
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK--K-DIEAINVTGPNGIPV 83 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~--~-g~~A~~v~~~~~~~~ 83 (191)
...|+++. ..+||||+.+++ ...|+||....+..++ .||.|.+++.... + .+.|.-+.+
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~a~---------~GD~Vlv~I~~~~~~~~~~eg~Vv~I------ 130 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNGAM---------HGDRVLVRITGKPDGGDRFEARVIKI------ 130 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCcCC---------CCCEEEEEEecccCCCCCceEEEEEE------
Confidence 35688875 589999999886 4579999998887764 8999999986532 2 234433322
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVD 161 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~ 161 (191)
+.+...-.|+.|...++++|+.|+|.. .+||+..++. ..+..|+.|.
T Consensus 131 ----------------------l~r~~~~~VG~~~~~~~~~~v~p~d~~~~~~I~i~~~~~---------~~~~~g~~v~ 179 (709)
T TIGR02063 131 ----------------------LERANDQIVGTFYIENGIGFVIPDDKRIYLDIFIPPEQI---------LGAEEGDKVL 179 (709)
T ss_pred ----------------------EeeCCCEEEEEEEEcCcEEEEEECCCCCCCCEEECCccc---------cCCCCCCEEE
Confidence 233334455556667789999999874 5788875543 3567899999
Q ss_pred EEEEEcC---CCceeEEeecCCC
Q psy9900 162 FNIGVGK---KDIEAINVTGPNG 181 (191)
Q Consensus 162 f~i~~~~---kg~~A~~V~~~~~ 181 (191)
++|..-+ +-+.+.-++.++.
T Consensus 180 v~i~~~p~~~~~~~g~i~~~lg~ 202 (709)
T TIGR02063 180 VEITKYPDRNRPAIGKVVEILGH 202 (709)
T ss_pred EEEccCCCCCCCceEEEEEEeCC
Confidence 9998643 2266666666654
No 35
>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=98.15 E-value=8.7e-06 Score=52.65 Aligned_cols=49 Identities=29% Similarity=0.361 Sum_probs=35.9
Q ss_pred CCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC--ceeEEee
Q psy9900 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEAINVT 177 (191)
Q Consensus 120 ~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg--~~A~~V~ 177 (191)
.+||||+.+++..+|||++..++..+ -.||+|.+.+...+++ +++.-|+
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITPPSRGKRPEGEVVE 57 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSEEEEEEEEEE
T ss_pred cCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEecCCCCCCCCEEEEe
Confidence 79999999999889999999999865 6899999999994443 5555443
No 36
>PF14444 S1-like: S1-like
Probab=97.35 E-value=0.00087 Score=43.07 Aligned_cols=48 Identities=21% Similarity=0.324 Sum_probs=40.0
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
+..+|.|..+. ..|||| .++|||+.+.+.+. .++.||+|.++...++.
T Consensus 2 r~~~GvVTkl~--~~yG~I-----De~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~ 49 (58)
T PF14444_consen 2 RVFTGVVTKLC--DDYGFI-----DEDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPN 49 (58)
T ss_pred ceEEEEEEEEe--CCcceE-----cccEEEEcccEecC-------CCccCCEEEEEEEeCCC
Confidence 35789999994 679999 36899999998863 56999999999998876
No 37
>PF14444 S1-like: S1-like
Probab=97.32 E-value=0.00096 Score=42.86 Aligned_cols=47 Identities=21% Similarity=0.327 Sum_probs=39.8
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
..+|.|..+. -.|||| .+||||+.+.+.+. .|+.||+|.++...+++
T Consensus 3 ~~~GvVTkl~--~~yG~I-----De~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~ 49 (58)
T PF14444_consen 3 VFTGVVTKLC--DDYGFI-----DEDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPN 49 (58)
T ss_pred eEEEEEEEEe--CCcceE-----cccEEEEcccEecC-------CCccCCEEEEEEEeCCC
Confidence 3589999995 789999 46899999998753 55899999999998877
No 38
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.95 E-value=0.038 Score=46.31 Aligned_cols=127 Identities=20% Similarity=0.186 Sum_probs=84.3
Q ss_pred CceeceeccceEEEEeeCCCCeeEEE-eCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-ceeeEeecC
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFIT-RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGP 78 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~-~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A~~v~~~ 78 (191)
|........+..|..+. .||... -.+.++.|+.|.+.... ..+.+||.|.+-+=.+.++ +.|.-...
T Consensus 1 ~~~~iG~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~-------~e~evGdev~vFiY~D~~~rl~aTt~~p- 69 (287)
T COG2996 1 MMIKIGQINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEE-------DELEVGDEVTVFIYVDSEDRLIATTREP- 69 (287)
T ss_pred CcccccceEEEEEEEee---ceeEEEecCCCceEEeccccCCcC-------CccccCcEEEEEEEECCCCceeheeecc-
Confidence 33445566778888774 556554 44444589999998854 5889999999988877665 44443322
Q ss_pred CCCCccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCccccccc--CCC
Q psy9900 79 NGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS--LGL 156 (191)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~--l~~ 156 (191)
.+..-..|-.+--...+.-|-.....-.+|+++..+++... .+ +++
T Consensus 70 --------------------------~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~------~~~wpq~ 117 (287)
T COG2996 70 --------------------------KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL------KSLWPQK 117 (287)
T ss_pred --------------------------eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc------cccCCCC
Confidence 00111123333333444555544444459999999999853 45 899
Q ss_pred CCEEEEEEEEcCCC
Q psy9900 157 GEIVDFNIGVGKKD 170 (191)
Q Consensus 157 G~~V~f~i~~~~kg 170 (191)
||.+.+.+..+++|
T Consensus 118 Gd~l~v~l~~Dkk~ 131 (287)
T COG2996 118 GDKLLVYLYVDKKG 131 (287)
T ss_pred CCEEEEEEEEccCC
Confidence 99999999999998
No 39
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.78 E-value=0.032 Score=50.78 Aligned_cols=142 Identities=20% Similarity=0.182 Sum_probs=87.0
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcC--CCceeeEeecCCCCCc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGPNGIPV 83 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~--~g~~A~~v~~~~~~~~ 83 (191)
....|+|+... -||....-+.+-+.|+|.+++... ...+....++.||.|.+.+..-+ ++.....+......|-
T Consensus 294 ~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~ 370 (491)
T PRK13806 294 DKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPW 370 (491)
T ss_pred CEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChh
Confidence 45678888774 488877665568899999998631 00011235789999999987532 2322333322111110
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
.. . ...........|+|+... .||.+..-+.+-+-|+|.+.+.......-...++.||.|.+.
T Consensus 371 ~~--~------------~~~~~vG~~v~G~V~~i~---~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~ 433 (491)
T PRK13806 371 AD--V------------AERFAPGTTVTGTVEKRA---QFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLV 433 (491)
T ss_pred HH--h------------hhhCCCCCEEEEEEEEEe---cCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEE
Confidence 00 0 001223457889998863 466654444489999999998753211224678999999998
Q ss_pred EEEcC
Q psy9900 164 IGVGK 168 (191)
Q Consensus 164 i~~~~ 168 (191)
|..-+
T Consensus 434 V~~id 438 (491)
T PRK13806 434 VEEID 438 (491)
T ss_pred EEEEe
Confidence 77644
No 40
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=96.66 E-value=0.0044 Score=42.43 Aligned_cols=62 Identities=23% Similarity=0.498 Sum_probs=37.7
Q ss_pred ceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900 10 RGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG 80 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~ 80 (191)
.|.+-- ...|||||... -+..||||..+.++. -.|+.||.|+-.+.....+ ..-..|..+++
T Consensus 4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg 73 (78)
T PF07497_consen 4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREGEKYFALLRVESVNG 73 (78)
T ss_dssp EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence 455552 35799999987 245899999999986 4789999999998875544 23344444433
No 41
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.59 E-value=0.031 Score=53.01 Aligned_cols=124 Identities=23% Similarity=0.215 Sum_probs=89.6
Q ss_pred ceEEEEeeCCCCeeEEEeCC--CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-C--ceeeEeecCCCCCcc
Q psy9900 10 RGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D--IEAINVTGPNGIPVQ 84 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~--~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g--~~A~~v~~~~~~~~~ 84 (191)
.|++.+ ..+||||+.+++ ...|+|+....+..++ .||.|.+++....+ + ..|.-+
T Consensus 71 ~~~~~~--~~~gf~f~~~~~~~~~~d~~v~~~~~~~a~---------~gD~V~v~~~~~~~~~~~~~~~v~--------- 130 (706)
T COG0557 71 EGIVEA--SAKGFGFLSPDDSKDADDIFVPKDPLNRAL---------HGDRVLVELLPSDKRGRFKEAAVV--------- 130 (706)
T ss_pred cceEEe--ccCCceeeccCccCCCCcEEeccccccccc---------cCCEEEEEECcccccCCCceEEEE---------
Confidence 344443 379999999998 6789999999988775 99999999865444 3 122222
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCC--CcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNK--EDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 162 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~--~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f 162 (191)
.++.+....+|+.|-...+.+++.+.|.. .++++--+... .+..|+.|.+
T Consensus 131 -------------------~il~r~~~~~vG~~~~~~~~~~~~p~d~r~~~~i~i~~~~~~---------~~~~~~~v~~ 182 (706)
T COG0557 131 -------------------RILERANSALVGELRPSQGIGRVLPDDKRLPFLIAIPPEQAP---------GAEEGHLVVV 182 (706)
T ss_pred -------------------eeeccccceeEEEEEecCCeEEEEecCCCCccceeecccccc---------ccccCCEEEE
Confidence 34556778888898888889999998854 25676554444 4578999999
Q ss_pred EEEEcCCC---ceeEEeecCCC
Q psy9900 163 NIGVGKKD---IEAINVTGPNG 181 (191)
Q Consensus 163 ~i~~~~kg---~~A~~V~~~~~ 181 (191)
+|..-... +...-+..++.
T Consensus 183 ~i~~~~~~~~~~~g~v~~~lG~ 204 (706)
T COG0557 183 EITRWPDTSRPPFGEVVEVLGD 204 (706)
T ss_pred EecccCCcCCCCceeEEEeecC
Confidence 99995543 55555665554
No 42
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.56 E-value=0.063 Score=48.85 Aligned_cols=150 Identities=17% Similarity=0.155 Sum_probs=89.0
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE-cCC-CceeeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKK-DIEAINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~-~~~-g~~A~~v~~~~~~~~~ 84 (191)
...+|+|+... .||.+..-. +-+.|+|.++|......+....++.||.|++.+.. ++. +............|-.
T Consensus 210 ~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~ 285 (486)
T PRK07899 210 QVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQ 285 (486)
T ss_pred CEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchh
Confidence 34679999874 466655444 58999999999753211112346899999999765 332 3222222221111110
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
.. .........+.|+|... ..||++..-+.+-+-++|++++.......--..++.||.|.+.|
T Consensus 286 --------~~------~~~~~vG~vv~G~V~~I---~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkI 348 (486)
T PRK07899 286 --------QF------ARTHAIGQIVPGKVTKL---VPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKV 348 (486)
T ss_pred --------hh------HHhcCCCCEEEEEEEEE---eccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEE
Confidence 00 00022345688999887 34888777665789999999997531111113479999999998
Q ss_pred EEcC--CCceeEEee
Q psy9900 165 GVGK--KDIEAINVT 177 (191)
Q Consensus 165 ~~~~--kg~~A~~V~ 177 (191)
..-+ ++.-...++
T Consensus 349 i~ID~e~rrI~LSlK 363 (486)
T PRK07899 349 IDIDLERRRISLSLK 363 (486)
T ss_pred EEEECCCCEEEEEEE
Confidence 7744 343333444
No 43
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=96.45 E-value=0.012 Score=40.38 Aligned_cols=64 Identities=25% Similarity=0.549 Sum_probs=41.2
Q ss_pred eeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---ceeEEeecCCCC
Q psy9900 111 RGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNGI 182 (191)
Q Consensus 111 ~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---~~A~~V~~~~~~ 182 (191)
.|++-.. .+||||+...+ +..||||..+.+.. -.|+.||.|+=.+.....+ ..-+.|.-++|.
T Consensus 4 ~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~ 74 (78)
T PF07497_consen 4 EGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREGEKYFALLRVESVNGR 74 (78)
T ss_dssp EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STTSSSEEECEECEETTE
T ss_pred EEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCc
Confidence 4555533 57999999972 35899999999986 5899999999888886555 345566666654
Q ss_pred C
Q psy9900 183 P 183 (191)
Q Consensus 183 ~ 183 (191)
+
T Consensus 75 ~ 75 (78)
T PF07497_consen 75 P 75 (78)
T ss_dssp C
T ss_pred C
Confidence 3
No 44
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.19 E-value=0.15 Score=46.40 Aligned_cols=153 Identities=19% Similarity=0.164 Sum_probs=88.9
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--c----eeeEeecCCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--I----EAINVTGPNG 80 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~----~A~~v~~~~~ 80 (191)
...+|+|+... .||.+..-..+-+.|+|.+++......+.-..+..||.|.+.+..-... . -.........
T Consensus 204 ~iv~G~V~~v~---~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~ 280 (491)
T PRK13806 204 DVVEGTVTRLA---PFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGG 280 (491)
T ss_pred CEEEEEEEEEe---CCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhc
Confidence 34579999874 3666655544689999999996431111123467999999998653321 1 1122221110
Q ss_pred CCccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCE
Q psy9900 81 IPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEI 159 (191)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~ 159 (191)
.|- .. -.........+.|+|.... .||.+.....+-+.|+|.+++.... ...--..++.||.
T Consensus 281 ~p~--------~~------~~~~~~~G~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~ 343 (491)
T PRK13806 281 DPW--------DT------VGDRLKAGDKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDA 343 (491)
T ss_pred ccc--------hh------hhccCCCCCEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCE
Confidence 000 00 0011233467889998873 4888776655789999999986310 0001135899999
Q ss_pred EEEEEEEcC--CCceeEEeecC
Q psy9900 160 VDFNIGVGK--KDIEAINVTGP 179 (191)
Q Consensus 160 V~f~i~~~~--kg~~A~~V~~~ 179 (191)
|.+.|..-+ ++.-...++.+
T Consensus 344 v~vkVl~iD~e~~ri~Ls~K~~ 365 (491)
T PRK13806 344 VAVKIKDIDPAKRRISLSLRDA 365 (491)
T ss_pred EEEEEEEEEccCCEEEEEEeec
Confidence 999998643 33333444433
No 45
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=95.92 E-value=0.23 Score=48.26 Aligned_cols=152 Identities=16% Similarity=0.140 Sum_probs=90.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG 85 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~ 85 (191)
..+|+|+... .||.+..-+ +-+-|+|.|.+....-.+....+..|+.|++.+..-++ +.-..........|
T Consensus 496 ~V~G~Vk~i~---~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p--- 568 (863)
T PRK12269 496 SVSGVVKSFT---SFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDP--- 568 (863)
T ss_pred EEEEEEEEEe---CCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccch---
Confidence 4689999885 467766554 56899999998643100012336789999999875443 32222222111100
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc-CcccccccCCCCCEEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~-~~~~~~~~l~~G~~V~f~i 164 (191)
... -.........++|+|+... .||.+..-..+-+-++|++++... ....-...++.||.|.+.|
T Consensus 569 --~~~---------~~~~~~vG~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkV 634 (863)
T PRK12269 569 --WLE---------FENKFGVNDVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMI 634 (863)
T ss_pred --hhh---------hhccCCCCCEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEE
Confidence 000 0011334467899999884 488766665578889999998641 1011124589999999998
Q ss_pred EEcCC--CceeEEeecCC
Q psy9900 165 GVGKK--DIEAINVTGPN 180 (191)
Q Consensus 165 ~~~~k--g~~A~~V~~~~ 180 (191)
..-+. +.-...++-+.
T Consensus 635 l~iD~e~~rIsLS~K~l~ 652 (863)
T PRK12269 635 LGYDIQAGRVSLGLKQVT 652 (863)
T ss_pred EEEecccCceEEEehhcc
Confidence 88543 34444554433
No 46
>PRK11642 exoribonuclease R; Provisional
Probab=95.80 E-value=0.027 Score=54.26 Aligned_cols=63 Identities=21% Similarity=0.183 Sum_probs=49.4
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE-cCCC-ceeEEeecCCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKD-IEAINVTGPNGI 182 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~-~~kg-~~A~~V~~~~~~ 182 (191)
.+.|+|..- .+||||+.++++++|||++-..+..+ -.||.|.+.+.. +.+| ++|.-|.++..+
T Consensus 84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~A---------~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~ 148 (813)
T PRK11642 84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKTC---------IHGDQVLAQPLGADRKGRREARIVRVLVPK 148 (813)
T ss_pred eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHccC---------CCCCEEEEEEccCCCCCCcEEEEEEEEecC
Confidence 467888864 79999999987678999998887754 579999999876 3333 788888887764
No 47
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=95.70 E-value=0.22 Score=48.44 Aligned_cols=143 Identities=14% Similarity=0.147 Sum_probs=89.2
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPV 83 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~ 83 (191)
...+|+|+... -||.+..-..+-+-|+|.|++.-. ...+....++.||.|.+.+-.-+. +.....+......|-
T Consensus 580 ~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw 656 (863)
T PRK12269 580 DVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPW 656 (863)
T ss_pred CEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCch
Confidence 45689999885 488776665567889999998641 111123457999999999876432 333333322111110
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc-ccccccCCCCCEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDF 162 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~-~~~~~~l~~G~~V~f 162 (191)
. .. ..........+|+|+.. ..||.+..-..+-+-|+|.+++.-... ...-..+++||.|.+
T Consensus 657 ~--------~~------~~~~~vG~~v~G~V~~i---~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~Vkv 719 (863)
T PRK12269 657 E--------EI------EARYPVGARFTRRIVKV---TNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIEC 719 (863)
T ss_pred H--------HH------HHhCCCCCEEEEEEEEE---ecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEE
Confidence 0 00 01133456788999886 347777666568899999999864210 001135899999999
Q ss_pred EEEEcCC
Q psy9900 163 NIGVGKK 169 (191)
Q Consensus 163 ~i~~~~k 169 (191)
.|..-+.
T Consensus 720 kVl~ID~ 726 (863)
T PRK12269 720 MVIECDP 726 (863)
T ss_pred EEEEEec
Confidence 9888654
No 48
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=95.70 E-value=0.025 Score=37.71 Aligned_cols=41 Identities=32% Similarity=0.464 Sum_probs=33.7
Q ss_pred CCCeeEEEeCC-----CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 19 KRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 19 ~kGfGFI~~~~-----~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
..|||||...+ ...||||+.+-++. -.|+.||.|+-.+...
T Consensus 9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p 54 (68)
T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPP 54 (68)
T ss_pred CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCC
Confidence 34999999762 45899999999996 4789999999988753
No 49
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=95.64 E-value=0.52 Score=40.56 Aligned_cols=148 Identities=14% Similarity=0.040 Sum_probs=91.2
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC-Cce-eeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-DIE-AINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~-g~~-A~~v~~~~~~~~~ 84 (191)
...+|+|+..+ .+|++..-+ +-+-|+|.|.+.... ......|+.|.+.+..-+. ..+ ...........
T Consensus 120 ~~V~g~V~~~~---~~G~~V~l~-Gv~gfip~s~ls~~~----~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~-- 189 (318)
T PRK07400 120 ATVRSEVFATN---RGGALVRIE-GLRGFIPGSHISTRK----PKEELVGEELPLKFLEVDEERNRLVLSHRRALVER-- 189 (318)
T ss_pred CEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcCccC----CccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhh--
Confidence 44678888885 346666554 668899999997532 1233499999999865332 211 11111000000
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
. .........+.|+|+... .||...... +-+-++|.+++.......-...++.||.|.+.+
T Consensus 190 ---------~------~~~~k~G~vv~G~V~~I~---~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkV 250 (318)
T PRK07400 190 ---------K------MNRLEVGEVVVGTVRGIK---PYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMI 250 (318)
T ss_pred ---------h------hccCCCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEE
Confidence 0 001223456889998874 488877664 678999999997542112234579999999999
Q ss_pred EEcC--CCceeEEeecCCCCC
Q psy9900 165 GVGK--KDIEAINVTGPNGIP 183 (191)
Q Consensus 165 ~~~~--kg~~A~~V~~~~~~~ 183 (191)
..-+ +|.-...++.+...|
T Consensus 251 l~iD~e~~rI~LS~K~l~~~P 271 (318)
T PRK07400 251 IDLDAERGRISLSTKQLEPEP 271 (318)
T ss_pred EEEeCCCCEEEEEEeccccCh
Confidence 8865 456666666666544
No 50
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.59 E-value=0.18 Score=46.28 Aligned_cols=140 Identities=16% Similarity=0.195 Sum_probs=92.9
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG 85 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~ 85 (191)
-..|+|+...+ ||-...-.+ -|=++|.+++.-....++..-+..||.|...+-.-+. +.....+......|-.
T Consensus 195 vV~G~V~~It~---~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~- 269 (541)
T COG0539 195 VVEGVVKNITD---YGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWE- 269 (541)
T ss_pred eEEEEEEEeec---CcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHH-
Confidence 45799998864 886666653 8999999999866544456667899999999987554 3334443332211100
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG 165 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~ 165 (191)
. -...........|+|..+. .||.+..-..+-+=|+|+|.+.-.....--.-|+.||.|++.|-
T Consensus 270 ----~---------i~~~~~~g~~v~G~Vt~i~---~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl 333 (541)
T COG0539 270 ----G---------IEKKYPVGDKVEGKVTNLT---DYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVL 333 (541)
T ss_pred ----H---------HhhhcCCCCEEEEEEEEee---cCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEE
Confidence 0 0111444567889998873 47766666668889999998865432112244799999999987
Q ss_pred EcC
Q psy9900 166 VGK 168 (191)
Q Consensus 166 ~~~ 168 (191)
.=+
T Consensus 334 ~id 336 (541)
T COG0539 334 DID 336 (541)
T ss_pred eeC
Confidence 744
No 51
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=95.42 E-value=0.049 Score=36.31 Aligned_cols=48 Identities=31% Similarity=0.514 Sum_probs=37.3
Q ss_pred eeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 112 GIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
|++-.. ..||||+...+ +..||||+.+.+.. -.|+.||.|+=.+....
T Consensus 3 GiLdi~--~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p~ 55 (68)
T cd04459 3 GVLEIL--PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPPK 55 (68)
T ss_pred EEEEEc--CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCCC
Confidence 444433 34899999863 35899999999997 58999999998887643
No 52
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=95.37 E-value=0.96 Score=39.70 Aligned_cols=156 Identities=19% Similarity=0.196 Sum_probs=88.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~~ 84 (191)
....|+|+.... ||....-. +-+.|+|.+.+......+....++.||.|.+.+..- +. +.-..........|-
T Consensus 194 ~~v~g~V~~v~~---~G~fV~l~-~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~- 268 (390)
T PRK06676 194 DVVEGTVARLTD---FGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPW- 268 (390)
T ss_pred CEEEEEEEEEec---ceEEEEeC-CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc-
Confidence 456788988642 55444333 478999999986431100113468999999998653 32 322222221110000
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
... .........+.|+|.... .||+...-+.+-+-++|.+++.......--..++.||.|...+
T Consensus 269 -------~~~------~~~~~~G~~v~g~V~~i~---~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V 332 (390)
T PRK06676 269 -------EGV------EEKLPEGDVIEGTVKRLT---DFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKV 332 (390)
T ss_pred -------ccc------hhhhcCCcEEEEEEEEEe---CceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEE
Confidence 000 001223456889998864 3887666555678899999986421000113478999999998
Q ss_pred EEcC--CCceeEEeecCCCCC
Q psy9900 165 GVGK--KDIEAINVTGPNGIP 183 (191)
Q Consensus 165 ~~~~--kg~~A~~V~~~~~~~ 183 (191)
..-+ ++.-...++.+...|
T Consensus 333 ~~id~e~~~i~ls~k~~~~~~ 353 (390)
T PRK06676 333 LEVNEEEKRISLSIKALEEAP 353 (390)
T ss_pred EEEECCCCEEEEEEEecccCh
Confidence 8865 344444455444433
No 53
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=95.30 E-value=0.64 Score=43.79 Aligned_cols=154 Identities=23% Similarity=0.162 Sum_probs=89.6
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~~ 84 (191)
....|+|+... .||++..- ++-+.|+|.+++...........++.||.|.+.+..- +. +.-..........|-.
T Consensus 479 ~iV~g~V~~v~---~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~ 554 (647)
T PRK00087 479 DVVEGEVKRLT---DFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWE 554 (647)
T ss_pred CEEEEEEEEEe---CCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhh
Confidence 45688998874 35655444 4678999999986421111123578999999998653 22 3222222211111100
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
.. .........+.|+|.... .||+...-+.+-+-++|.+++.......--..++.||.|...+
T Consensus 555 --------~~------~~~~~~G~~v~g~V~~i~---~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV 617 (647)
T PRK00087 555 --------NV------EEKYPVGSIVLGKVVRIA---PFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKI 617 (647)
T ss_pred --------hh------hhhccCCeEEEEEEEEEE---CCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEE
Confidence 00 000123456889998874 3777666555789999999987531111113579999999998
Q ss_pred EEcC--CCceeEEeecCCC
Q psy9900 165 GVGK--KDIEAINVTGPNG 181 (191)
Q Consensus 165 ~~~~--kg~~A~~V~~~~~ 181 (191)
..-+ ++.-...++.+..
T Consensus 618 ~~id~e~~rI~lslk~~~~ 636 (647)
T PRK00087 618 LEVDPEEKRIRLSIKEVEE 636 (647)
T ss_pred EEEeCCCCEEEEEEeeccc
Confidence 8754 3444444554443
No 54
>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=95.26 E-value=0.069 Score=50.31 Aligned_cols=63 Identities=27% Similarity=0.372 Sum_probs=48.8
Q ss_pred eeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEE-cCCC-ceeEEeecCCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKD-IEAINVTGPNGI 182 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~-~~kg-~~A~~V~~~~~~ 182 (191)
...|+|+.- .+||||+.++++ ++|||+.-.++..+ -.||.|.+.+.. +++| ++|.-+.++..+
T Consensus 16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~a---------~~GD~V~v~i~~~~~~~~~~g~v~~il~r~ 81 (654)
T TIGR00358 16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKKV---------MHGDLVEACPLSQPQRGRFEAEVERILEPA 81 (654)
T ss_pred eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCcC---------CCCCEEEEEEeecCCCCCceEEEEEEeccC
Confidence 467999874 799999999863 68999998877654 579999999865 3344 588888877653
No 55
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=95.11 E-value=0.092 Score=49.37 Aligned_cols=62 Identities=23% Similarity=0.256 Sum_probs=46.9
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~ 181 (191)
....|+|+.- .+||||+.+++ .+|||++-..+..+ -.||.|.+.+....++.+|.-+.++..
T Consensus 17 ~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A---------~~GD~V~v~i~~~~~r~~~~v~~iver 78 (639)
T TIGR02062 17 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDKIIAVIHSEKERESAEPEELIEP 78 (639)
T ss_pred ceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecCCCCcEEEEEEEEcc
Confidence 4567999864 79999997654 57999999988754 579999999876444466666666644
No 56
>PRK05054 exoribonuclease II; Provisional
Probab=95.07 E-value=0.084 Score=49.64 Aligned_cols=62 Identities=23% Similarity=0.240 Sum_probs=46.8
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNG 181 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~~~ 181 (191)
....|+|..- .+||||+.+++ .+|||++-..+..+ -.||.|.+.+....++.+|.-+.++..
T Consensus 20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a---------~~GD~V~v~i~~~~~r~~g~v~~il~r 81 (644)
T PRK05054 20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHTEKDREIAEPEELIEP 81 (644)
T ss_pred CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecCCCCcEEEEEEEEec
Confidence 3467999864 79999998854 56999999988754 579999999876444467776666654
No 57
>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=95.01 E-value=1.3 Score=40.32 Aligned_cols=142 Identities=16% Similarity=0.169 Sum_probs=85.3
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC-CCcccCCCCCEEEEEEEEcC-C-CceeeEeecCCCCCc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-KFFQSLGLGEIVDFNIGVGK-K-DIEAINVTGPNGIPV 83 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~-~g~~~l~~Gd~V~f~~~~~~-~-g~~A~~v~~~~~~~~ 83 (191)
....|+|+.- ..||+...-+.+-+.|+|.+++...... .....++.||.|.+.+..-+ . +.-..........|-
T Consensus 361 ~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~ 437 (516)
T TIGR00717 361 DRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPW 437 (516)
T ss_pred CEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCch
Confidence 4567888875 4567776666678999999998632100 01246789999999865433 2 332222221111110
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
... ...........|+|... ..||+...-+.+-+-|+|.+++.......-...++.||.|.+.
T Consensus 438 --------~~~------~~~~~~G~~v~g~V~~v---~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~ 500 (516)
T TIGR00717 438 --------EKF------AAKYKVGSVVKGKVTEI---KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAK 500 (516)
T ss_pred --------hhh------hhccCcceEEEEEEEEE---ecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEE
Confidence 000 00122345688999886 3478655555578999999998643111124578999999999
Q ss_pred EEEcC
Q psy9900 164 IGVGK 168 (191)
Q Consensus 164 i~~~~ 168 (191)
|..-+
T Consensus 501 V~~id 505 (516)
T TIGR00717 501 VVDID 505 (516)
T ss_pred EEEEe
Confidence 87643
No 58
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=94.77 E-value=1.4 Score=40.67 Aligned_cols=140 Identities=19% Similarity=0.238 Sum_probs=83.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE-cC-CCceeeEeecCCCCCccC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GK-KDIEAINVTGPNGIPVQG 85 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~-~~-~g~~A~~v~~~~~~~~~~ 85 (191)
...|+|+... -||....-+ +-+.|+|.+.+......+....++.||.|.+.+.. ++ ++.-..........|-..
T Consensus 204 iv~g~V~~v~---~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~ 279 (565)
T PRK06299 204 VVEGVVKNIT---DYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEA 279 (565)
T ss_pred EEEEEEEEEe---CCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHH
Confidence 3678888764 467666555 68999999998643110112336899999999764 33 343333332211111000
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCEEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i 164 (191)
. .........+.|+|... ..||+...-..+-+.|+|.+++.... .......++.|+.|.+.|
T Consensus 280 --------~------~~~~~~G~~v~g~V~~i---~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V 342 (565)
T PRK06299 280 --------I------EKKYPVGSKVKGKVTNI---TDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMV 342 (565)
T ss_pred --------H------HhhCCCCCEEEEEEEEE---eCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEE
Confidence 0 00123345788999886 34787766555789999999986321 000113478999999988
Q ss_pred EEcC
Q psy9900 165 GVGK 168 (191)
Q Consensus 165 ~~~~ 168 (191)
..-+
T Consensus 343 ~~id 346 (565)
T PRK06299 343 LEID 346 (565)
T ss_pred EEEc
Confidence 7643
No 59
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=94.75 E-value=0.47 Score=43.66 Aligned_cols=144 Identities=19% Similarity=0.171 Sum_probs=87.9
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCc
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPV 83 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~ 83 (191)
.....|+|..+- -||.+..-..+-+-|+|.|.+.-..-..+-..|+.||.|++.+-.-+. ..--.++.-....|-
T Consensus 278 g~~v~G~Vt~i~---~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw 354 (541)
T COG0539 278 GDKVEGKVTNLT---DYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPW 354 (541)
T ss_pred CCEEEEEEEEee---cCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChh
Confidence 345779998874 577776666688999999977544211123457999999999865332 221222222111111
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
.. -....+.....+|.|+... .||-+.-.+++-|=|+|.+++.-..+..-...++.|+.|+..
T Consensus 355 ~~--------------~~~~~~~g~~v~g~v~~~t---~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~ 417 (541)
T COG0539 355 EE--------------FADKHPVGDVVEGKVKSIT---DFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAK 417 (541)
T ss_pred hh--------------hhhhcCCCCeEEEEEeeec---ccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEE
Confidence 00 0011344567899998873 366444444579999999999743221212266899999998
Q ss_pred EEEcCC
Q psy9900 164 IGVGKK 169 (191)
Q Consensus 164 i~~~~k 169 (191)
+..-+.
T Consensus 418 vl~vd~ 423 (541)
T COG0539 418 VLAVDK 423 (541)
T ss_pred EEEEec
Confidence 877544
No 60
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=94.52 E-value=1.2 Score=41.06 Aligned_cols=150 Identities=16% Similarity=0.143 Sum_probs=88.5
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCC-CCCcccCCCCCEEEEEEEEc-CC-CceeeEeecCCCCCc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDFNIGVG-KK-DIEAINVTGPNGIPV 83 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~-~~g~~~l~~Gd~V~f~~~~~-~~-g~~A~~v~~~~~~~~ 83 (191)
....|+|+... .||+...-+.+-+.|+|.+++..... ......++.||.|.+.+..- +. +.-..........|.
T Consensus 375 ~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~ 451 (565)
T PRK06299 375 DVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPF 451 (565)
T ss_pred CEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCch
Confidence 45678888864 56777666556899999999974210 11235678999999987643 22 332333322111110
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCce-eEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFG-FITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 162 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfG-FI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f 162 (191)
. .. ...........|+|..... || |+... .+-.-|+|.+.+.......-...++.||.|..
T Consensus 452 ~--------~~------~~~~~~G~vV~G~V~~v~~---~G~fV~l~-~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~ 513 (565)
T PRK06299 452 E--------EF------AKKHKKGSIVTGTVTEVKD---KGAFVELE-DGVEGLIRASELSRDRVEDATEVLKVGDEVEA 513 (565)
T ss_pred h--------HH------HhhcCCCCEEEEEEEEEec---CceEEecC-CCcEEEEEHHHhcchhccCccccCCCCCEEEE
Confidence 0 00 0001234568899988753 46 45554 37889999999854311122456799999999
Q ss_pred EEEEcC--CCceeEEee
Q psy9900 163 NIGVGK--KDIEAINVT 177 (191)
Q Consensus 163 ~i~~~~--kg~~A~~V~ 177 (191)
.+..-+ ++.-...++
T Consensus 514 ~V~~vd~~~~~i~LS~k 530 (565)
T PRK06299 514 KVINIDRKNRRISLSIK 530 (565)
T ss_pred EEEEEccccCEEEEEee
Confidence 988744 343333333
No 61
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.21 E-value=0.15 Score=33.03 Aligned_cols=52 Identities=19% Similarity=0.292 Sum_probs=33.2
Q ss_pred eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeE
Q psy9900 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAI 174 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~ 174 (191)
-+|...+ .+|+....+.+.+|++|.+.+. ..++.||.|++-+-.+.++ +.|+
T Consensus 7 L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~D~~~rl~AT 59 (61)
T PF13509_consen 7 LKVVDKN---EFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYLDKEGRLVAT 59 (61)
T ss_dssp --EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-EEEE
T ss_pred eEEEEEe---CCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEECCCCCEEEe
Confidence 3454443 5777777666799999999987 3689999999999999988 5553
No 62
>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=93.79 E-value=0.19 Score=47.74 Aligned_cols=63 Identities=25% Similarity=0.323 Sum_probs=47.3
Q ss_pred eeeeeEEEeecCCCceeEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc---CCCceeEEeecCCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG---KKDIEAINVTGPNGI 182 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~---~kg~~A~~V~~~~~~ 182 (191)
.+.|+++. ..+||||+.+++ ...|+|+...++.. +..||.|.+.+... .+.++|.-|++++.+
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~---------a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~ 134 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG---------AMHGDRVLVRITGKPDGGDRFEARVIKILERA 134 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc---------CCCCCEEEEEEecccCCCCCceEEEEEEEeeC
Confidence 46787765 378999999986 35799998776654 46899999998764 234788877777654
No 63
>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=93.53 E-value=2.2 Score=38.86 Aligned_cols=142 Identities=16% Similarity=0.167 Sum_probs=83.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC-CCCCcccCCCCCEEEEEEEE-cCC-CceeeEeecCCCCCc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGV-GKK-DIEAINVTGPNGIPV 83 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~-~~~g~~~l~~Gd~V~f~~~~-~~~-g~~A~~v~~~~~~~~ 83 (191)
...+|+|+... .||.+..-..+-+.|+|.+++.... ..+....+..||.|.+.+.. ++. +.-..........|-
T Consensus 274 ~i~~g~V~~v~---~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~ 350 (516)
T TIGR00717 274 DKITGRVTNLT---DYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPW 350 (516)
T ss_pred CEEEEEEEEee---CCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcH
Confidence 34578898864 5675544334678999999886320 00011247899999999764 443 333333222111110
Q ss_pred cCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcc-cccccCCCCCEEEE
Q psy9900 84 QGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-KFFQSLGLGEIVDF 162 (191)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~-~~~~~l~~G~~V~f 162 (191)
... ...........|+|+.. ..||....-+.+.+.|+|.+++....+. .-...++.|+.|.+
T Consensus 351 --------~~~------~~~~~~G~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~ 413 (516)
T TIGR00717 351 --------EQF------EEKHPVGDRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEA 413 (516)
T ss_pred --------HHH------HHhCCCCCEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEE
Confidence 000 00122345688999875 4567766666689999999998632100 01246789999999
Q ss_pred EEEEcC
Q psy9900 163 NIGVGK 168 (191)
Q Consensus 163 ~i~~~~ 168 (191)
.+..-+
T Consensus 414 ~Vl~vd 419 (516)
T TIGR00717 414 VVLAVD 419 (516)
T ss_pred EEEEEe
Confidence 876643
No 64
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=93.34 E-value=0.22 Score=44.30 Aligned_cols=70 Identities=29% Similarity=0.430 Sum_probs=52.3
Q ss_pred eeeeeEEEeecCCCceeEEeCCC-----CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC---CCceeEEeecCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDN-----KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK---KDIEAINVTGPN 180 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~-----~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~---kg~~A~~V~~~~ 180 (191)
...|++... ..||||+...+. ..||||..+.+.. -.|+.||.|+=.+..-+ |.+.-..|..++
T Consensus 50 ~~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vn 120 (416)
T PRK09376 50 FGEGVLEIL--PDGFGFLRSPDANYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKIRPPKEGERYFALLKVETVN 120 (416)
T ss_pred EEEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEeeCCCCCCCccceEEEeeeC
Confidence 356777665 349999998643 3899999999997 58999999998887643 335667888888
Q ss_pred CCCCCCC
Q psy9900 181 GIPVQGA 187 (191)
Q Consensus 181 ~~~~~~~ 187 (191)
|.+....
T Consensus 121 g~~~~~~ 127 (416)
T PRK09376 121 GEDPEKA 127 (416)
T ss_pred CCCHHHh
Confidence 7664433
No 65
>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=93.11 E-value=0.82 Score=31.72 Aligned_cols=62 Identities=18% Similarity=0.086 Sum_probs=40.8
Q ss_pred cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc---CcccccccCCCCCEEEEEEEEcC
Q psy9900 106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM---NPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~---~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....+.|+|+...+.- +|.+..-+.+.+-|+|++++... ....--..++.||.|.+.+..-.
T Consensus 7 ~G~iy~g~V~~i~~~~-~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~ 71 (88)
T cd04453 7 VGNIYLGRVKKIVPGL-QAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP 71 (88)
T ss_pred CCCEEEEEEEEeccCC-cEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence 3456889999884322 45555544478999999998430 00001246899999999998843
No 66
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.60 E-value=1 Score=29.17 Aligned_cols=59 Identities=17% Similarity=0.181 Sum_probs=41.0
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
.+.|+|.... .||.+..-..+-+-|+|.+++.......-...++.||.|++.+..-++.
T Consensus 3 ~~~g~V~~v~---~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 3 KTHGTIVKVK---PNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred EEEEEEEEEe---cCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCC
Confidence 4678888873 3666665555689999999997432111123488999999999886654
No 67
>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=92.50 E-value=1.1 Score=30.31 Aligned_cols=60 Identities=15% Similarity=0.051 Sum_probs=43.6
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
...+.|+|+... .||.+..-..+-+.|+|.+++.......-...++.||.|++.+..-+.
T Consensus 15 G~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 15 GMVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CCEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 356789998874 388877766678999999999654211112457889999999988654
No 68
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=92.48 E-value=2.8 Score=38.30 Aligned_cols=140 Identities=16% Similarity=0.102 Sum_probs=79.2
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCccc--CCCCCEEEEEEEEcCCCceeeEeecCCCCCccC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS--LGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQG 85 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~--l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~ 85 (191)
..+|+|+... + +|++..- +-.-|+|.|.+.... ... ...|+.|.|.+..-++...-..+........
T Consensus 125 ~V~G~V~~v~--k-~G~~Vdl--Gi~gflP~Sel~~~~----~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~-- 193 (486)
T PRK07899 125 VVTGTVIEVV--K-GGLILDI--GLRGFLPASLVEMRR----VRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQ-- 193 (486)
T ss_pred EEEEEEEEEE--C-CeEEEEE--CCEEEEEhhHhcccc----cCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHh--
Confidence 5689999985 2 4666655 357999999876431 112 2489999999987544322111111000000
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG 165 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~ 165 (191)
.. .... . .-.........+.|+|+... .||.+..-. +-+.|+|.+++.......--..++.||.|++.|.
T Consensus 194 -~~--~~~~-~--~~~~~lk~G~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl 263 (486)
T PRK07899 194 -TQ--SEVR-S--EFLNQLQKGQVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVL 263 (486)
T ss_pred -hh--HHHH-H--HHHHhccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEE
Confidence 00 0000 0 00001223456889999873 366655544 6899999999975311011134689999999977
Q ss_pred EcC
Q psy9900 166 VGK 168 (191)
Q Consensus 166 ~~~ 168 (191)
.-+
T Consensus 264 ~iD 266 (486)
T PRK07899 264 DVD 266 (486)
T ss_pred EEE
Confidence 633
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=92.43 E-value=2.7 Score=36.86 Aligned_cols=141 Identities=12% Similarity=0.036 Sum_probs=79.3
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~ 84 (191)
...+|+|+..+. .+=||..+..+-+.|+|.+++......+....+..||.|++.+..... +.-...........
T Consensus 19 ~iv~G~V~~i~~--~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~-- 94 (390)
T PRK06676 19 DVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEK-- 94 (390)
T ss_pred CEEEEEEEEEEC--CeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhh--
Confidence 446799999963 334454434467899999999653222233457899999999876543 21111111110000
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i 164 (191)
.. ... ....-......|+|.... + +|++..-+ +-..|+|.+++..... ..... ..|+.|.|.|
T Consensus 95 ---~~--~~~------~~~~~~G~~v~g~V~~v~--~-~G~~V~~~-G~~gflp~~el~~~~~-~~~~~-~vG~~v~~~V 157 (390)
T PRK06676 95 ---AW--DKL------EEKFEEGEVVEVKVTEVV--K-GGLVVDVE-GVRGFIPASLISTRFV-EDFSD-FKGKTLEVKI 157 (390)
T ss_pred ---hH--HHH------HHhccCCCEEEEEEEEEE--C-CeEEEEEC-CEEEEEEHHHcCCccC-CChHH-cCCCEEEEEE
Confidence 00 000 000122345789998874 3 45555554 4488999998864310 00112 2799999999
Q ss_pred EEcC
Q psy9900 165 GVGK 168 (191)
Q Consensus 165 ~~~~ 168 (191)
..-+
T Consensus 158 l~~d 161 (390)
T PRK06676 158 IELD 161 (390)
T ss_pred EEEE
Confidence 7533
No 70
>COG1158 Rho Transcription termination factor [Transcription]
Probab=92.28 E-value=0.29 Score=42.67 Aligned_cols=72 Identities=26% Similarity=0.422 Sum_probs=54.2
Q ss_pred eeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC--c-eeEEeecCCC
Q psy9900 110 VRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--I-EAINVTGPNG 181 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg--~-~A~~V~~~~~ 181 (191)
..|+.... ..||||+.+.+ +..|||+.-|.+.. -.|+.||.|+=.+..-+.| + .-+.|..+++
T Consensus 54 ~~GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRr-------f~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~ 124 (422)
T COG1158 54 GDGVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKVRPPKEGERYFALLKVEAVNG 124 (422)
T ss_pred eeeEEEec--cCCcceeecCccccCCCCCceEECHHHHhh-------ccCccCCEEeeeecCCCcccceeeeEEEeecCC
Confidence 34676665 48999999876 24899999999997 5899999999998887666 3 3457777777
Q ss_pred CCCCCCCCC
Q psy9900 182 IPVQGAPKV 190 (191)
Q Consensus 182 ~~~~~~~~~ 190 (191)
.+...++.+
T Consensus 125 ~~pe~~~~R 133 (422)
T COG1158 125 DDPEKAKNR 133 (422)
T ss_pred CCHHHhhcc
Confidence 765554443
No 71
>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=92.23 E-value=1.2 Score=29.07 Aligned_cols=60 Identities=20% Similarity=0.237 Sum_probs=44.8
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
..+.|+|...+. +|++..-..+-+.|+|.+++...........+..||.|.+.+..-+..
T Consensus 6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~ 65 (74)
T PF00575_consen 6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKE 65 (74)
T ss_dssp SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETT
T ss_pred CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECC
Confidence 467899998865 777666556899999999998521112347889999999999886554
No 72
>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=91.97 E-value=0.65 Score=28.81 Aligned_cols=55 Identities=20% Similarity=0.222 Sum_probs=38.0
Q ss_pred ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
.|+|+..+ .+|+....+.+.+.|+|.+.+......+....++.||.|.+.+..-.
T Consensus 2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD 56 (65)
T ss_pred EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence 68888886 45554444446899999999875311112356899999999987643
No 73
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=91.94 E-value=2.7 Score=36.22 Aligned_cols=137 Identities=17% Similarity=0.082 Sum_probs=78.7
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCCCCccC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNGIPVQG 85 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~~~~~~ 85 (191)
...|+|.... +. |.+..-...-+-|+|.+++......+....+..||.|+|.+..-.. +.-.........
T Consensus 34 iv~G~V~~i~--~~-g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~----- 105 (318)
T PRK07400 34 IVNGTVFSLE--PR-GALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEY----- 105 (318)
T ss_pred EEEEEEEEEE--CC-EEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhh-----
Confidence 3579999975 33 4444444456889999999754211122347899999999875332 321111111000
Q ss_pred CCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEE
Q psy9900 86 APKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG 165 (191)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~ 165 (191)
..+=.+. ..........+|+|+..+ .+|++..-+ +-.-|+|.+.+.... ......|+.|.+.|.
T Consensus 106 --~~~w~~l------~~~~~~~~~V~g~V~~~~---~~G~~V~l~-Gv~gfip~s~ls~~~----~~~~~vG~~i~~kVl 169 (318)
T PRK07400 106 --MRAWERV------RQLQKEDATVRSEVFATN---RGGALVRIE-GLRGFIPGSHISTRK----PKEELVGEELPLKFL 169 (318)
T ss_pred --hhHHHHH------HHhccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcCccC----CccccCCCEEEEEEE
Confidence 0000000 001112345788888874 356766664 678899999997532 123358999999987
Q ss_pred EcC
Q psy9900 166 VGK 168 (191)
Q Consensus 166 ~~~ 168 (191)
+-+
T Consensus 170 ~id 172 (318)
T PRK07400 170 EVD 172 (318)
T ss_pred EEE
Confidence 644
No 74
>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=91.48 E-value=2 Score=28.31 Aligned_cols=56 Identities=16% Similarity=-0.009 Sum_probs=37.6
Q ss_pred eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
|+|.... ..||.+..-..+-+-|+|.|++.......-...++.||.|++.+..-++
T Consensus 7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~ 62 (71)
T cd05696 7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSP 62 (71)
T ss_pred eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeC
Confidence 7787763 3476655544468999999998643211123459999999999876443
No 75
>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=91.40 E-value=0.62 Score=30.56 Aligned_cols=59 Identities=20% Similarity=0.226 Sum_probs=43.6
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
....|+|..-+. +|++..-..+-+.|+|.+++...........+..||.|.+.+..-+.
T Consensus 6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence 456899998875 66666555678999999999853212235788999999999876444
No 76
>PRK12608 transcription termination factor Rho; Provisional
Probab=90.57 E-value=0.67 Score=40.89 Aligned_cols=68 Identities=24% Similarity=0.419 Sum_probs=47.9
Q ss_pred eeccceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCc-eeeEeecCC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI-EAINVTGPN 79 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~-~A~~v~~~~ 79 (191)
.....|++.-.. .||||+... .+..||||..+.++. ..|+.||.|.-.... +-+. ---.|..+.
T Consensus 16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~-------~~l~~Gd~V~~~~r~-~~~~~~LgrV~~~~ 85 (380)
T PRK12608 16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRR-------FNLRTGDVVEGVARP-RERYRVLVRVDSVN 85 (380)
T ss_pred CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHH-------hCCCCCCEEEeccCC-CCChhheEEEeccC
Confidence 445678887653 599999985 335899999999986 478999999988766 3332 233455555
Q ss_pred CCCc
Q psy9900 80 GIPV 83 (191)
Q Consensus 80 ~~~~ 83 (191)
+.|.
T Consensus 86 G~p~ 89 (380)
T PRK12608 86 GTDP 89 (380)
T ss_pred CcCc
Confidence 5553
No 77
>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=90.43 E-value=2.4 Score=27.95 Aligned_cols=61 Identities=16% Similarity=0.089 Sum_probs=42.9
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
..+.|+|.... ..||.+..-..+.+-++|++++.......-...++.||.|...+..-++|
T Consensus 5 ~iv~G~V~~i~--~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~ 65 (72)
T cd05704 5 AVTLGMVTKVI--PHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG 65 (72)
T ss_pred CEEEEEEEEee--CCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence 45788888863 23666666666899999999996542111123468899999999887655
No 78
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=90.40 E-value=0.33 Score=43.78 Aligned_cols=51 Identities=25% Similarity=0.411 Sum_probs=42.3
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
.++..|+||.= +|||||+..|. .+..|+.--..+..| .||++.-.+.....
T Consensus 19 ~prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~MKkvM---------HGDkIiA~i~te~e 69 (645)
T COG4776 19 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKVM---------HGDKIIAVIHTEKE 69 (645)
T ss_pred Ccccceeeeec--cccceeEEEcC-ccccccCCHHHhhhc---------ccCeEEEEEEecCc
Confidence 45788999975 89999999997 678999998888877 89999888765433
No 79
>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=90.33 E-value=1 Score=30.48 Aligned_cols=58 Identities=16% Similarity=0.079 Sum_probs=41.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
...|+|+... -||++..-.++-+.|+|.+++......+-...++.||.|++.+..-..
T Consensus 17 i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 17 VVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred EEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 4578888775 488887766678999999999654211122447889999999876543
No 80
>PRK08582 hypothetical protein; Provisional
Probab=90.23 E-value=4.5 Score=30.57 Aligned_cols=74 Identities=18% Similarity=0.219 Sum_probs=49.7
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC-CCceeEEeecCCCCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTGPNGIP 183 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~-kg~~A~~V~~~~~~~ 183 (191)
...+.|+|... ..||+....+.+.+-++|++++.......-...++.||.|.+.|..-+ .|.-...++.+...|
T Consensus 6 G~iv~G~V~~I---~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~ 80 (139)
T PRK08582 6 GSKLQGKVTGI---TNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80 (139)
T ss_pred CCEEEEEEEEE---ECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCc
Confidence 34578999886 347877666667899999999974321111246899999999988855 365455555544433
No 81
>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=90.11 E-value=2.7 Score=27.13 Aligned_cols=59 Identities=14% Similarity=0.149 Sum_probs=41.6
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
.+.|+|.... .||.+..-+.+-+-|+|.+++.......-...++.||.+.+.+..-+..
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~ 61 (69)
T cd05697 3 VVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPE 61 (69)
T ss_pred EEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECC
Confidence 4678888874 4777766655789999999986532111124589999999999886553
No 82
>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=90.10 E-value=1.8 Score=26.67 Aligned_cols=56 Identities=20% Similarity=0.215 Sum_probs=37.8
Q ss_pred eeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 111 ~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.|+|...+ .+|.+...+.+.+.|+|.+++...........++.||.|.+.+..-+.
T Consensus 2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence 57888875 345444444568999999998753110112468999999999987553
No 83
>PRK08582 hypothetical protein; Provisional
Probab=90.00 E-value=3.9 Score=30.89 Aligned_cols=73 Identities=18% Similarity=0.184 Sum_probs=48.1
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC-CCceeeEee
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVT 76 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~-~g~~A~~v~ 76 (191)
|.--.-....|+|+.-. .||+...-+.+.+-++|.+.+.......-...+..||.|.+.+..-. .|.....+.
T Consensus 1 m~~kvG~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk 74 (139)
T PRK08582 1 MSIEVGSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIK 74 (139)
T ss_pred CCCcCCCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEE
Confidence 33334456788998864 47877666657899999999975421111245789999999987644 354333443
No 84
>PRK12608 transcription termination factor Rho; Provisional
Probab=89.63 E-value=1 Score=39.72 Aligned_cols=65 Identities=25% Similarity=0.442 Sum_probs=46.4
Q ss_pred eeeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPNGI 182 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~~ 182 (191)
...|+..... .||||+...+ +..||||..+.+.. ..|+.|+.|.-.... .-| .--..|--+.|.
T Consensus 18 ~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~-------~~l~~Gd~V~~~~r~-~~~~~~LgrV~~~~G~ 87 (380)
T PRK12608 18 EVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRR-------FNLRTGDVVEGVARP-RERYRVLVRVDSVNGT 87 (380)
T ss_pred cceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHH-------hCCCCCCEEEeccCC-CCChhheEEEeccCCc
Confidence 3568887663 5999999853 34899999999997 589999999988766 333 223344444454
Q ss_pred C
Q psy9900 183 P 183 (191)
Q Consensus 183 ~ 183 (191)
|
T Consensus 88 p 88 (380)
T PRK12608 88 D 88 (380)
T ss_pred C
Confidence 4
No 85
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=89.63 E-value=3.1 Score=26.36 Aligned_cols=58 Identities=21% Similarity=0.199 Sum_probs=40.7
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|....+ ||+...-..+.+-|+|.+++.......-...++.||.|.+.+..-+.
T Consensus 3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC
Confidence 45788877753 88877765568999999998653110111346899999999888654
No 86
>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=89.23 E-value=2 Score=29.80 Aligned_cols=61 Identities=18% Similarity=0.081 Sum_probs=39.4
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec---CCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM---NPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~---~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
....|+|+.... .-||.+..-+.+.+-|+|.+++... ...+-...++.||.|.+++..-+.
T Consensus 9 ~iy~g~V~~i~~-~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~ 72 (88)
T cd04453 9 NIYLGRVKKIVP-GLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPI 72 (88)
T ss_pred CEEEEEEEEecc-CCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecC
Confidence 346789998842 2245555444468999999998430 000012458999999999987544
No 87
>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=89.20 E-value=1.8 Score=28.54 Aligned_cols=53 Identities=17% Similarity=0.019 Sum_probs=35.7
Q ss_pred eEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE
Q psy9900 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 65 (191)
Q Consensus 11 G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~ 65 (191)
|+|+.-. ..||.+..-..+-+-|+|.|.+...........++.||.|++.+..
T Consensus 7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~ 59 (71)
T cd05696 7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG 59 (71)
T ss_pred eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence 7888864 3466655444368999999998543111123458999999999764
No 88
>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=89.15 E-value=2.2 Score=27.56 Aligned_cols=58 Identities=17% Similarity=0.169 Sum_probs=39.7
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
...|+|+... -||.+..-.++-+-|+|.+++....-.+....++.||.|++.+..-..
T Consensus 3 ~~~g~V~~v~---~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 3 KTHGTIVKVK---PNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred EEEEEEEEEe---cCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 3578888885 366666555468999999999743211122347899999999876444
No 89
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=89.13 E-value=3.2 Score=26.02 Aligned_cols=59 Identities=20% Similarity=0.212 Sum_probs=41.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
..+.|+|...+. +|++..-+.+...|+|.+++...........++.||.|.+.+..-+.
T Consensus 4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 357789988855 56655555568899999998753100111348999999999988654
No 90
>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=89.08 E-value=3.7 Score=25.85 Aligned_cols=58 Identities=24% Similarity=0.218 Sum_probs=39.7
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|.... .||+...-+.+.+.|+|.+++.......-...++.||.|...+..-+.
T Consensus 3 ~~~g~V~~i~---~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 3 VVEGTVTRLK---PFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred EEEEEEEEEE---eeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC
Confidence 4578887764 377776666678999999998743100011347899999999877553
No 91
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=88.88 E-value=1.4 Score=39.28 Aligned_cols=64 Identities=30% Similarity=0.486 Sum_probs=45.2
Q ss_pred cceEEEEeeCCCCeeEEEeCCC-----CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC---ceeeEeecCCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDN-----KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINVTGPNG 80 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~-----~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g---~~A~~v~~~~~ 80 (191)
..|.+--. ..||||+...+. ..||||..+.++. -.|+.||.|.-.+.....+ ..-..|..+++
T Consensus 51 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng 121 (416)
T PRK09376 51 GEGVLEIL--PDGFGFLRSPDANYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKIRPPKEGERYFALLKVETVNG 121 (416)
T ss_pred EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEeeCCCCCCCccceEEEeeeCC
Confidence 45666644 349999998532 4899999999996 4789999999988764333 34455655554
Q ss_pred C
Q psy9900 81 I 81 (191)
Q Consensus 81 ~ 81 (191)
.
T Consensus 122 ~ 122 (416)
T PRK09376 122 E 122 (416)
T ss_pred C
Confidence 3
No 92
>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=88.86 E-value=2 Score=27.18 Aligned_cols=57 Identities=25% Similarity=0.236 Sum_probs=39.3
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|..... ||+...-+.+.+.|+|.+++......+....++.||.|.+.+..-.
T Consensus 3 ~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 3 VVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred EEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 35688888653 7777766657899999999975421111134789999999986544
No 93
>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=88.70 E-value=2.2 Score=27.03 Aligned_cols=57 Identities=21% Similarity=0.200 Sum_probs=40.1
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|..... ||+...-....+-|+|.+++......+-...++.||.|.+.+...+
T Consensus 3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD 59 (68)
T ss_pred EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence 35678887764 8888876556899999999975421111134689999999987654
No 94
>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=88.56 E-value=5 Score=26.08 Aligned_cols=59 Identities=12% Similarity=-0.019 Sum_probs=40.3
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
....|+|+... .+|.+..-+.+-+-|+|.+++.......--..++.||.|++.+..-+.
T Consensus 5 ~iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 5 DILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CEEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 35678888863 356555544468999999999753211112347899999999988654
No 95
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=88.36 E-value=1.3 Score=28.58 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=31.9
Q ss_pred ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC-cee
Q psy9900 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEA 72 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g-~~A 72 (191)
+-+|+.-+ .+|+....+..++||+|.+.+.. .+..||.|++-+=.+.++ +.|
T Consensus 6 ~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~D~~~rl~A 58 (61)
T PF13509_consen 6 TLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE--------PLKVGDEVEVFVYLDKEGRLVA 58 (61)
T ss_dssp ---EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-EEE
T ss_pred ceEEEEEe---CCEEEEECCCCCEEEechHHcCC--------CCCCCCEEEEEEEECCCCCEEE
Confidence 44566665 56777766667999999998863 578999999999888776 444
No 96
>PRK12678 transcription termination factor Rho; Provisional
Probab=88.21 E-value=1.2 Score=41.71 Aligned_cols=70 Identities=20% Similarity=0.381 Sum_probs=48.9
Q ss_pred eeeeEEEeecCCCceeEEeCC---CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC---------ceeEEee
Q psy9900 110 VRGIVKFYDSKRGFGFITRLD---NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---------IEAINVT 177 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d---~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg---------~~A~~V~ 177 (191)
..|++-.. .|||||...+ +..||||..+.+.. ..|+.||.|.=.+..-..| ..-+.|.
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr-------~~Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~ 365 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRK-------NGLRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLD 365 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHH-------cCCCCCCEEEEeecCCCCCccccccceeeeeeeEe
Confidence 44555444 5999999863 35899999999997 5899999999777653332 2345677
Q ss_pred cCCCCCCCCCCC
Q psy9900 178 GPNGIPVQGAPK 189 (191)
Q Consensus 178 ~~~~~~~~~~~~ 189 (191)
-+++.+....+.
T Consensus 366 ~vNg~~~e~~~~ 377 (672)
T PRK12678 366 SVNGMSPEEAKK 377 (672)
T ss_pred eeCCCChHHhcc
Confidence 777766444433
No 97
>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=88.07 E-value=4.3 Score=26.18 Aligned_cols=59 Identities=17% Similarity=0.224 Sum_probs=40.9
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
.+.|+|+... .+|.+..-..+-+-|+|.+++.....+.-...++.||.|++.+..-+..
T Consensus 3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~ 61 (73)
T cd05691 3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK 61 (73)
T ss_pred EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCC
Confidence 3578888773 4677666555688999999987542111123468999999999886653
No 98
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=87.88 E-value=1.8 Score=27.31 Aligned_cols=59 Identities=20% Similarity=0.212 Sum_probs=40.6
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
....|+|...+. +|++..-+.+-+.|+|.+++......+....++.||.|.+.+..-..
T Consensus 4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 346789998875 56655555468899999999754111112347999999999876543
No 99
>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=86.93 E-value=2.4 Score=27.39 Aligned_cols=58 Identities=14% Similarity=0.136 Sum_probs=40.7
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
...|+|+.-+ .||.+..-+.+-+-|+|.+++......+....++.||.+.+.+..-+.
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 3 VVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred EEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 3578888875 478777665568999999999653211112458899999999876443
No 100
>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=86.86 E-value=5.1 Score=26.67 Aligned_cols=54 Identities=19% Similarity=0.279 Sum_probs=41.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
....|+|+... .||++..-. .+-+-|+|.+++... ..+++||.|.+.+..-++.
T Consensus 6 ~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~ 60 (74)
T cd05694 6 MVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDD 60 (74)
T ss_pred CEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECC
Confidence 34789998863 588866653 357899999999852 5789999999998865543
No 101
>COG1158 Rho Transcription termination factor [Transcription]
Probab=86.85 E-value=0.91 Score=39.64 Aligned_cols=63 Identities=30% Similarity=0.525 Sum_probs=44.5
Q ss_pred eEEEEeeCCCCeeEEEeCC-----CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC--cee-eEeecCCCCC
Q psy9900 11 GIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD--IEA-INVTGPNGIP 82 (191)
Q Consensus 11 G~vk~~~~~kGfGFI~~~~-----~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g--~~A-~~v~~~~~~~ 82 (191)
|++.-- .-||||+...+ +..||||.-|.+... .|+.||.|+-.+.....| .-| ..|..+++.+
T Consensus 56 GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf-------~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~ 126 (422)
T COG1158 56 GVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRRF-------NLRTGDTVEGKVRPPKEGERYFALLKVEAVNGDD 126 (422)
T ss_pred eEEEec--cCCcceeecCccccCCCCCceEECHHHHhhc-------cCccCCEEeeeecCCCcccceeeeEEEeecCCCC
Confidence 444444 48999999765 348999999999863 789999999998765555 223 4455444433
No 102
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=86.58 E-value=5.9 Score=26.18 Aligned_cols=59 Identities=8% Similarity=-0.045 Sum_probs=39.4
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC--cccccccCCCCCEEEEEEEEcCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN--PKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~--~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
...|+|+... .+|....-..+-+-|+|.+++.... ...-...++.||.|++.|..=++.
T Consensus 3 ~V~g~V~~i~---~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~ 63 (73)
T cd05703 3 EVTGFVNNVS---KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKE 63 (73)
T ss_pred EEEEEEEEEe---CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCC
Confidence 3578888873 3455443333689999999996320 112235689999999998875543
No 103
>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=86.57 E-value=6.7 Score=25.38 Aligned_cols=59 Identities=19% Similarity=0.175 Sum_probs=41.0
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-cccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-PKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
..+.|+|... +.||+...-+.+.+-++|.+++.... .......++.||.|.+.+..-+.
T Consensus 5 ~~~~g~V~~i---~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~ 64 (72)
T cd05689 5 TRLFGKVTNL---TDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDE 64 (72)
T ss_pred CEEEEEEEEE---EeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeC
Confidence 3578888886 34888776655789999999996321 00112356899999999877554
No 104
>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=86.16 E-value=4.3 Score=26.38 Aligned_cols=57 Identities=12% Similarity=-0.012 Sum_probs=38.9
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|+.-. .||.+..-+.+-+-|+|.+++......+....++.||.|++.+..-.
T Consensus 6 iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 6 ILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD 62 (73)
T ss_pred EEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence 4578888864 35666555546899999999975421111234789999999987644
No 105
>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=85.08 E-value=4.6 Score=26.00 Aligned_cols=57 Identities=18% Similarity=0.233 Sum_probs=39.8
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
..|+|+... .+|.+..-..+-+-|+|.+++......+-...++.||.|++.+..-..
T Consensus 4 v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 4 VTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred EEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 568888874 467776655567899999998764211112346899999999876544
No 106
>PRK07252 hypothetical protein; Provisional
Probab=84.89 E-value=12 Score=27.44 Aligned_cols=59 Identities=20% Similarity=0.200 Sum_probs=42.3
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
..+.|+|.... .||++..-+.+.+-|+|.+++.......-...++.||.|.+.|..-+.
T Consensus 5 ~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 5 DKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence 35788888874 488877766678999999998643110111347899999999998654
No 107
>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=84.84 E-value=9.2 Score=25.41 Aligned_cols=50 Identities=16% Similarity=0.263 Sum_probs=39.8
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 167 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~ 167 (191)
...+.|+|... ..||+...-+.+.+-++|.+++. ..++.||.|...+..-
T Consensus 17 G~~~~g~V~~i---~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 17 GKLYKGKVNGV---AKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCEEEEEEEeE---ecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence 35678888876 34888777666789999999985 4689999999998775
No 108
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=84.82 E-value=25 Score=33.21 Aligned_cols=136 Identities=13% Similarity=0.130 Sum_probs=76.4
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE--cCCCceeeEeecCCCCCcc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV--GKKDIEAINVTGPNGIPVQ 84 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~--~~~g~~A~~v~~~~~~~~~ 84 (191)
....|+|...+. . |.+..-...-+-|++.+++...........+..||.|++.+.. .+++.-......+....
T Consensus 304 ~iV~G~V~~v~~-~--gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~-- 378 (647)
T PRK00087 304 DIVKGTVVSVNE-N--EVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREK-- 378 (647)
T ss_pred CEEEEEEEEEEC-C--EEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchh--
Confidence 346799999964 2 3333333345789999988743222233567899999999876 33342111111110000
Q ss_pred CCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccC--CCCCEEEE
Q psy9900 85 GAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSL--GLGEIVDF 162 (191)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l--~~G~~V~f 162 (191)
+-... ....-......|+|.... .+|++..-+ +-+.|+|.+++.... ...+ ..|+.|.|
T Consensus 379 -----~~~~l------~~~~~~G~iv~g~V~~v~---~~G~~V~lg-gi~gfiP~sel~~~~----~~d~~~~vG~~v~v 439 (647)
T PRK00087 379 -----AWKEL------EEAFENGEPVKGKVKEVV---KGGLLVDYG-GVRAFLPASHVELGY----VEDLSEYKGQELEV 439 (647)
T ss_pred -----HHHHH------HHHhhCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHhCccc----cCCHHHhCCCEEEE
Confidence 00000 000122345788888763 246665554 489999999876431 1222 28999999
Q ss_pred EEEE
Q psy9900 163 NIGV 166 (191)
Q Consensus 163 ~i~~ 166 (191)
.+..
T Consensus 440 ~Vl~ 443 (647)
T PRK00087 440 KIIE 443 (647)
T ss_pred EEEE
Confidence 9844
No 109
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=84.62 E-value=1.8 Score=38.62 Aligned_cols=51 Identities=29% Similarity=0.519 Sum_probs=39.8
Q ss_pred eeeeeEEEeecCCCceeEEeCC-----CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLD-----NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d-----~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
...|++... ..||||+...+ +..||||..+.+.. -.|+.||.|+=.+..-.
T Consensus 50 ~~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~-------~~lr~gd~v~g~~R~~~ 105 (415)
T TIGR00767 50 FGEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRR-------FNLRTGDTIEGQIRSPK 105 (415)
T ss_pred EEEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeccc
Confidence 356777655 35999999863 35899999999997 58999999998776543
No 110
>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=84.41 E-value=4.4 Score=26.09 Aligned_cols=56 Identities=14% Similarity=0.056 Sum_probs=38.1
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
..+|+|...+. ..-||.. ....+-|+|.+++......+....++.||.|++.+..-
T Consensus 3 iv~g~V~~i~~--~~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 3 IVKGTVVSVDD--DEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV 58 (70)
T ss_pred EEEEEEEEEeC--CEEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence 35799999863 2345554 43578999999997532111234579999999998763
No 111
>PRK07252 hypothetical protein; Provisional
Probab=84.20 E-value=9.3 Score=28.10 Aligned_cols=59 Identities=20% Similarity=0.200 Sum_probs=41.8
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
....|+|.... .||++..-+.+.+-|+|.++|....-..-...++.||.|.+.+..-..
T Consensus 5 ~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 5 DKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence 34678888885 488887766668999999999653211112457899999999987543
No 112
>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=83.93 E-value=7.8 Score=25.43 Aligned_cols=60 Identities=17% Similarity=0.113 Sum_probs=40.9
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g 69 (191)
...|+|+.-... ||.+..-..+.+-++|.+++......+....++.||.|...+..-.++
T Consensus 6 iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~ 65 (72)
T cd05704 6 VTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG 65 (72)
T ss_pred EEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence 457888886422 666666666789999999997643211223468899999998776543
No 113
>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=83.92 E-value=7.6 Score=24.73 Aligned_cols=57 Identities=25% Similarity=0.194 Sum_probs=39.4
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhc-cCcccccccCCCCCEEEEEEEEcC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVK-MNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~-~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
.+.|+|.... .||+...-+.+.+-++|.+++.. ...+.-...++.||.|...+..-+
T Consensus 3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence 3678887763 48877766667899999999862 110111234689999999987754
No 114
>PRK05807 hypothetical protein; Provisional
Probab=83.83 E-value=4.7 Score=30.30 Aligned_cols=72 Identities=17% Similarity=0.151 Sum_probs=47.4
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC-CCceeeEee
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVT 76 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~-~g~~A~~v~ 76 (191)
|.-.......|+|.... .||+...-+ +..-++|.+.+......+-...++.||.|.+.+..-. .|.....+.
T Consensus 1 m~~~vG~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk 73 (136)
T PRK05807 1 MTLKAGSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIK 73 (136)
T ss_pred CCccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEE
Confidence 44445567889999874 477766554 5689999999975432222355799999999987643 454333443
No 115
>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=83.68 E-value=7.4 Score=25.83 Aligned_cols=59 Identities=19% Similarity=0.148 Sum_probs=40.5
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC---cccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN---PKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~---~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
....|+|+... .||....-..+-+-|+|++++.... +..-...++.||.|.+.+..-+.
T Consensus 5 ~~V~g~V~~i~---~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 5 QLLRGYVSSVT---KQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CEEEEEEEEEe---CCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence 35789999874 4555444445789999999987642 10012457999999999987654
No 116
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=83.67 E-value=2 Score=28.52 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=22.2
Q ss_pred cccCCCCCEEEEEEEEcCCC-ceeEEeec
Q psy9900 151 FQSLGLGEIVDFNIGVGKKD-IEAINVTG 178 (191)
Q Consensus 151 ~~~l~~G~~V~f~i~~~~kg-~~A~~V~~ 178 (191)
+..|++||.|.|.+..++.| +.-+.++.
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~~ 68 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIEP 68 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence 57899999999999999998 87777653
No 117
>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=82.78 E-value=7.2 Score=25.00 Aligned_cols=58 Identities=24% Similarity=0.236 Sum_probs=39.6
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|+... .+|.+..-..+-+-|+|.+++.......-...++.||.|++.+..-+.
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence 3678888863 466655554568999999998643111112348999999999887554
No 118
>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=82.64 E-value=7 Score=34.96 Aligned_cols=74 Identities=16% Similarity=0.089 Sum_probs=51.1
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC------------cccccccCCCCCEEEEEEEEcC---CCc
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN------------PKKFFQSLGLGEIVDFNIGVGK---KDI 171 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~------------~~~~~~~l~~G~~V~f~i~~~~---kg~ 171 (191)
...+.|+|+...+.-.--||.-.+ ++.-|+|++++.... ...-...|++||.|.++|...+ ||+
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp 104 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA 104 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence 346789999987766688888765 678999999985310 0000114899999999999954 664
Q ss_pred e-eEEeecCCC
Q psy9900 172 E-AINVTGPNG 181 (191)
Q Consensus 172 ~-A~~V~~~~~ 181 (191)
. ..++++++.
T Consensus 105 ~lT~~Isl~Gr 115 (414)
T TIGR00757 105 RLTTDISLPGR 115 (414)
T ss_pred eEEEEEEeccc
Confidence 4 336666554
No 119
>PRK08059 general stress protein 13; Validated
Probab=82.62 E-value=11 Score=27.69 Aligned_cols=71 Identities=20% Similarity=0.243 Sum_probs=47.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC--CceeEEeecCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNG 181 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k--g~~A~~V~~~~~ 181 (191)
..+.|+|..... ||+...-+.+.+-++|.+++.......-...++.||.|.+.|..-+. |.-...++.+..
T Consensus 9 ~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 9 SVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred CEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 467888887643 78777766678999999998543111112356899999999988543 544444554444
No 120
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=82.58 E-value=29 Score=29.41 Aligned_cols=117 Identities=15% Similarity=0.035 Sum_probs=69.6
Q ss_pred CeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCc-eeeEeecCCCCCccCCCCCCCcccccccc
Q psy9900 21 GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI-EAINVTGPNGIPVQGAPKSSSETVSGTYR 99 (191)
Q Consensus 21 GfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~-~A~~v~~~~~~~~~~~~~~~~~~~~~~~~ 99 (191)
.-|--....-..|++|..+++..- --..|+.||.+.+.+..+.++. .|.-... . ....-+.++..
T Consensus 87 ~lGaFlD~Gl~KDl~vp~~elp~~----~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~a~~--~-~l~~l~~~~~~------- 152 (287)
T COG2996 87 DLGAFLDWGLPKDLLVPLDELPTL----KSLWPQKGDKLLVYLYVDKKGRIWGTLAIE--K-ILENLATPAYN------- 152 (287)
T ss_pred CcceEEecCCCcceeeehhhcccc----cccCCCCCCEEEEEEEEccCCcEEEEecch--h-HHHhcCCccch-------
Confidence 334333334458999999999853 1235899999999999999883 2221111 0 00000000000
Q ss_pred CCcccccceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE
Q psy9900 100 NDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 166 (191)
Q Consensus 100 ~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~ 166 (191)
-.......|+|-.+... |++...+.+--.|+|.|+.. ..++.|++|.-.+..
T Consensus 153 ----~l~nq~v~~tVYr~~~~---G~fv~~e~~~~GfIh~sEr~--------~~prlG~~l~~rVi~ 204 (287)
T COG2996 153 ----NLKNQEVDATVYRLLES---GTFVITENGYLGFIHKSERF--------AEPRLGERLTARVIG 204 (287)
T ss_pred ----hhhcCeeeeEEEEEecc---ceEEEEcCCeEEEEcchhhc--------ccccCCceEEEEEEE
Confidence 01123467888777332 33222245788999999886 467899999887765
No 121
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=82.49 E-value=1.4 Score=39.40 Aligned_cols=50 Identities=28% Similarity=0.508 Sum_probs=38.6
Q ss_pred cceEEEEeeCCCCeeEEEeC-----CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 9 VRGIVKFYDSKRGFGFITRL-----DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~-----~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
..|.+--. ..||||+... .+..||||..+.++. -.|+.||.|.-.+....
T Consensus 51 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~-------~~lr~gd~v~g~~R~~~ 105 (415)
T TIGR00767 51 GEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRR-------FNLRTGDTIEGQIRSPK 105 (415)
T ss_pred EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEeccc
Confidence 45666644 3599999985 345899999999996 37899999999876543
No 122
>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=82.28 E-value=6.8 Score=25.70 Aligned_cols=58 Identities=17% Similarity=0.225 Sum_probs=38.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCC-CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~-~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....|+|+... -||....-++ ..+-|+|.+.+.......-...++.||+|.+.+..-.
T Consensus 5 ~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 5 QIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE 63 (73)
T ss_pred CEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEEC
Confidence 34678888875 4787765543 3689999999965421001122578999999987643
No 123
>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=82.17 E-value=11 Score=24.31 Aligned_cols=57 Identities=18% Similarity=0.160 Sum_probs=38.9
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheec-CCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM-NPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~-~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|+.-. -||+...-+.+.+-|+|.+++... ........++.||.|.+.+..-+
T Consensus 6 ~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 6 RLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred EEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence 4678888764 488887665568999999999631 10012234688999999886643
No 124
>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=81.88 E-value=6.2 Score=25.17 Aligned_cols=55 Identities=25% Similarity=0.198 Sum_probs=38.1
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeehee-cCCCCCcccCCCCCEEEEEEEEc
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVK-MNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~-~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
..|+|+... .||+...-+.+.+-++|.+++.. .........++.||.|.+.+..-
T Consensus 4 ~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i 59 (69)
T cd05690 4 VSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI 59 (69)
T ss_pred EEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE
Confidence 567787764 58888766667899999999962 11111123468999999987654
No 125
>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=81.33 E-value=8.9 Score=25.13 Aligned_cols=59 Identities=17% Similarity=0.213 Sum_probs=39.2
Q ss_pred eeeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
..+.|+|.... .||....-++ ..+-++|.+++.......-..-++.||.|.+.+..-+.
T Consensus 5 ~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 5 QIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM 64 (73)
T ss_pred CEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence 35778888874 3787666543 36899999999653210111225889999999877544
No 126
>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=81.29 E-value=13 Score=24.57 Aligned_cols=68 Identities=15% Similarity=0.166 Sum_probs=43.2
Q ss_pred eeeeeEEEeecCCCceeEEeCC---CCCcEEEeccchhccCc-ccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLD---NKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d---~~~dvF~h~s~~~~~~~-~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
.+.|+|.... .||+...-+ .+.+-|+|.+++..... ..-...++.||.|...+..-+++.-...++.+
T Consensus 3 ~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k~~ 74 (79)
T cd05684 3 IYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDV 74 (79)
T ss_pred EEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCCEEEEEEEec
Confidence 3567777763 367766544 25789999999964310 01113468999999999886655444444433
No 127
>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=81.04 E-value=11 Score=24.23 Aligned_cols=57 Identities=14% Similarity=0.088 Sum_probs=38.0
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
.+.|+|..... +|.+..-..+.+-|+|.+++...........+++||.|++.+..-+
T Consensus 3 iv~g~V~~i~~---~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 3 IVKGTVVSVDD---DEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59 (70)
T ss_pred EEEEEEEEEeC---CEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEE
Confidence 46788888743 3444444446789999999975321111245899999999988744
No 128
>PRK05807 hypothetical protein; Provisional
Probab=81.03 E-value=19 Score=26.99 Aligned_cols=70 Identities=14% Similarity=0.141 Sum_probs=46.7
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC-CCceeEEeecCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTGPN 180 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~-kg~~A~~V~~~~ 180 (191)
...+.|+|.... .||.+...+ +..-++|++++.......-...++.||.|.+.|..-+ .|.-...++.+.
T Consensus 6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 356789998863 477766664 5789999999964321111245799999999987754 454445555443
No 129
>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=80.42 E-value=13 Score=24.08 Aligned_cols=59 Identities=14% Similarity=0.032 Sum_probs=39.7
Q ss_pred eeeeeeEEEeecCCCceeEEeCC--CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d--~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
..+.|+|.... .||.+..-. .+.+-++|.+++.......-...++.||.|+..+..-+.
T Consensus 5 ~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 5 ELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred CEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence 35778888763 477766543 247899999998753211111347899999999887554
No 130
>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=80.40 E-value=9.3 Score=25.40 Aligned_cols=49 Identities=16% Similarity=0.293 Sum_probs=38.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
...+|+|.... .||+...-+.+.+-|+|.+++. ..++.||.|...+..-
T Consensus 18 ~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 18 KLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CEEEEEEEeEe---cceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence 45678888753 5888877666689999999975 4588999999988664
No 131
>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=80.27 E-value=11 Score=24.26 Aligned_cols=51 Identities=24% Similarity=0.215 Sum_probs=37.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....|+|...+. +|.+...+ +-+-|++.+.+... ..++.||.|.+.+..-+
T Consensus 5 ~iV~G~V~~~~~---~~~~vdig-~~eg~lp~~e~~~~------~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 5 EIVTGIVKRVDR---GNVIVDLG-KVEAILPKKEQIPG------ESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CEEEEEEEEEcC---CCEEEEcC-CeEEEeeHHHCCCC------CcCCCCCEEEEEEEEEe
Confidence 356899988854 24444443 37889999999743 46799999999998754
No 132
>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=79.86 E-value=7.6 Score=24.88 Aligned_cols=57 Identities=25% Similarity=0.243 Sum_probs=38.5
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|+.-. .||.+..-..+-+-|+|.+.+....-.+....++.||.|++.+..-+
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSID 59 (68)
T ss_pred EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEe
Confidence 3578888874 46665555446899999999965321112234789999999887543
No 133
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=79.16 E-value=3.4 Score=32.26 Aligned_cols=48 Identities=25% Similarity=0.326 Sum_probs=41.2
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEE
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 62 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~ 62 (191)
.-|+||.|+.+..-|.+.-.+ -+|+=+|-..+..-. -.|.+||.|..-
T Consensus 36 rIG~iK~F~~~tQe~iVti~e-~e~LeI~T~nISN~~-----leLs~~D~VlLL 83 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTIPE-YEDLEIHTKNISNIN-----LELSKGDEVLLL 83 (181)
T ss_pred EEeeeeecccccceEEEEeec-ccCceEEeeecccce-----eEecCCCEEEEE
Confidence 359999999999999999888 589999999998753 589999998763
No 134
>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=78.62 E-value=14 Score=23.87 Aligned_cols=58 Identities=16% Similarity=0.179 Sum_probs=38.5
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc--CcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM--NPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~--~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
...|+|..... +|.+..-..+-+-++|.+++... ....-...+++||.|.+.+..-+.
T Consensus 3 iV~g~V~~i~~---~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 3 LVKAKVKSVKP---TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred EEEEEEEEEEC---CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence 46788888743 44444444578999999998643 111123458999999999876543
No 135
>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=78.36 E-value=7.3 Score=25.86 Aligned_cols=58 Identities=17% Similarity=0.060 Sum_probs=39.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCC---cccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKF---FQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g---~~~l~~Gd~V~f~~~~~~ 67 (191)
....|+|+... .||....-..+-+-|+|.+++......+. ...++.||.|.+.+..-+
T Consensus 5 ~~V~g~V~~i~---~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id 65 (74)
T cd05705 5 QLLRGYVSSVT---KQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN 65 (74)
T ss_pred CEEEEEEEEEe---CCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence 34679999974 55554444446899999999876420011 245699999999987543
No 136
>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=77.70 E-value=14 Score=22.96 Aligned_cols=58 Identities=19% Similarity=0.289 Sum_probs=39.0
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|.... .||....-..+.+-|+|.+++.......--..++.||.|.+.+..-+.
T Consensus 3 ~~~g~V~~i~---~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 3 VLEGVVTNVT---DFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60 (68)
T ss_pred EEEEEEEEEe---cccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEEC
Confidence 3678887764 367666655568899999988643100001247999999999887554
No 137
>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=76.04 E-value=12 Score=24.19 Aligned_cols=51 Identities=22% Similarity=0.209 Sum_probs=36.7
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...+|+|..-+. .+=||.. + +-+-|++.+.+... ..+..||.|.+.+..-.
T Consensus 5 ~iV~G~V~~~~~--~~~~vdi-g-~~eg~lp~~e~~~~------~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 5 EIVTGIVKRVDR--GNVIVDL-G-KVEAILPKKEQIPG------ESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CEEEEEEEEEcC--CCEEEEc-C-CeEEEeeHHHCCCC------CcCCCCCEEEEEEEEEe
Confidence 456899999965 3334433 3 36889999999742 46799999999987643
No 138
>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=75.99 E-value=16 Score=23.64 Aligned_cols=57 Identities=12% Similarity=0.012 Sum_probs=38.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCC--CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~--~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|.... .||.+..-. .+-+-|+|.+.+.......-...++.||.|++.+..-+
T Consensus 6 ~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 6 LVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred EEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEE
Confidence 4578888774 478766543 24789999999975421111234789999999987644
No 139
>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=75.79 E-value=8.8 Score=25.33 Aligned_cols=55 Identities=9% Similarity=-0.081 Sum_probs=37.2
Q ss_pred ccceEEEEeeCCCCeeE-EEeCCCCccEEEEeeeheecC--CCCCcccCCCCCEEEEEEEEc
Q psy9900 8 TVRGIVKFYDSKRGFGF-ITRLDNKEDIFVHKSSIVKMN--PKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGF-I~~~~~~~dvFvh~s~l~~~~--~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
..+|+|+... .||. +...+ +-+-|+|.+++.... ..+....++.||.|++.+..-
T Consensus 3 ~V~g~V~~i~---~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~i 60 (73)
T cd05703 3 EVTGFVNNVS---KEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGV 60 (73)
T ss_pred EEEEEEEEEe---CCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEE
Confidence 3578999884 3454 45444 689999999986320 111234589999999998753
No 140
>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=75.67 E-value=10 Score=23.67 Aligned_cols=56 Identities=20% Similarity=0.292 Sum_probs=37.5
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
..|+|+.-. .||....-..+.+-|+|.+++......+-...++.||.|.+.+..-+
T Consensus 4 ~~g~V~~i~---~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 4 LEGVVTNVT---DFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred EEEEEEEEe---cccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEE
Confidence 567888764 36766655556889999999965310000124689999999987644
No 141
>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=75.62 E-value=20 Score=23.54 Aligned_cols=58 Identities=21% Similarity=0.268 Sum_probs=38.3
Q ss_pred eeeeeEEEeecCCCceeEEeCCC-CCcEEEeccchhccC-----------cccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMN-----------PKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~-~~dvF~h~s~~~~~~-----------~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|.... .||++..-.. +-+-++|.+++.... .+.....++.||.|...+..-+.
T Consensus 4 ~~~g~V~~v~---~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 4 EFDGVISGVT---SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred EEEEEEEeEE---eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEecc
Confidence 4567777663 3777766554 567799998886320 00112467889999999988764
No 142
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=74.12 E-value=6.2 Score=28.94 Aligned_cols=65 Identities=14% Similarity=-0.006 Sum_probs=41.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCC------CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeec
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDN------KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTG 178 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~------~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~ 178 (191)
...+|+|+..+...+-=-|.-..- ..-.-|-..+-. -+..|++||.|.|.+...+.++...+|+.
T Consensus 43 ~~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~------~l~~lk~G~~V~F~~~~~~~~~~i~~i~~ 113 (115)
T PRK09838 43 ISGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQT------KMSEIKTGDKVAFNFVQQGNLSLLQDIKV 113 (115)
T ss_pred EEEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChh------hhccCCCCCEEEEEEEEcCCcEEEEEEee
Confidence 456899999987765444443221 011112111111 24689999999999999999987777764
No 143
>PRK08059 general stress protein 13; Validated
Probab=73.97 E-value=21 Score=26.13 Aligned_cols=58 Identities=24% Similarity=0.268 Sum_probs=40.6
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....|+|..... ||+...-+.+.+-|+|.+++......+-...++.||.|.+.+..-.
T Consensus 9 ~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 9 SVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEE
Confidence 456788888653 7877766667899999999965321111234689999999988643
No 144
>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=73.63 E-value=23 Score=23.33 Aligned_cols=58 Identities=17% Similarity=0.198 Sum_probs=38.4
Q ss_pred cceEEEEeeCCCCeeEEEeCC---CCccEEEEeeeheecCC-CCCcccCCCCCEEEEEEEEcCCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLD---NKEDIFVHKSSIVKMNP-KKFFQSLGLGEIVDFNIGVGKKD 69 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~---~~~dvFvh~s~l~~~~~-~~g~~~l~~Gd~V~f~~~~~~~g 69 (191)
..|+|.... .||+...-+ .+.+-|+|.+++..... .+....++.||.|.+.+...+++
T Consensus 4 ~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~ 65 (79)
T cd05684 4 YKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG 65 (79)
T ss_pred EEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence 467777764 467766544 35789999999975410 11123468999999998775544
No 145
>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=73.49 E-value=8.4 Score=24.61 Aligned_cols=53 Identities=21% Similarity=0.190 Sum_probs=36.5
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccC--CCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSL--GLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l--~~Gd~V~f~~~~~~~ 68 (191)
...|+|+..+. +|++..- .+-+.|+|.+.+.... ...+ ..|+.+++.+..-++
T Consensus 3 iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~----~~~~~~~vG~~i~~~i~~vd~ 57 (67)
T cd04465 3 IVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRP----VEDLDEYVGKELKFKIIEIDR 57 (67)
T ss_pred EEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcc----cCChHHhCCCEEEEEEEEEeC
Confidence 35789999862 5666655 4689999999996431 1111 379999999876443
No 146
>PRK12678 transcription termination factor Rho; Provisional
Probab=72.02 E-value=13 Score=35.04 Aligned_cols=48 Identities=21% Similarity=0.385 Sum_probs=37.8
Q ss_pred cceEEEEeeCCCCeeEEEeC---CCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 9 VRGIVKFYDSKRGFGFITRL---DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~---~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
..|++--. .|||||... -+..||||..+.+... .|+.||.|.-.+...
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~-------~Lr~Gd~v~G~vr~p 346 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKN-------GLRKGDAVTGAVRAP 346 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHc-------CCCCCCEEEEeecCC
Confidence 56776655 399999975 3458999999999974 789999999887653
No 147
>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=71.50 E-value=20 Score=23.13 Aligned_cols=56 Identities=16% Similarity=0.145 Sum_probs=37.4
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC--CCCCcccCCCCCEEEEEEEEc
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN--PKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~--~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
...|+|+.... +|.+..-..+-+-++|.+++.... ..+....++.||.|.+.+..-
T Consensus 3 iV~g~V~~i~~---~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~ 60 (70)
T cd05702 3 LVKAKVKSVKP---TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGG 60 (70)
T ss_pred EEEEEEEEEEC---CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEE
Confidence 35788888753 455544444689999999986431 111234579999999988653
No 148
>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=71.01 E-value=14 Score=23.07 Aligned_cols=56 Identities=23% Similarity=0.232 Sum_probs=36.8
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
..+|+|...+. +|++..-+ ..+-|+|.+++.....+.....++.||.|.+.+..-+
T Consensus 4 ~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 4 VVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred EEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEE
Confidence 45788888763 56665544 4789999998863211111234689999999887643
No 149
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=70.70 E-value=8.1 Score=25.53 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=20.3
Q ss_pred cccCCCCCEEEEEEEEcCCC-ceeeEee
Q psy9900 50 FQSLGLGEIVDFNIGVGKKD-IEAINVT 76 (191)
Q Consensus 50 ~~~l~~Gd~V~f~~~~~~~g-~~A~~v~ 76 (191)
+..|++||+|.|.+...+.+ +....+.
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 46889999999999999888 7655554
No 150
>PRK11712 ribonuclease G; Provisional
Probab=69.99 E-value=24 Score=32.33 Aligned_cols=73 Identities=18% Similarity=0.158 Sum_probs=51.2
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc------Ccccc------cccCCCCCEEEEEEEEcC---CCce
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM------NPKKF------FQSLGLGEIVDFNIGVGK---KDIE 172 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~------~~~~~------~~~l~~G~~V~f~i~~~~---kg~~ 172 (191)
.-+.|+|+..-+.-.--||.-.. ++.-|.|++++... +.... -..|++||.|.++|...+ ||+.
T Consensus 40 nIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~ 118 (489)
T PRK11712 40 NIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGAR 118 (489)
T ss_pred cEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCCCe
Confidence 45789999998888888988775 78999999987321 00000 012899999999999965 5643
Q ss_pred -eEEeecCCC
Q psy9900 173 -AINVTGPNG 181 (191)
Q Consensus 173 -A~~V~~~~~ 181 (191)
..++++++.
T Consensus 119 lT~~Isl~Gr 128 (489)
T PRK11712 119 LTTDITLPSR 128 (489)
T ss_pred EEEEEEeccc
Confidence 336776654
No 151
>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=69.42 E-value=16 Score=23.61 Aligned_cols=57 Identities=18% Similarity=0.240 Sum_probs=38.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|+.-. .||++..-. .+.+-++|.+++...........++.||.|.+.+..-+
T Consensus 5 ~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 5 KIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred EEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 4678888874 467666544 35789999999975421111234689999999887644
No 152
>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=69.40 E-value=18 Score=23.01 Aligned_cols=55 Identities=18% Similarity=0.126 Sum_probs=37.4
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|+..+ .+|.+... .+-+.|+|.+.+...... .... ..|+.+.+.+.+=++
T Consensus 3 iv~g~V~~v~---~~G~~v~l-~g~~gfip~s~~~~~~~~-~~~~-~vG~~i~~~i~~vd~ 57 (67)
T cd04465 3 IVEGKVTEKV---KGGLIVDI-EGVRAFLPASQVDLRPVE-DLDE-YVGKELKFKIIEIDR 57 (67)
T ss_pred EEEEEEEEEE---CCeEEEEE-CCEEEEEEHHHCCCcccC-ChHH-hCCCEEEEEEEEEeC
Confidence 3578888874 36666666 478999999999743100 0111 379999999988554
No 153
>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=68.45 E-value=26 Score=21.82 Aligned_cols=57 Identities=25% Similarity=0.246 Sum_probs=37.5
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|...+. +|.+..-+ +.+-|+|.+++.....+.-...++.||.|.+.+..-+.
T Consensus 4 ~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 4 VVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred EEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEEC
Confidence 46788887753 56655554 57899999988632111111346999999999887554
No 154
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=67.75 E-value=27 Score=30.22 Aligned_cols=75 Identities=11% Similarity=-0.048 Sum_probs=51.3
Q ss_pred cceeeeeeEEEeecCCCceeEEeCC--CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEc--CCCceeEEeecCCC
Q psy9900 106 AVHTVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG--KKDIEAINVTGPNG 181 (191)
Q Consensus 106 ~~~~~~G~Vk~~~~~kgfGFI~~~d--~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~--~kg~~A~~V~~~~~ 181 (191)
....+.|+|+... .||.+..-. ++-+-|+|+|.+...-.+.--.-+++||.|.+.|-.- ++|.-...++.+..
T Consensus 17 ~GdvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~ 93 (319)
T PTZ00248 17 EDDLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP 93 (319)
T ss_pred CCCEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc
Confidence 3456889999874 477665543 4789999999997642222223479999999999863 45766666665554
Q ss_pred CC
Q psy9900 182 IP 183 (191)
Q Consensus 182 ~~ 183 (191)
.|
T Consensus 94 ~p 95 (319)
T PTZ00248 94 ED 95 (319)
T ss_pred ch
Confidence 33
No 155
>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=66.79 E-value=34 Score=22.60 Aligned_cols=52 Identities=17% Similarity=0.268 Sum_probs=38.6
Q ss_pred ccceEEEEeeCCCCeeEEEeCC-CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~-~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
..+|+|+... -||++..-+ .+-+-|+|.+++... ..+++|+.|.+.+..-++
T Consensus 7 ~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 7 VLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred EEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEEC
Confidence 3679999885 567765543 346899999999752 578999999999875433
No 156
>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=65.90 E-value=35 Score=22.33 Aligned_cols=57 Identities=21% Similarity=0.285 Sum_probs=37.2
Q ss_pred ccceEEEEeeCCCCeeEEEeCCC-CccEEEEeeeheecC-----------CCCCcccCCCCCEEEEEEEEcC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDN-KEDIFVHKSSIVKMN-----------PKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~-~~dvFvh~s~l~~~~-----------~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...|+|..-. -||+...-.. +.+-|+|.+++.... .......++.||.|...+....
T Consensus 4 ~~~g~V~~v~---~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 4 EFDGVISGVT---SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEEEEEEeEE---eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 3567777764 4788776554 577899999986320 0001245688999998887654
No 157
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=65.76 E-value=10 Score=34.54 Aligned_cols=51 Identities=25% Similarity=0.406 Sum_probs=38.8
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.++..|+||.- +|||||+..|. .+..|+.=..++.. --||++.-.|.....
T Consensus 19 ~prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~MKkv---------MHGDkIiA~i~te~e 69 (645)
T COG4776 19 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDKIIAVIHTEKE 69 (645)
T ss_pred Ccccceeeeec--cccceeEEEcC-ccccccCCHHHhhh---------cccCeEEEEEEecCc
Confidence 35678999986 89999999986 67888877666643 469998877766443
No 158
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=62.06 E-value=17 Score=27.18 Aligned_cols=71 Identities=17% Similarity=0.217 Sum_probs=44.5
Q ss_pred cceEEEEeeCCCCee-EEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE-cCCCceeeEeecCCCCCc
Q psy9900 9 VRGIVKFYDSKRGFG-FITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKDIEAINVTGPNGIPV 83 (191)
Q Consensus 9 ~~G~vk~~~~~kGfG-FI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~-~~~g~~A~~v~~~~~~~~ 83 (191)
.+|+|.-- .-|| |+..++ +..=+||+|.+...+-..=...|++||.|.+.+-. +++|.--..+......|.
T Consensus 9 l~GkItgI---~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe 81 (129)
T COG1098 9 LKGKITGI---TPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPE 81 (129)
T ss_pred EEEEEEee---EecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCcc
Confidence 45555432 3455 555554 67889999999764321123567999999999764 556755566665444443
No 159
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=61.22 E-value=16 Score=27.21 Aligned_cols=73 Identities=16% Similarity=0.224 Sum_probs=45.6
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE-cCCCceeEEeecCCCCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKDIEAINVTGPNGIP 183 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~-~~kg~~A~~V~~~~~~~ 183 (191)
..++|+|.-. ..||-....++++.=+||+|.+...--..=..-|.+||.|...|-. +++|---..++-+...|
T Consensus 7 ~~l~GkItgI---~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~p 80 (129)
T COG1098 7 SKLKGKITGI---TPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEP 80 (129)
T ss_pred ceEEEEEEee---EecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCc
Confidence 3467777654 3366444444578899999999764111112468999999998766 44565555555554433
No 160
>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=60.83 E-value=41 Score=21.49 Aligned_cols=55 Identities=16% Similarity=-0.079 Sum_probs=37.1
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
...|+|+... .+|-+..-.++-+-|+|.+.+.... .....++.|+.|.+.+..-+
T Consensus 3 ~V~g~V~~i~---~~G~~v~l~~~v~g~v~~~~l~~~~--~~~~~~~~G~~i~~kVi~id 57 (66)
T cd05695 3 LVNARVKKVL---SNGLILDFLSSFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILYVD 57 (66)
T ss_pred EEEEEEEEEe---CCcEEEEEcCCceEEEEHHHcCCcc--CcccCcCCCCEEEEEEEEEe
Confidence 3568888774 3555444333689999999986421 11356899999999977644
No 161
>KOG3209|consensus
Probab=59.92 E-value=33 Score=33.04 Aligned_cols=51 Identities=18% Similarity=0.110 Sum_probs=33.5
Q ss_pred EEEEeeCCCCeeEEEe--CCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEE
Q psy9900 12 IVKFYDSKRGFGFITR--LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIG 64 (191)
Q Consensus 12 ~vk~~~~~kGfGFI~~--~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~ 64 (191)
.|--|--+-||||=.. ++.++.|||..--..++.- ---.|++||++.+.-.
T Consensus 652 dV~L~rkesGFGFRiLGG~ep~qpi~iG~Iv~lGaAe--~DGRL~~gDElv~iDG 704 (984)
T KOG3209|consen 652 DVFLRRKESGFGFRILGGDEPGQPIYIGAIVPLGAAE--EDGRLREGDELVCIDG 704 (984)
T ss_pred eEEEEeeccccceEEecCCCCCCeeEEeeeeeccccc--ccCcccCCCeEEEecC
Confidence 3555666779999764 5556789887655544321 2247999999877543
No 162
>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=59.28 E-value=45 Score=21.37 Aligned_cols=58 Identities=17% Similarity=0.233 Sum_probs=39.6
Q ss_pred eeeeeEEEeecCCCceeEEeCC-CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLD-NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d-~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
.+.|+|.... .+|.+..-. .+.+-++|.+++.......-...++.||.|...+..-+.
T Consensus 5 ~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 5 KIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred EEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeC
Confidence 4678888774 467666544 367899999999753211112346999999999887654
No 163
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=57.80 E-value=24 Score=33.71 Aligned_cols=61 Identities=33% Similarity=0.420 Sum_probs=45.8
Q ss_pred eeeeEEEeecCCCceeEEeCC--CCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC-C--ceeEEeecCCC
Q psy9900 110 VRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D--IEAINVTGPNG 181 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d--~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k-g--~~A~~V~~~~~ 181 (191)
..|++..- .+||||+.+++ ...|+|+....+... ..||.|.+++...++ + .+|.-++.+..
T Consensus 70 ~~~~~~~~--~~gf~f~~~~~~~~~~d~~v~~~~~~~a---------~~gD~V~v~~~~~~~~~~~~~~~v~~il~r 135 (706)
T COG0557 70 VEGIVEAS--AKGFGFLSPDDSKDADDIFVPKDPLNRA---------LHGDRVLVELLPSDKRGRFKEAAVVRILER 135 (706)
T ss_pred ccceEEec--cCCceeeccCccCCCCcEEecccccccc---------ccCCEEEEEECcccccCCCceEEEEeeecc
Confidence 45666553 78999999998 568999999886643 689999999766544 4 56777776663
No 164
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=57.65 E-value=23 Score=34.90 Aligned_cols=55 Identities=13% Similarity=0.110 Sum_probs=38.8
Q ss_pred ceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
.|+|+... .||....-..+.+-|+|+|.|......+....++.||.|.+.+..-+
T Consensus 759 ~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID 813 (891)
T PLN00207 759 NCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN 813 (891)
T ss_pred CcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEEC
Confidence 35888764 58887666556899999999965421112235788999999987644
No 165
>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=57.58 E-value=34 Score=32.92 Aligned_cols=60 Identities=22% Similarity=0.196 Sum_probs=42.1
Q ss_pred cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhc----cCcccccccCCCCCEEEEEEEEcC
Q psy9900 106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVK----MNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~----~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....+.|+|+... .||.+..-..+.+-++|+|.+.. .....-..-++.||.|.+.+..-+
T Consensus 647 vG~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 647 VGERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred CCCEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 4566889998873 48887776667999999998731 100011235889999999987744
No 166
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=57.16 E-value=18 Score=22.46 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=24.0
Q ss_pred ccCCCCCEEEEEEEEcCCC-ceeEEeecCCC
Q psy9900 152 QSLGLGEIVDFNIGVGKKD-IEAINVTGPNG 181 (191)
Q Consensus 152 ~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~ 181 (191)
..+..||.|+|.|.-...| ..|.+|.+-+-
T Consensus 6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~D~ 36 (53)
T TIGR01451 6 TVATIGDTITYTITVTNNGNVPATNVVVTDI 36 (53)
T ss_pred cccCCCCEEEEEEEEEECCCCceEeEEEEEc
Confidence 5678999999999998888 55667776554
No 167
>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=57.08 E-value=55 Score=21.77 Aligned_cols=59 Identities=12% Similarity=0.039 Sum_probs=39.8
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhcc----CcccccccCCCCCEEEEEEEEcCC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKM----NPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~----~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
....|+|... ..+|....-+.+-+-++|.+++... ....-...++.||.|.+.+..-+.
T Consensus 8 diV~g~V~~i---~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 8 DVVIGRVTEV---GFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CEEEEEEEEE---CCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 4567888875 3355655555578999999998631 000011248999999999988654
No 168
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=56.54 E-value=49 Score=32.63 Aligned_cols=67 Identities=13% Similarity=0.103 Sum_probs=43.7
Q ss_pred eee-eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC-CCceeEEeec
Q psy9900 109 TVR-GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTG 178 (191)
Q Consensus 109 ~~~-G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~-kg~~A~~V~~ 178 (191)
.+. |+|+.. ..||.+..-..+.+-++|+|++.......-...++.||.|.+.+..-+ +|.-....+.
T Consensus 756 iy~~g~V~~I---~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~ 824 (891)
T PLN00207 756 IYRNCEIKSI---APYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA 824 (891)
T ss_pred EEECcEEEEE---eccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence 453 577776 348877665557899999999965311111245889999999988865 4543444443
No 169
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=55.77 E-value=61 Score=31.01 Aligned_cols=60 Identities=23% Similarity=0.152 Sum_probs=43.2
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
...+.|+|.... .||+...-..+.+-++|++.+.....+.-..-++.||.|...+..-+.
T Consensus 622 G~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~ 681 (693)
T PRK11824 622 GEIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK 681 (693)
T ss_pred CeEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECC
Confidence 456888888873 488877766679999999999753111112347999999999888653
No 170
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=55.75 E-value=60 Score=24.06 Aligned_cols=61 Identities=16% Similarity=0.155 Sum_probs=42.1
Q ss_pred eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCC
Q psy9900 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPN 180 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~ 180 (191)
|.|.|-.....+=|+..|+ +.++-|+++.... ...++|+.|..+=.-++.| ..|.+|-.-+
T Consensus 62 gSv~~~~~~~~~~F~i~D~-~~~i~V~Y~G~~P-------d~F~eg~~VVv~G~~~~~g~F~A~~lL~Kc 123 (131)
T PF03100_consen 62 GSVEYDPDGNTLTFTITDG-GKEIPVVYTGPLP-------DLFREGQGVVVEGRLGEDGVFEATELLAKC 123 (131)
T ss_dssp TTEEE-TTSSEEEEEEE-S-S-EEEEEEES--C-------TT--TTSEEEEEEEECCTSEEEEEEEEETS
T ss_pred CCEEEcCCCCEEEEEEEEC-CcEEEEEECCCCC-------ccccCCCeEEEEEEECCCCEEEEEEEEeCC
Confidence 4444543567888988877 6779999988775 3678999999998887777 8999988655
No 171
>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=55.55 E-value=58 Score=21.53 Aligned_cols=59 Identities=19% Similarity=0.136 Sum_probs=39.5
Q ss_pred eeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC
Q psy9900 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170 (191)
Q Consensus 109 ~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg 170 (191)
...|+|.... ..+.+..-....+-++|.+++.......-...++.||.|.+.+..-+++
T Consensus 9 iV~G~V~~v~---~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 9 IVIGIVTEVN---SRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred EEEEEEEEEc---CCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 4678887763 2344444444689999999986532111224589999999999987664
No 172
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=53.94 E-value=46 Score=31.82 Aligned_cols=58 Identities=22% Similarity=0.158 Sum_probs=42.1
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....|+|+... .||+...-..+.+-++|+|.+......+-...++.||.|.+.+..-+
T Consensus 623 ~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD 680 (693)
T PRK11824 623 EIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680 (693)
T ss_pred eEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEEC
Confidence 45678888885 48888776667899999999975421112234689999999987654
No 173
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=53.17 E-value=48 Score=30.24 Aligned_cols=117 Identities=15% Similarity=0.130 Sum_probs=67.3
Q ss_pred ccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCCCccCCCCCCCccccccccCCcccccceeee
Q psy9900 32 EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVR 111 (191)
Q Consensus 32 ~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 (191)
.+-++..++..... ..+..||.+++.+.....|..|.......- .+.-..+........+ ..-....+.
T Consensus 71 ~~~eI~L~eAk~~~-----~~~~vGD~ie~~I~~~~fgRia~q~aKq~i--~Qkire~ere~i~~ey----k~~~GeIV~ 139 (470)
T PRK09202 71 PTKEISLEEARKID-----PDAEVGDYIEEEIESVDFGRIAAQTAKQVI--VQKIREAERERVYEEY----KDRVGEIIT 139 (470)
T ss_pred CcceeeHHHHhhhC-----ccccCCCeEEEEEccccCChHHHHHHHHHH--HHHHHHHHHHHHHHHH----HhhcCCEEE
Confidence 34666666665432 456799999999987666643322211000 0000000000000000 011235689
Q ss_pred eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
|+|+... + +|++... ++-+.|+|.+.+... ..++.||+|.+.|..=++
T Consensus 140 G~V~ri~--~-~giiVDL-ggvea~LP~sE~ip~------E~~~~GdrIka~I~~Vd~ 187 (470)
T PRK09202 140 GVVKRVE--R-GNIIVDL-GRAEAILPRKEQIPR------ENFRPGDRVRAYVYEVRK 187 (470)
T ss_pred EEEEEEe--c-CCEEEEE-CCeEEEecHHHcCCC------ccCCCCCEEEEEEEEEec
Confidence 9999985 3 4666655 468999999998754 578999999998877443
No 174
>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=53.02 E-value=46 Score=31.79 Aligned_cols=60 Identities=23% Similarity=0.154 Sum_probs=42.0
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k 169 (191)
...+.|+|+... .||.+..-..+.+-|+|+|.+.......-...++.||.|.+.+..-++
T Consensus 619 G~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 619 GKIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred CcEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC
Confidence 356888888873 488777665578999999999643111112346889999999887553
No 175
>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=52.17 E-value=62 Score=21.39 Aligned_cols=59 Identities=19% Similarity=0.136 Sum_probs=37.9
Q ss_pred ccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g 69 (191)
...|+|..-. ..+++..-...-+-++|.+++......+-...++.||.|.+.+..-.+.
T Consensus 9 iV~G~V~~v~---~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 9 IVIGIVTEVN---SRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred EEEEEEEEEc---CCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 3567888773 2233333344578999999996432111234579999999999876553
No 176
>PHA02945 interferon resistance protein; Provisional
Probab=52.03 E-value=80 Score=22.07 Aligned_cols=63 Identities=17% Similarity=0.209 Sum_probs=40.2
Q ss_pred eeeeeeEEEeecCCCceeEEe-CC-CCCcEEEeccch--hccCcccccccCCCCCEEEEEEEEcCCCceeEEe
Q psy9900 108 HTVRGIVKFYDSKRGFGFITR-LD-NKEDIFVHKSSI--VKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINV 176 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~-~d-~~~dvF~h~s~~--~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V 176 (191)
+...|+|+. +.||+-.. ++ ++.+-|+|+|.+ ...-.+. -.-| +|++|.+.+-.-++...-+++
T Consensus 13 elvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDl 79 (88)
T PHA02945 13 DVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred cEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 345677765 56776444 43 378999999966 3321111 2456 999999999887765443444
No 177
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=50.25 E-value=71 Score=26.75 Aligned_cols=67 Identities=21% Similarity=0.213 Sum_probs=44.1
Q ss_pred eeeeeeEEEeecCCCceeEEeCCC--CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC--CceeEEee
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDN--KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVT 177 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~--~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k--g~~A~~V~ 177 (191)
....|+|+.. ..||+...-+. +.+-|+|.+++.....+.--..++.||.|.+.+..-++ |.-...++
T Consensus 10 diV~G~V~~I---~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 10 ELVVGTVKEV---KDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CEEEEEEEEE---ECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence 4578888876 34777665432 68999999998653211111347899999999988664 44344444
No 178
>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=49.95 E-value=73 Score=21.99 Aligned_cols=55 Identities=25% Similarity=0.230 Sum_probs=34.6
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCC-----------CcccCCCCCEEEEEEEEcC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKK-----------FFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~-----------g~~~l~~Gd~V~f~~~~~~ 67 (191)
..|+|..-+. +|+...-+ ..+.|+|.+++....-.. .-..++.||.|.+.+..-.
T Consensus 3 v~g~V~~i~~---~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 3 VEGEVVEVVD---FGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred EEEEEEEEEe---ccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence 4577777653 56655544 378999999986431000 0134688999999886543
No 179
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=49.64 E-value=1.5e+02 Score=24.62 Aligned_cols=128 Identities=13% Similarity=0.009 Sum_probs=73.4
Q ss_pred eceeccceEEEEeeCCCCeeEEE--eCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCCCceeeEeecCCCC
Q psy9900 4 FEIHTVRGIVKFYDSKRGFGFIT--RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGI 81 (191)
Q Consensus 4 ~~~~~~~G~vk~~~~~kGfGFI~--~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~g~~A~~v~~~~~~ 81 (191)
-..+...|+|........-+.+. .+.++..+...++.-... .-.|.+|+.|.+.+.. ..|......
T Consensus 125 SarN~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~-----~L~l~~G~~v~~~Ika-------~~V~l~~~~ 192 (263)
T PRK10676 125 SARNQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAE-----RLGLDEGKEVLVLIKA-------PWVGITQDP 192 (263)
T ss_pred chhhcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHh-----hcCCCCCCeEEEEEEC-------CEEEEEcCC
Confidence 34456789999996553345543 444344577766655433 2467899999887643 333331111
Q ss_pred CccCCCCCCCccccccccCCcccccceeeeeeEEEeecCCCceeEEeC-CCCCcEEEeccchhccCcccccccCCCCCEE
Q psy9900 82 PVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRL-DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIV 160 (191)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~Vk~~~~~kgfGFI~~~-d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V 160 (191)
|.. ........|+|.........=-|.-+ +++..+...++.-.-. --.|++|+.|
T Consensus 193 ~~~-------------------~SarN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~-----~L~L~~G~~V 248 (263)
T PRK10676 193 AVA-------------------QAADNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAA-----RLSLQQGDAV 248 (263)
T ss_pred CCC-------------------CChhheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHH-----hcCCCCCCEE
Confidence 100 12234688999998655444334433 3345566655553322 2478899999
Q ss_pred EEEEEEc
Q psy9900 161 DFNIGVG 167 (191)
Q Consensus 161 ~f~i~~~ 167 (191)
...+..+
T Consensus 249 ~a~iKas 255 (263)
T PRK10676 249 TAYFNAD 255 (263)
T ss_pred EEEEEcc
Confidence 9887654
No 180
>PRK10811 rne ribonuclease E; Reviewed
Probab=49.31 E-value=73 Score=31.88 Aligned_cols=72 Identities=13% Similarity=0.069 Sum_probs=49.9
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCccc--------cc-ccCCCCCEEEEEEEEcC---CCc-eeE
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKK--------FF-QSLGLGEIVDFNIGVGK---KDI-EAI 174 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~--------~~-~~l~~G~~V~f~i~~~~---kg~-~A~ 174 (191)
..+.|+|+..-+.-+--||.-.+ ++.-|+|++++....... .. ..|++||.|.+.|.... ||+ -..
T Consensus 40 nIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 40 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred ceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 45789999888888888998876 688999988885210000 01 24889999999999855 553 344
Q ss_pred EeecCC
Q psy9900 175 NVTGPN 180 (191)
Q Consensus 175 ~V~~~~ 180 (191)
+|++.+
T Consensus 119 ~ISLpG 124 (1068)
T PRK10811 119 FISLAG 124 (1068)
T ss_pred eEEecc
Confidence 666554
No 181
>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=48.38 E-value=58 Score=29.20 Aligned_cols=62 Identities=16% Similarity=0.048 Sum_probs=43.8
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC------------CCCCcccCCCCCEEEEEEEEcCC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN------------PKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~------------~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
..-..|+|+...+--.--||.... +..-|+|++++.... .+.-...|++||.|.+.+...+.
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~ 99 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPR 99 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCc
Confidence 344678999887766678888865 579999999985310 00001148899999999998664
No 182
>KOG0109|consensus
Probab=48.27 E-value=29 Score=29.75 Aligned_cols=21 Identities=29% Similarity=0.409 Sum_probs=18.0
Q ss_pred ceEEEEeeCCCCeeEEEeCCC
Q psy9900 10 RGIVKFYDSKRGFGFITRLDN 30 (191)
Q Consensus 10 ~G~vk~~~~~kGfGFI~~~~~ 30 (191)
-|+|..-|..|-|||+..++.
T Consensus 26 ygkVlECDIvKNYgFVHiEdk 46 (346)
T KOG0109|consen 26 YGKVLECDIVKNYGFVHIEDK 46 (346)
T ss_pred hCceEeeeeecccceEEeecc
Confidence 599999999999999987653
No 183
>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=48.23 E-value=68 Score=20.18 Aligned_cols=61 Identities=11% Similarity=-0.071 Sum_probs=37.1
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCc-cEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKE-DIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~-dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
|.....++..|+|.+-.....+--|..+-++. .+....+.-... -..|++|+.|...+...
T Consensus 1 ~~~s~~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~-----~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 1 LQTSARNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA-----ELGLKPGKEVYAVIKAP 62 (69)
T ss_pred CCcccccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh-----hCCCCCCCEEEEEEECc
Confidence 45555677899999997554444344433223 555555443221 24678999999877543
No 184
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=47.46 E-value=1.9e+02 Score=25.86 Aligned_cols=60 Identities=20% Similarity=0.215 Sum_probs=42.8
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCCCCC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPNGIP 183 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~~~ 183 (191)
...++.+|..+. ..|.|....+ +.-|||. ..-+||+|++.|.+..++ ..|.-+.++.-+|
T Consensus 13 ~~~~~l~i~~l~-~~G~Gv~~~~--~~~vfV~--------------~~lPGe~v~v~i~~~~~~~~~~~~~~vl~~sp 73 (443)
T PRK13168 13 RQIITVTIESLD-HDGRGVARHN--GKTVFIE--------------GALPGERVEVQVTEDKKQYARAKVVRILKPSP 73 (443)
T ss_pred CcEEEEEEEEcC-CCCceEEEEC--CEEEEeC--------------CCCCCCEEEEEEEEecCcEEEEEEEEEecCCc
Confidence 344567787774 7788887653 4677773 335899999999997776 6677777766555
No 185
>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=47.36 E-value=52 Score=31.43 Aligned_cols=58 Identities=22% Similarity=0.160 Sum_probs=40.8
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....|+|+... .||....-..+.+-|+|.|.+.......-...++.||.|.+++..-.
T Consensus 620 ~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id 677 (684)
T TIGR03591 620 KIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677 (684)
T ss_pred cEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEEC
Confidence 44678888884 48877766557899999999965421111234688999999987644
No 186
>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=47.32 E-value=50 Score=31.81 Aligned_cols=57 Identities=21% Similarity=0.197 Sum_probs=39.7
Q ss_pred eccceEEEEeeCCCCeeEEEeCCCCccEEEEeeehe----ecCCCCCcccCCCCCEEEEEEEEc
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIV----KMNPKKFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~----~~~~~~g~~~l~~Gd~V~f~~~~~ 66 (191)
....|+|+.-- -||....-..+.+-|+|+|.+. .....+-...++.||.|.+++..-
T Consensus 649 ~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~I 709 (719)
T TIGR02696 649 ERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADI 709 (719)
T ss_pred CEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEE
Confidence 45679999874 4898776666789999999773 110011233578999999998653
No 187
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=47.30 E-value=33 Score=25.09 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=21.8
Q ss_pred cccCCCCCEEEEEEEEcCCCceeeEee
Q psy9900 50 FQSLGLGEIVDFNIGVGKKDIEAINVT 76 (191)
Q Consensus 50 ~~~l~~Gd~V~f~~~~~~~g~~A~~v~ 76 (191)
+..|++||.|.|.+.....+.....|.
T Consensus 86 l~~lk~G~~V~F~~~~~~~~~~i~~i~ 112 (115)
T PRK09838 86 MSEIKTGDKVAFNFVQQGNLSLLQDIK 112 (115)
T ss_pred hccCCCCCEEEEEEEEcCCcEEEEEEe
Confidence 357899999999999988887665554
No 188
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=45.65 E-value=88 Score=27.09 Aligned_cols=68 Identities=12% Similarity=-0.011 Sum_probs=44.9
Q ss_pred eccceEEEEeeCCCCeeEEEeCC--CCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEc--CCCceeeEeec
Q psy9900 7 HTVRGIVKFYDSKRGFGFITRLD--NKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG--KKDIEAINVTG 77 (191)
Q Consensus 7 ~~~~G~vk~~~~~kGfGFI~~~~--~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~--~~g~~A~~v~~ 77 (191)
....|+|+... -||.+..-. ++-+-|+|.|.|......+-...++.||.|.+.+-.- .+|.....+..
T Consensus 19 dvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~ 90 (319)
T PTZ00248 19 DLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKR 90 (319)
T ss_pred CEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeee
Confidence 34678998875 477765543 3689999999996542111223479999999998753 34554554443
No 189
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=43.37 E-value=53 Score=29.94 Aligned_cols=52 Identities=17% Similarity=0.295 Sum_probs=39.4
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
...++|+|+... ++ |++..-+ +-+.|+|.+.+... ..++.||+|.+.+..-.
T Consensus 135 GeIV~G~V~ri~--~~-giiVDLg-gvea~LP~sE~ip~------E~~~~GdrIka~I~~Vd 186 (470)
T PRK09202 135 GEIITGVVKRVE--RG-NIIVDLG-RAEAILPRKEQIPR------ENFRPGDRVRAYVYEVR 186 (470)
T ss_pred CCEEEEEEEEEe--cC-CEEEEEC-CeEEEecHHHcCCC------ccCCCCCEEEEEEEEEe
Confidence 356789999996 44 5555443 57999999999643 67899999999987543
No 190
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=43.11 E-value=39 Score=22.09 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=25.0
Q ss_pred ccCCCCCEEEEEEEEcCCC-ceeEEeecCCC
Q psy9900 152 QSLGLGEIVDFNIGVGKKD-IEAINVTGPNG 181 (191)
Q Consensus 152 ~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~ 181 (191)
..+.+||.|+|.|.-...| .-|.+|++-+-
T Consensus 35 ~~~~~Gd~v~ytitvtN~G~~~a~nv~v~D~ 65 (76)
T PF01345_consen 35 STANPGDTVTYTITVTNTGPAPATNVVVTDT 65 (76)
T ss_pred CcccCCCEEEEEEEEEECCCCeeEeEEEEEc
Confidence 5778999999999998888 55778887664
No 191
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=42.20 E-value=31 Score=24.69 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=20.4
Q ss_pred cccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900 151 FQSLGLGEIVDFNIGVGKKDIEAINVT 177 (191)
Q Consensus 151 ~~~l~~G~~V~f~i~~~~kg~~A~~V~ 177 (191)
+..|++||.|+|..++-+.-+.-.+|+
T Consensus 81 lsglKeGdkV~fvferv~gk~tv~qvk 107 (108)
T COG5569 81 LSGLKEGDKVEFVFERVNGKLTVQQVK 107 (108)
T ss_pred hhccccCCcEEEEEEeeCCEEEEEEec
Confidence 578999999999988766555555543
No 192
>PF06523 DUF1106: Protein of unknown function (DUF1106); InterPro: IPR009490 This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=41.34 E-value=92 Score=21.02 Aligned_cols=58 Identities=22% Similarity=0.380 Sum_probs=40.4
Q ss_pred ccccceeeeeeEEEeecCCCceeEE----eCCCCCcEEE-eccchhccCcccccccCCCCCEEEEEEE
Q psy9900 103 FFPAVHTVRGIVKFYDSKRGFGFIT----RLDNKEDIFV-HKSSIVKMNPKKFFQSLGLGEIVDFNIG 165 (191)
Q Consensus 103 ~~~~~~~~~G~Vk~~~~~kgfGFI~----~~d~~~dvF~-h~s~~~~~~~~~~~~~l~~G~~V~f~i~ 165 (191)
..++..+.+|.|-++...+|-=++. |++ ...||. |..+..- +.+..+-+.+.++|+|+
T Consensus 26 fsiicgrlrgiv~t~kcs~g~iylsi~v~pnn-~~hi~ly~kk~yi~----dklkeifpde~iefsie 88 (91)
T PF06523_consen 26 FSIICGRLRGIVLTIKCSNGIIYLSIKVNPNN-SNHIFLYHKKNYIF----DKLKEIFPDEAIEFSIE 88 (91)
T ss_pred EEEEeeceeeEEEEEEecCcEEEEEEEeCCCC-cceEEEEecchhHH----HHHHHhCCCCceEEEEE
Confidence 3577888999999998888865543 344 456665 4444322 23678889999999986
No 193
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=40.66 E-value=54 Score=24.64 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=35.7
Q ss_pred eeeeEEEeecCC-----CceeEEeCCCCCcEEE-eccchhccCcccccccCCCCCEEEEE--EEEcCCC
Q psy9900 110 VRGIVKFYDSKR-----GFGFITRLDNKEDIFV-HKSSIVKMNPKKFFQSLGLGEIVDFN--IGVGKKD 170 (191)
Q Consensus 110 ~~G~Vk~~~~~k-----gfGFI~~~d~~~dvF~-h~s~~~~~~~~~~~~~l~~G~~V~f~--i~~~~kg 170 (191)
-.|+|...-++. --=||...+.+..+.| |--++. ..+..|++||.|+|. ..-++||
T Consensus 41 g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla-----prip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 41 GCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA-----PRIPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred ccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc-----ccCcCcCCCCEEEEEEEEEECCCC
Confidence 367777764442 2347777766766665 444443 247889999999995 4445565
No 194
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=39.64 E-value=69 Score=24.08 Aligned_cols=58 Identities=21% Similarity=0.181 Sum_probs=39.1
Q ss_pred ccceEEEEeeCCC-----CeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEE--EEEcCCC
Q psy9900 8 TVRGIVKFYDSKR-----GFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN--IGVGKKD 69 (191)
Q Consensus 8 ~~~G~vk~~~~~k-----GfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~--~~~~~~g 69 (191)
.-.|+|+.-.++. --=||.....+..++|- .++..+. -...|+.||.|+|. ..-+++|
T Consensus 40 ~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIa-hNIDlap---rip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 40 SGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIA-HNIDLAP---RIPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred eccEEEEEECcccCCCCcceEEEEEeCCCCEEEEE-eccCccc---cCcCcCCCCEEEEEEEEEECCCC
Confidence 3468888876663 23488877777777775 5555442 46679999999995 3445554
No 195
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=39.09 E-value=54 Score=25.73 Aligned_cols=48 Identities=25% Similarity=0.326 Sum_probs=38.7
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEE
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
.-|+||.|+.+..-|.++-.+ -+|+=+|-..+..-. -.|.+||.|..-
T Consensus 36 rIG~iK~F~~~tQe~iVti~e-~e~LeI~T~nISN~~-----leLs~~D~VlLL 83 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTIPE-YEDLEIHTKNISNIN-----LELSKGDEVLLL 83 (181)
T ss_pred EEeeeeecccccceEEEEeec-ccCceEEeeecccce-----eEecCCCEEEEE
Confidence 359999999999999988775 678888887777653 578999998753
No 196
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=38.48 E-value=1.4e+02 Score=28.97 Aligned_cols=74 Identities=18% Similarity=0.165 Sum_probs=50.5
Q ss_pred cceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC--CCceeEEeecCCCC
Q psy9900 106 AVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK--KDIEAINVTGPNGI 182 (191)
Q Consensus 106 ~~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~--kg~~A~~V~~~~~~ 182 (191)
..+...|+|... ..||-+..-+-..|..+|+|.+...--.....-++.||.|...+.+-+ ++.-+...+..+..
T Consensus 658 ~Gm~leg~Vrnv---~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~ 733 (780)
T COG2183 658 PGMILEGTVRNV---VDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEE 733 (780)
T ss_pred CCCEEEEEEEEe---eeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence 346788999875 347777777778999999999986311111367899999999988744 33445555544443
No 197
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=38.18 E-value=63 Score=21.97 Aligned_cols=36 Identities=19% Similarity=0.355 Sum_probs=22.4
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCC---ccEEEEeeeh
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNK---EDIFVHKSSI 41 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~---~dvFvh~s~l 41 (191)
.....|+|......+++|-...-+.+ .-+|.|.+.+
T Consensus 17 ~A~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~ 55 (96)
T PF01551_consen 17 YAPADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSV 55 (96)
T ss_dssp EESSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEE
T ss_pred EeCccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccc
Confidence 34578999999887777766543323 3455555443
No 198
>CHL00010 infA translation initiation factor 1
Probab=36.89 E-value=1.3e+02 Score=20.18 Aligned_cols=59 Identities=14% Similarity=0.030 Sum_probs=35.3
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 65 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~ 65 (191)
|.|...-.++|+|..--. .+|=.+..++ +..+-.|..-.... ....+..||.|+|++..
T Consensus 1 m~~~~~~~~~G~Vik~lg-~~~y~V~~~~-g~~~~c~~rGklr~----~~i~~~vGD~V~ve~~~ 59 (78)
T CHL00010 1 MKKENKIEMEGLVTESLP-NGMFRVRLDN-GCQVLGYISGKIRR----NSIRILPGDRVKVELSP 59 (78)
T ss_pred CCccceEEEEEEEEEEcC-CCEEEEEeCC-CCEEEEEeccceec----CCcccCCCCEEEEEEcc
Confidence 666666678899887532 3444455544 44454554433221 12457799999999644
No 199
>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=35.37 E-value=89 Score=19.61 Aligned_cols=49 Identities=29% Similarity=0.240 Sum_probs=32.4
Q ss_pred eeeeEEEe-ecCCCceeEEeCCCCCcEEEeccc--hhccCcccccccCCCCCEEEEE
Q psy9900 110 VRGIVKFY-DSKRGFGFITRLDNKEDIFVHKSS--IVKMNPKKFFQSLGLGEIVDFN 163 (191)
Q Consensus 110 ~~G~Vk~~-~~~kgfGFI~~~d~~~dvF~h~s~--~~~~~~~~~~~~l~~G~~V~f~ 163 (191)
..|.|... ...+.+-|++-.|+...+-+.+.. ... ....|++|+.|.+.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~-----~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYER-----FREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHH-----HHHTS-TTSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhH-----HhhcCCCCeEEEEE
Confidence 45777777 777888998887765444433333 222 24789999999987
No 200
>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=34.97 E-value=1.6e+02 Score=20.62 Aligned_cols=59 Identities=19% Similarity=0.168 Sum_probs=38.9
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccC-------------------cccccccCCCCCEEEEEEEEcC
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN-------------------PKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~-------------------~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....|+|+... .+|-+..-..+-+-|+|++++.... ...-...++.||.|.+.|..-+
T Consensus 5 ~vV~G~V~~v~---~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 5 MLVLGQVKEIT---KLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CEEEEEEEEEc---CCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence 35678888863 3354444444789999999996420 0001245799999999998866
Q ss_pred C
Q psy9900 169 K 169 (191)
Q Consensus 169 k 169 (191)
+
T Consensus 82 ~ 82 (100)
T cd05693 82 K 82 (100)
T ss_pred C
Confidence 4
No 201
>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=34.86 E-value=1.2e+02 Score=23.57 Aligned_cols=58 Identities=22% Similarity=0.069 Sum_probs=36.2
Q ss_pred eceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC-----------CCcccCCCCCEEEEEEEE
Q psy9900 4 FEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-----------KFFQSLGLGEIVDFNIGV 65 (191)
Q Consensus 4 ~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~-----------~g~~~l~~Gd~V~f~~~~ 65 (191)
.......|+|+.-+. +|+...-+ .-+-++|.+++....-. +.-..+..||.|.|.+..
T Consensus 80 ~~gEvv~G~V~~v~~---~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 148 (179)
T TIGR00448 80 ELGEIVEGEVIEIVE---FGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVA 148 (179)
T ss_pred cCCCEEEEEEEEEEe---eEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEE
Confidence 344567888888864 78877664 46778888887533100 011346777777777654
No 202
>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=34.73 E-value=1.1e+02 Score=20.18 Aligned_cols=49 Identities=10% Similarity=0.108 Sum_probs=37.5
Q ss_pred CCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 120 ~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
.+.|-.|.-.+++.-.+|..+.=....++.+-..|+.|+.+...+....
T Consensus 12 ~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~ 60 (69)
T cd05701 12 DKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPN 60 (69)
T ss_pred hhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCc
Confidence 5678888888888888887666555555556689999999999887644
No 203
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=34.46 E-value=90 Score=26.13 Aligned_cols=58 Identities=21% Similarity=0.158 Sum_probs=38.5
Q ss_pred ccceEEEEeeCCCCeeEEEe-CCC-CccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC
Q psy9900 8 TVRGIVKFYDSKRGFGFITR-LDN-KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~~-~~~-~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~ 68 (191)
...|+|+... .||+... ++. +-+-|+|.|.+.......-...++.||.|.+.+..-..
T Consensus 11 iV~G~V~~I~---~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~ 70 (262)
T PRK03987 11 LVVGTVKEVK---DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDP 70 (262)
T ss_pred EEEEEEEEEE---CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEec
Confidence 4568888773 5676654 332 57899999998654211112346899999999876543
No 204
>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=33.91 E-value=1.3e+02 Score=26.18 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=38.8
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....+|+|...+ .+||=||.. ++-+-|++.+.+... ..+..||+|.+.+..-.
T Consensus 132 GeiV~G~V~~v~-~~g~v~Vdi--G~~ea~LP~~E~ip~------E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 132 GEIISGTVKRVN-RRGNLYVEL--GKTEGILPKKEQIPG------EKFRIGDRIKAYVYEVR 184 (341)
T ss_pred CCEEEEEEEEEe-cCCcEEEEE--CCeEEEecHHHcCCC------cCCCCCCEEEEEEEEEE
Confidence 455789999985 335434544 467899999988753 56899999999987543
No 205
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=33.67 E-value=55 Score=31.71 Aligned_cols=69 Identities=19% Similarity=0.200 Sum_probs=48.3
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcCC--CceeeEeecCCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVTGPNG 80 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~~--g~~A~~v~~~~~ 80 (191)
..|+|+.. .-||-+..-+-..|.+||+|.+....-+.+..-++.||.|...+..-+. ...+......+.
T Consensus 662 leg~Vrnv---~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~ 732 (780)
T COG2183 662 LEGTVRNV---VDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEE 732 (780)
T ss_pred EEEEEEEe---eeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence 56888765 3577776666689999999999876544456778999999999876433 333444444333
No 206
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=32.43 E-value=1.3e+02 Score=18.67 Aligned_cols=55 Identities=13% Similarity=-0.026 Sum_probs=34.2
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCc-EEEeccchhccCcccccccCCCCCEEEEEEEEc
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKED-IFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 167 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~d-vF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~ 167 (191)
-...|+|.........-+|.-.-++.. +....+.-... --.|++|+.|.+.+...
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-----~L~L~~G~~V~~~ik~~ 60 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-----ELGLKPGDEVYASIKAS 60 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-----HCT-STT-EEEEEE-GG
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-----HcCCCCCCEEEEEEehh
Confidence 457899998877776666666543434 66666543322 13588999999988653
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=31.68 E-value=1.4e+02 Score=19.09 Aligned_cols=52 Identities=19% Similarity=0.128 Sum_probs=33.0
Q ss_pred eeeeEEEee-cCCCceeEEeCCCC---CcEEEeccchhccCcccccccCCCCCEEEEEEEEc
Q psy9900 110 VRGIVKFYD-SKRGFGFITRLDNK---EDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVG 167 (191)
Q Consensus 110 ~~G~Vk~~~-~~kgfGFI~~~d~~---~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~ 167 (191)
+.|.|..+. ..+|+.|++..|.. +-++|+ +.+... ...|++|+.|.+.-.-.
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~-~~~~~~-----~~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDEDASIRCVMWR-SNARRL-----GFPLEEGMEVLVRGKVS 59 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeCCeEEEEEEEc-chhhhC-----CCCCCCCCEEEEEEEEE
Confidence 445555554 47789999987654 334555 333322 26889999998876544
No 208
>PRK10811 rne ribonuclease E; Reviewed
Probab=30.89 E-value=1.5e+02 Score=29.77 Aligned_cols=60 Identities=13% Similarity=0.084 Sum_probs=39.9
Q ss_pred cceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCC---------cccCCCCCEEEEEEEEcCCC
Q psy9900 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKF---------FQSLGLGEIVDFNIGVGKKD 69 (191)
Q Consensus 9 ~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g---------~~~l~~Gd~V~f~~~~~~~g 69 (191)
..|+|+.-..--+=-||.... +...|+|++++....-... -..|++||.|.+.+...+.+
T Consensus 42 YkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 42 YKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred EEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence 456666665555556887776 5789999988852210000 12488999999999986654
No 209
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=30.00 E-value=1.7e+02 Score=25.75 Aligned_cols=52 Identities=13% Similarity=0.111 Sum_probs=37.9
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....+|+|...+. .|++... ++-+-|+|.++.... ..++.||+|.+.+..=+
T Consensus 135 GeiV~G~V~~~~~---~~~~Vdl-g~vEa~LP~~E~ip~------e~~~~Gd~Ika~V~~V~ 186 (362)
T PRK12327 135 GDIVTGVVQRRDN---RFVYVNL-GKIEAVLPPAEQIPG------ETYKHGDRIKVYVVKVE 186 (362)
T ss_pred CCEEEEEEEEEeC---CcEEEEe-CCeEEEecHHHcCCC------CCCCCCCEEEEEEEEEe
Confidence 3567999999753 3455444 357889998887654 57899999999887644
No 210
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=29.10 E-value=1.1e+02 Score=24.01 Aligned_cols=47 Identities=19% Similarity=0.159 Sum_probs=37.0
Q ss_pred EeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCC-ceeEEeecCCC
Q psy9900 127 TRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD-IEAINVTGPNG 181 (191)
Q Consensus 127 ~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg-~~A~~V~~~~~ 181 (191)
..++....+.++.+-+. +.+.+|+.|.+.+.--..| -.|.+|++.+.
T Consensus 15 ~~~~~~a~llv~K~il~--------~~~v~g~~v~V~~~iyN~G~~~A~dV~l~D~ 62 (181)
T PF05753_consen 15 AQEDSPARLLVSKQILN--------KYLVEGEDVTVTYTIYNVGSSAAYDVKLTDD 62 (181)
T ss_pred ccCCCCcEEEEEEeecc--------ccccCCcEEEEEEEEEECCCCeEEEEEEECC
Confidence 34455677888777766 4778999999999998888 67889999883
No 211
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=27.92 E-value=1.1e+02 Score=24.41 Aligned_cols=68 Identities=22% Similarity=0.136 Sum_probs=43.5
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCc-----------ccccccCCCCCEEEEEEEEcCCC---cee
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNP-----------KKFFQSLGLGEIVDFNIGVGKKD---IEA 173 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~-----------~~~~~~l~~G~~V~f~i~~~~kg---~~A 173 (191)
+-..|.|..- ..||+...-. ..|.|+|.+.+..... +..-..++.||.|.+.|...... ++.
T Consensus 83 EVV~GeVv~~---~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~ 158 (183)
T COG1095 83 EVVEGEVVEV---VEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE 158 (183)
T ss_pred cEEEEEEEEE---eecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence 4466777664 4477766654 6789999998865400 00113688999999999886543 345
Q ss_pred EEeecC
Q psy9900 174 INVTGP 179 (191)
Q Consensus 174 ~~V~~~ 179 (191)
..|.+.
T Consensus 159 ~~I~lT 164 (183)
T COG1095 159 SKIGLT 164 (183)
T ss_pred ceEEEE
Confidence 555543
No 212
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=27.63 E-value=1.8e+02 Score=19.02 Aligned_cols=59 Identities=14% Similarity=0.140 Sum_probs=33.1
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 65 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~ 65 (191)
|.+.....++|+|..-- ..+|=.+..++ +..+-.|..-.... ....+..||.|+|++..
T Consensus 1 ~~~~~~~~~~G~Vi~~~-~~~~y~V~~~~-g~~~~c~~~Gklr~----~~i~i~vGD~V~ve~~~ 59 (72)
T PRK00276 1 MAKEDVIEMEGTVVEAL-PNAMFRVELEN-GHEVLAHISGKMRK----NYIRILPGDKVTVELSP 59 (72)
T ss_pred CCccceEEEEEEEEEEc-CCCEEEEEeCC-CCEEEEEEccceee----CCcccCCCCEEEEEEcc
Confidence 44555556788888752 12244455544 44444554432221 12457899999999654
No 213
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=27.50 E-value=1.3e+02 Score=26.59 Aligned_cols=52 Identities=13% Similarity=0.116 Sum_probs=37.0
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEEcC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~~~ 67 (191)
....+|+|+..+. + |++...+ +-+-|++.+++... ..++.||+|.+.+..-.
T Consensus 135 GeiV~G~V~~~~~--~-~~~Vdlg-~vEa~LP~~E~ip~------e~~~~Gd~Ika~V~~V~ 186 (362)
T PRK12327 135 GDIVTGVVQRRDN--R-FVYVNLG-KIEAVLPPAEQIPG------ETYKHGDRIKVYVVKVE 186 (362)
T ss_pred CCEEEEEEEEEeC--C-cEEEEeC-CeEEEecHHHcCCC------CCCCCCCEEEEEEEEEe
Confidence 3457899999853 4 4444333 46789998877643 67899999999987543
No 214
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=26.84 E-value=2.2e+02 Score=19.79 Aligned_cols=59 Identities=20% Similarity=0.197 Sum_probs=43.0
Q ss_pred CceeceeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEEEE
Q psy9900 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 65 (191)
Q Consensus 1 ~~~~~~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~~~ 65 (191)
|.|-....+.|+|..--..-- |-...+++..|--|++---.. ....+-+||+|.+++..
T Consensus 1 M~ke~~ie~~G~V~e~Lp~~~--frV~LenG~~vla~isGKmR~----~rIrIl~GD~V~VE~sp 59 (87)
T PRK12442 1 MAKEELIELDGIVDEVLPDSR--FRVTLENGVEVGAYASGRMRK----HRIRILAGDRVTLELSP 59 (87)
T ss_pred CCccceEEEEEEEEEECCCCE--EEEEeCCCCEEEEEeccceee----eeEEecCCCEEEEEECc
Confidence 666677778899998854443 333334478899999876554 35788899999999875
No 215
>PRK11637 AmiB activator; Provisional
Probab=26.17 E-value=72 Score=28.39 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=15.1
Q ss_pred ccceEEEEeeCCCCeeEEE
Q psy9900 8 TVRGIVKFYDSKRGFGFIT 26 (191)
Q Consensus 8 ~~~G~vk~~~~~kGfGFI~ 26 (191)
-..|+|.+-+...|||-+.
T Consensus 345 ~~~G~V~~~~~~~~~G~~v 363 (428)
T PRK11637 345 IADGRVLLADWLQGYGLVV 363 (428)
T ss_pred cCCeEEEEeeccCCcccEE
Confidence 4679999888889999544
No 216
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=26.11 E-value=1.6e+02 Score=18.64 Aligned_cols=53 Identities=23% Similarity=0.203 Sum_probs=36.7
Q ss_pred eecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEeecC
Q psy9900 117 YDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 179 (191)
Q Consensus 117 ~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~~~ 179 (191)
|+....|=|..+++ =+.+.+....+... ..-|++|..|...+-.+. ++.|++|
T Consensus 9 Y~dg~~~~FMd~et-yeQ~~i~~~~igd~-----~~~L~e~~~v~v~~~~~~----~i~v~lP 61 (61)
T cd04470 9 YKDGDNYVFMDTET-YEQIELPKEALGDA-----AKFLKEGMEVIVLFYNGE----PIGVELP 61 (61)
T ss_pred EeCCCEEEEeCCCC-ceEEEECHHHhhhH-----HhhCcCCCEEEEEEECCE----EEEEECc
Confidence 55556666766654 68899988888654 478999999988876432 5555543
No 217
>KOG0125|consensus
Probab=26.04 E-value=39 Score=29.44 Aligned_cols=15 Identities=33% Similarity=0.944 Sum_probs=11.6
Q ss_pred eeCC--CCeeEEEeCCC
Q psy9900 16 YDSK--RGFGFITRLDN 30 (191)
Q Consensus 16 ~~~~--kGfGFI~~~~~ 30 (191)
||.+ |||||++.++.
T Consensus 130 fNERGSKGFGFVTmen~ 146 (376)
T KOG0125|consen 130 FNERGSKGFGFVTMENP 146 (376)
T ss_pred eccCCCCccceEEecCh
Confidence 6654 89999998763
No 218
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=24.14 E-value=1.9e+02 Score=18.16 Aligned_cols=51 Identities=14% Similarity=0.186 Sum_probs=26.3
Q ss_pred eeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEE
Q psy9900 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGV 166 (191)
Q Consensus 110 ~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~ 166 (191)
++|+|..-- ..++-.+..++ ++.+=.+..-.... ....+.+||.|.|++..
T Consensus 3 ~~G~Vi~~~-~g~~~~V~~~~-g~~~~c~~rGklr~----~~~~~~vGD~V~~~~~~ 53 (64)
T cd04451 3 MEGVVTEAL-PNAMFRVELEN-GHEVLAHISGKMRM----NYIRILPGDRVKVELSP 53 (64)
T ss_pred EEEEEEEEe-CCCEEEEEeCC-CCEEEEEECceeec----CCcccCCCCEEEEEEee
Confidence 356665431 13455566544 33333333221110 12347899999999764
No 219
>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=23.16 E-value=2.5e+02 Score=24.52 Aligned_cols=53 Identities=15% Similarity=0.177 Sum_probs=38.0
Q ss_pred ceeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 107 ~~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
....+|+|...+. +||=|| +-++-+-|++.+..... ..+..||+|.+.+..-+
T Consensus 132 GeiV~G~V~~v~~-~g~v~V--diG~~ea~LP~~E~ip~------E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 132 GEIISGTVKRVNR-RGNLYV--ELGKTEGILPKKEQIPG------EKFRIGDRIKAYVYEVR 184 (341)
T ss_pred CCEEEEEEEEEec-CCcEEE--EECCeEEEecHHHcCCC------cCCCCCCEEEEEEEEEE
Confidence 3567999999743 233233 32467899999998854 46899999999887744
No 220
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=22.29 E-value=61 Score=22.17 Aligned_cols=27 Identities=15% Similarity=0.335 Sum_probs=15.8
Q ss_pred ccccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900 150 FFQSLGLGEIVDFNIGVGKKDIEAINVT 177 (191)
Q Consensus 150 ~~~~l~~G~~V~f~i~~~~kg~~A~~V~ 177 (191)
-+..|++||.++|.+..+.+ +.+..+.
T Consensus 39 ~L~~L~pGq~l~f~~d~~g~-L~~L~~~ 65 (85)
T PF04225_consen 39 PLTRLKPGQTLEFQLDEDGQ-LTALRYE 65 (85)
T ss_dssp -GGG--TT-EEEEEE-TTS--EEEEEEE
T ss_pred hHhhCCCCCEEEEEECCCCC-EEEEEEE
Confidence 47899999999999986422 6666554
No 221
>PRK11712 ribonuclease G; Provisional
Probab=21.84 E-value=3.1e+02 Score=25.26 Aligned_cols=63 Identities=16% Similarity=0.074 Sum_probs=43.4
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecC------CCCC------cccCCCCCEEEEEEEEcCCC
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMN------PKKF------FQSLGLGEIVDFNIGVGKKD 69 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~------~~~g------~~~l~~Gd~V~f~~~~~~~g 69 (191)
..-..|+|+.-.+--.=-||.-.. +..-|+|.+++.... .... ...|++||.|.+.+...+.|
T Consensus 39 GnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~ 113 (489)
T PRK11712 39 GNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLG 113 (489)
T ss_pred ccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcC
Confidence 344568888887777778888776 689999999873200 0000 01288999999999987643
No 222
>PF01796 DUF35: DUF35 OB-fold domain; InterPro: IPR002878 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA.
Probab=21.60 E-value=2.3e+02 Score=18.06 Aligned_cols=37 Identities=8% Similarity=0.029 Sum_probs=25.3
Q ss_pred eeEEEeCCCCccEEEEeeeheecCCCCCcccCCCCCEEEEEE
Q psy9900 22 FGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63 (191)
Q Consensus 22 fGFI~~~~~~~dvFvh~s~l~~~~~~~g~~~l~~Gd~V~f~~ 63 (191)
+|.|..++ +..++-++.+.... ....|+.|++|+...
T Consensus 31 v~~V~lde-g~rv~~~i~~~~~~----~~~~l~iG~~V~~vf 67 (68)
T PF01796_consen 31 VAIVELDE-GVRVMARIVDVDPE----DPDELRIGMRVRLVF 67 (68)
T ss_pred EEEEEeCC-CCEEEEEEecCCCC----CcccCCCCCEEEEEE
Confidence 57777865 56777777765432 235688999998754
No 223
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=21.59 E-value=2.4e+02 Score=27.06 Aligned_cols=60 Identities=25% Similarity=0.199 Sum_probs=42.7
Q ss_pred eeeeeeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCC-C
Q psy9900 108 HTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK-D 170 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~k-g 170 (191)
..+.|+|+.-.. ||-...--.++|-.+|+|.+...--..=-.-|+.||.|.+.+..-++ |
T Consensus 621 ~iy~G~V~ri~~---fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~G 681 (692)
T COG1185 621 EVYEGTVVRIVD---FGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQG 681 (692)
T ss_pred cEEEEEEEEEee---cceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccC
Confidence 558888888754 77655555589999999999763100112578999999999888554 6
No 224
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=21.58 E-value=2e+02 Score=24.22 Aligned_cols=67 Identities=18% Similarity=0.162 Sum_probs=41.9
Q ss_pred eeeeeeEEEeecCCCce-eEEeC-CCCCcEEEeccchhccCcccccccCCCCCEEEEEEEEcCCCceeEEee
Q psy9900 108 HTVRGIVKFYDSKRGFG-FITRL-DNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVT 177 (191)
Q Consensus 108 ~~~~G~Vk~~~~~kgfG-FI~~~-d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~kg~~A~~V~ 177 (191)
+..-|+|+... .|| |+..+ -++.+-|+|+|.+...--+.=-.-+++|+.|.+.+-.-+....-+++.
T Consensus 13 EiVv~tV~~V~---~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLS 81 (269)
T COG1093 13 EIVVGTVKQVA---DYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLS 81 (269)
T ss_pred cEEEEEEEEee---ccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeee
Confidence 45668887763 344 33333 246899999999975311111135789999999988866554444443
No 225
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=21.40 E-value=2e+02 Score=19.14 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=15.4
Q ss_pred cCCCCCEEEEEEEEcCCCc
Q psy9900 153 SLGLGEIVDFNIGVGKKDI 171 (191)
Q Consensus 153 ~l~~G~~V~f~i~~~~kg~ 171 (191)
.++.||.|.|.+..++.|+
T Consensus 2 ~~~~Ge~v~~~~~~~~~~Y 20 (83)
T PF14326_consen 2 VYRVGERVRFRVTSNRDGY 20 (83)
T ss_pred cccCCCEEEEEEEeCCCeE
Confidence 3578999999999988883
No 226
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=20.93 E-value=2.7e+02 Score=18.55 Aligned_cols=50 Identities=28% Similarity=0.335 Sum_probs=31.5
Q ss_pred eeeeEEEeecCC-CceeEEeCCC-------CCcEEEeccchhccCcccccccCCCCCEEEEEEEEcC
Q psy9900 110 VRGIVKFYDSKR-GFGFITRLDN-------KEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168 (191)
Q Consensus 110 ~~G~Vk~~~~~k-gfGFI~~~d~-------~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f~i~~~~ 168 (191)
.+|+|..-.... ..||-..+.. .+-||+.... . ..+++||.|++.=...+
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~--~-------~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGS--G-------ADVAVGDLVRVTGTVTE 59 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCC--C-------CCCCCCCEEEEEEEEEe
Confidence 457776554432 3566544431 2569998766 2 47789999999866555
No 227
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=20.75 E-value=2.4e+02 Score=21.83 Aligned_cols=57 Identities=25% Similarity=0.226 Sum_probs=36.5
Q ss_pred eeccceEEEEeeCCCCeeEEEeCCCCccEEEEeeeheecCCC-----------CCcccCCCCCEEEEEEEEc
Q psy9900 6 IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPK-----------KFFQSLGLGEIVDFNIGVG 66 (191)
Q Consensus 6 ~~~~~G~vk~~~~~kGfGFI~~~~~~~dvFvh~s~l~~~~~~-----------~g~~~l~~Gd~V~f~~~~~ 66 (191)
..-..|+|+.-+. +|+...-+ .-+.|+|.+++....-. +....+..||.|.|.+..-
T Consensus 82 GEVv~g~V~~v~~---~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v 149 (187)
T PRK08563 82 QEVVEGEVVEVVE---FGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAV 149 (187)
T ss_pred CCEEEEEEEEEEc---cEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEE
Confidence 4456788888863 56666554 47889999888643100 0113467888888887543
No 228
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=20.34 E-value=1.8e+02 Score=19.07 Aligned_cols=33 Identities=18% Similarity=0.400 Sum_probs=22.3
Q ss_pred eeeeEEEee--cCCCceeEEeCCCCCcEEEeccch
Q psy9900 110 VRGIVKFYD--SKRGFGFITRLDNKEDIFVHKSSI 142 (191)
Q Consensus 110 ~~G~Vk~~~--~~kgfGFI~~~d~~~dvF~h~s~~ 142 (191)
-.|+|+-|. +.+|.|+|..-+.+...+|--..|
T Consensus 28 ~~g~I~~fKmtDG~giG~vv~~~ng~~~WFFedEi 62 (64)
T PF11061_consen 28 PIGTIKGFKMTDGSGIGVVVEFSNGSRTWFFEDEI 62 (64)
T ss_pred CcEEEEEEEEecCCcEEEEEEecCCceeEEchhhc
Confidence 358888884 456788888766676666654443
No 229
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=20.23 E-value=2.6e+02 Score=18.20 Aligned_cols=41 Identities=17% Similarity=0.329 Sum_probs=30.8
Q ss_pred eeEEEeecCCCceeEEeCCCCCcEEEeccchhccCcccccccCCCCCEEEE
Q psy9900 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 162 (191)
Q Consensus 112 G~Vk~~~~~kgfGFI~~~d~~~dvF~h~s~~~~~~~~~~~~~l~~G~~V~f 162 (191)
++|-.| +.+|--+..+++...+-|+.+.|.. ..++||.+.+
T Consensus 2 ~ivDRi--E~~~AVl~~~~~~~~~~vp~~~LP~--------~~keGDvl~i 42 (71)
T PF11213_consen 2 AIVDRI--EGDYAVLELEDGEKEIDVPRSRLPE--------GAKEGDVLEI 42 (71)
T ss_pred eEEEEE--eCCEEEEEECCCeEEEEEEHHHCCC--------CCCcccEEEE
Confidence 567777 5677777777755478888888874 5689999887
Done!