Query 030172
Match_columns 182
No_of_seqs 167 out of 1538
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 09:39:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 1.5E-35 3.3E-40 259.0 14.5 168 4-179 129-310 (541)
2 COG0539 RpsA Ribosomal protein 100.0 1.3E-33 2.9E-38 246.8 13.6 167 5-178 217-395 (541)
3 PRK07899 rpsA 30S ribosomal pr 100.0 2.2E-31 4.7E-36 233.0 15.6 166 5-178 146-325 (486)
4 PRK13806 rpsA 30S ribosomal pr 100.0 1.1E-30 2.3E-35 230.1 14.9 167 5-178 228-411 (491)
5 PRK12269 bifunctional cytidyla 100.0 2.6E-30 5.6E-35 238.3 15.1 167 5-178 518-697 (863)
6 PRK13806 rpsA 30S ribosomal pr 100.0 9.8E-30 2.1E-34 224.1 13.8 167 5-178 140-324 (491)
7 PRK06299 rpsA 30S ribosomal pr 100.0 2.4E-28 5.2E-33 218.7 15.6 166 5-178 139-318 (565)
8 PRK06676 rpsA 30S ribosomal pr 100.0 3.3E-28 7.2E-33 209.0 15.2 167 5-179 130-310 (390)
9 PRK12269 bifunctional cytidyla 100.0 2.8E-28 6E-33 224.9 14.5 167 5-178 604-784 (863)
10 TIGR00717 rpsA ribosomal prote 99.9 1.3E-26 2.8E-31 205.4 14.0 166 5-178 125-304 (516)
11 TIGR00717 rpsA ribosomal prote 99.9 1.6E-26 3.4E-31 204.9 14.2 167 5-178 298-478 (516)
12 PRK00087 4-hydroxy-3-methylbut 99.9 1.9E-26 4.1E-31 209.1 14.6 167 5-179 414-595 (647)
13 PRK06299 rpsA 30S ribosomal pr 99.9 2.9E-26 6.3E-31 205.2 14.0 168 5-179 312-493 (565)
14 PRK07400 30S ribosomal protein 99.9 2.1E-23 4.5E-28 174.8 12.7 158 5-178 57-227 (318)
15 PRK07899 rpsA 30S ribosomal pr 99.9 3.8E-23 8.3E-28 181.2 12.6 162 5-178 61-239 (486)
16 PRK07400 30S ribosomal protein 99.9 4.1E-23 8.9E-28 173.0 12.0 127 5-137 143-274 (318)
17 PRK06676 rpsA 30S ribosomal pr 99.9 2.3E-22 5E-27 172.8 12.9 163 6-179 45-224 (390)
18 PTZ00248 eukaryotic translatio 99.9 2.4E-21 5.3E-26 160.9 10.4 119 54-177 12-143 (319)
19 PRK00087 4-hydroxy-3-methylbut 99.8 2.3E-20 5.1E-25 169.5 12.4 162 6-178 329-508 (647)
20 COG1098 VacB Predicted RNA bin 99.7 5.5E-18 1.2E-22 121.3 4.5 77 55-137 2-83 (129)
21 PRK08582 hypothetical protein; 99.6 8.5E-15 1.8E-19 109.2 9.8 77 55-137 2-83 (139)
22 cd05705 S1_Rrp5_repeat_hs14 S1 99.6 5.9E-15 1.3E-19 98.6 7.2 66 56-126 1-74 (74)
23 PHA02945 interferon resistance 99.5 5.1E-14 1.1E-18 95.3 9.1 74 54-132 7-86 (88)
24 PF00575 S1: S1 RNA binding do 99.5 2.9E-14 6.4E-19 94.7 7.6 69 55-128 1-74 (74)
25 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 2.7E-14 5.9E-19 97.2 7.4 70 53-127 9-83 (83)
26 cd04452 S1_IF2_alpha S1_IF2_al 99.5 1.1E-13 2.4E-18 92.3 9.2 71 56-129 1-76 (76)
27 PLN00207 polyribonucleotide nu 99.5 6.3E-14 1.4E-18 129.5 10.3 86 49-140 744-835 (891)
28 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 5.5E-14 1.2E-18 93.4 7.1 66 56-128 1-72 (72)
29 cd05703 S1_Rrp5_repeat_hs12_sc 99.5 6.9E-14 1.5E-18 93.2 7.5 65 59-128 1-72 (73)
30 cd05698 S1_Rrp5_repeat_hs6_sc5 99.5 8.5E-14 1.8E-18 91.5 7.2 65 59-128 1-70 (70)
31 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 2E-13 4.3E-18 90.9 9.0 66 57-127 2-72 (73)
32 cd05706 S1_Rrp5_repeat_sc10 S1 99.5 2.2E-13 4.7E-18 90.4 8.9 68 56-128 1-73 (73)
33 PRK07252 hypothetical protein; 99.5 2.1E-13 4.6E-18 99.2 9.4 73 57-134 2-79 (120)
34 COG1093 SUI2 Translation initi 99.5 4.3E-14 9.2E-19 113.3 5.2 78 55-135 8-90 (269)
35 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.5 2.4E-13 5.2E-18 89.2 7.6 64 59-127 1-69 (69)
36 KOG1070 rRNA processing protei 99.5 1E-12 2.2E-17 123.8 13.9 151 22-177 1115-1284(1710)
37 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.5 2.7E-13 5.9E-18 89.8 7.4 57 66-127 15-71 (71)
38 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 9.3E-13 2E-17 88.0 9.3 68 55-132 1-73 (74)
39 cd05684 S1_DHX8_helicase S1_DH 99.4 1.3E-12 2.8E-17 88.0 9.8 71 59-134 1-78 (79)
40 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 1.2E-12 2.5E-17 87.3 8.9 70 57-130 1-75 (77)
41 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 9E-13 1.9E-17 87.0 8.3 67 59-130 1-72 (73)
42 PRK08059 general stress protei 99.4 1E-12 2.2E-17 96.1 9.3 76 54-134 3-83 (123)
43 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 5.5E-13 1.2E-17 87.3 6.5 63 59-126 1-68 (68)
44 PRK05807 hypothetical protein; 99.4 2.1E-12 4.5E-17 96.0 9.7 70 55-131 2-76 (136)
45 cd05690 S1_RPS1_repeat_ec5 S1_ 99.4 1.2E-12 2.5E-17 85.7 7.3 63 59-126 1-69 (69)
46 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 2.5E-12 5.3E-17 84.6 7.6 65 59-128 1-70 (70)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 99.4 3.7E-12 8.1E-17 82.7 7.9 64 59-128 1-69 (69)
48 PRK03987 translation initiatio 99.4 4.4E-12 9.5E-17 103.7 9.4 85 55-142 5-94 (262)
49 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 7.1E-12 1.5E-16 82.8 8.1 66 56-126 1-72 (72)
50 cd05693 S1_Rrp5_repeat_hs1_sc1 99.3 4.4E-12 9.6E-17 89.5 5.7 70 56-130 1-97 (100)
51 cd05685 S1_Tex S1_Tex: The C-t 99.3 1.4E-11 3E-16 79.8 6.5 63 59-126 1-68 (68)
52 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.3 1.8E-11 3.9E-16 79.9 6.9 61 59-126 1-66 (66)
53 cd05688 S1_RPS1_repeat_ec3 S1_ 99.3 3.1E-11 6.6E-16 78.3 7.8 63 58-126 1-68 (68)
54 cd04472 S1_PNPase S1_PNPase: P 99.3 3.2E-11 6.9E-16 78.3 7.6 63 59-127 1-68 (68)
55 KOG1070 rRNA processing protei 99.2 5.6E-11 1.2E-15 112.3 11.0 156 22-181 470-634 (1710)
56 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 3.6E-11 7.8E-16 82.2 7.2 70 55-130 3-81 (86)
57 PRK09521 exosome complex RNA-b 99.2 6.7E-11 1.4E-15 92.5 9.2 101 22-129 29-142 (189)
58 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 6.7E-11 1.5E-15 77.1 7.4 62 59-128 1-67 (67)
59 PRK11824 polynucleotide phosph 99.2 9.8E-11 2.1E-15 107.4 11.2 91 33-130 589-692 (693)
60 TIGR02696 pppGpp_PNP guanosine 99.2 8.5E-11 1.9E-15 106.9 10.6 89 31-126 611-718 (719)
61 smart00316 S1 Ribosomal protei 99.2 1.1E-10 2.3E-15 75.7 8.0 67 57-128 1-72 (72)
62 cd04453 S1_RNase_E S1_RNase_E: 99.2 1.2E-10 2.6E-15 80.3 7.8 70 54-128 3-82 (88)
63 cd04471 S1_RNase_R S1_RNase_R: 99.1 4.9E-10 1.1E-14 75.6 9.1 65 59-127 2-82 (83)
64 cd04454 S1_Rrp4_like S1_Rrp4_l 99.1 5E-10 1.1E-14 75.9 7.7 69 55-129 3-76 (82)
65 COG2183 Tex Transcriptional ac 99.1 2.8E-10 6E-15 103.4 6.8 75 53-132 653-732 (780)
66 TIGR02063 RNase_R ribonuclease 99.1 1E-10 2.2E-15 107.8 4.0 120 2-127 556-708 (709)
67 COG1185 Pnp Polyribonucleotide 99.1 6.4E-10 1.4E-14 99.7 8.8 93 32-131 586-691 (692)
68 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 1.4E-09 3E-14 71.6 6.4 57 59-120 1-64 (70)
69 TIGR03591 polynuc_phos polyrib 99.0 1.7E-09 3.7E-14 99.1 9.1 87 32-125 585-684 (684)
70 cd00164 S1_like S1_like: Ribos 99.0 1.5E-09 3.2E-14 69.0 6.2 56 66-126 10-65 (65)
71 cd04473 S1_RecJ_like S1_RecJ_l 99.0 5.6E-09 1.2E-13 70.0 8.9 61 53-127 11-76 (77)
72 cd04460 S1_RpoE S1_RpoE: RpoE, 98.9 6.4E-09 1.4E-13 73.0 8.8 68 66-139 12-95 (99)
73 COG2996 Predicted RNA-bindinin 98.9 1.5E-08 3.2E-13 82.2 11.1 137 22-180 46-189 (287)
74 TIGR00358 3_prime_RNase VacB a 98.9 1.7E-10 3.7E-15 105.4 -0.1 119 2-127 504-653 (654)
75 TIGR00448 rpoE DNA-directed RN 98.9 1.2E-08 2.6E-13 79.2 8.7 131 1-137 13-175 (179)
76 PRK09202 nusA transcription el 98.9 4.8E-09 1E-13 92.2 7.1 108 8-129 71-200 (470)
77 PRK11642 exoribonuclease R; Pr 98.9 5.8E-10 1.3E-14 103.8 1.1 73 55-131 640-728 (813)
78 COG1095 RPB7 DNA-directed RNA 98.8 3.2E-08 7E-13 76.1 7.9 126 1-132 13-170 (183)
79 PRK04163 exosome complex RNA-b 98.8 2.4E-08 5.1E-13 80.7 7.4 71 54-130 59-138 (235)
80 KOG1067 Predicted RNA-binding 98.7 1.6E-08 3.5E-13 88.9 3.7 82 54-141 664-750 (760)
81 PRK08563 DNA-directed RNA poly 98.7 2.2E-07 4.7E-12 72.5 9.5 128 1-134 13-172 (187)
82 cd04455 S1_NusA S1_NusA: N-uti 98.6 2.1E-07 4.5E-12 60.7 7.1 59 57-127 2-67 (67)
83 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.6 2.5E-07 5.4E-12 64.3 6.5 74 55-129 3-86 (92)
84 PHA02858 EIF2a-like PKR inhibi 98.5 4.4E-07 9.5E-12 61.1 5.8 69 54-127 12-85 (86)
85 PRK05054 exoribonuclease II; P 98.5 7.4E-08 1.6E-12 88.0 2.6 117 2-127 498-643 (644)
86 TIGR01953 NusA transcription t 98.4 8.3E-07 1.8E-11 75.3 7.7 109 8-130 68-199 (341)
87 PRK12327 nusA transcription el 98.4 5.1E-07 1.1E-11 77.1 6.0 109 8-129 71-200 (362)
88 COG2996 Predicted RNA-bindinin 98.3 9.5E-06 2.1E-10 66.0 10.4 94 22-131 117-219 (287)
89 COG0557 VacB Exoribonuclease R 98.2 7.5E-07 1.6E-11 82.3 2.8 121 2-128 555-704 (706)
90 KOG2916 Translation initiation 98.2 1.1E-06 2.4E-11 71.0 3.2 85 56-143 14-103 (304)
91 PTZ00248 eukaryotic translatio 98.2 2E-07 4.3E-12 78.1 -1.3 108 5-116 45-173 (319)
92 TIGR02062 RNase_B exoribonucle 98.2 5.9E-07 1.3E-11 82.1 1.6 116 2-126 494-638 (639)
93 cd05705 S1_Rrp5_repeat_hs14 S1 98.1 2E-06 4.4E-11 57.2 3.2 34 146-179 3-36 (74)
94 COG1096 Predicted RNA-binding 98.1 2E-05 4.3E-10 60.9 8.7 75 52-129 58-142 (188)
95 COG1097 RRP4 RNA-binding prote 98.0 4.7E-05 1E-09 61.1 8.8 99 21-130 31-139 (239)
96 cd05689 S1_RPS1_repeat_ec4 S1_ 97.9 1E-05 2.2E-10 53.0 2.7 31 147-177 4-34 (72)
97 cd05697 S1_Rrp5_repeat_hs5 S1_ 97.9 1.3E-05 2.7E-10 52.2 3.1 32 147-178 1-32 (69)
98 cd05703 S1_Rrp5_repeat_hs12_sc 97.9 1.3E-05 2.8E-10 53.1 3.1 32 147-178 1-32 (73)
99 cd05694 S1_Rrp5_repeat_hs2_sc2 97.9 1.6E-05 3.4E-10 52.9 3.4 35 146-180 4-39 (74)
100 cd05690 S1_RPS1_repeat_ec5 S1_ 97.9 1.1E-05 2.4E-10 52.3 2.5 32 147-178 1-32 (69)
101 cd05698 S1_Rrp5_repeat_hs6_sc5 97.8 1.6E-05 3.5E-10 51.7 2.7 33 147-179 1-33 (70)
102 PF00575 S1: S1 RNA binding do 97.8 2.5E-05 5.3E-10 51.3 3.6 35 146-180 4-38 (74)
103 cd04461 S1_Rrp5_repeat_hs8_sc7 97.8 2.9E-05 6.4E-10 52.4 3.8 39 139-179 9-47 (83)
104 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.8 2.5E-05 5.3E-10 50.7 2.9 32 147-178 1-32 (66)
105 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.7 0.00019 4.2E-09 49.1 7.3 69 55-130 3-76 (86)
106 PTZ00162 DNA-directed RNA poly 97.7 0.00016 3.5E-09 55.9 7.6 123 1-129 13-165 (176)
107 cd05707 S1_Rrp5_repeat_sc11 S1 97.7 2.8E-05 6.1E-10 50.4 2.7 32 147-178 1-32 (68)
108 cd04453 S1_RNase_E S1_RNase_E: 97.7 3.6E-05 7.9E-10 52.9 2.9 33 146-178 7-41 (88)
109 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.7 4.2E-05 9.1E-10 50.3 2.9 32 147-178 1-34 (71)
110 cd05706 S1_Rrp5_repeat_sc10 S1 97.6 5.5E-05 1.2E-09 49.6 3.1 33 146-178 3-35 (73)
111 cd05704 S1_Rrp5_repeat_hs13 S1 97.5 0.00012 2.6E-09 48.2 3.4 35 146-180 3-38 (72)
112 TIGR00757 RNaseEG ribonuclease 97.5 0.00034 7.3E-09 61.0 7.1 58 54-116 21-97 (414)
113 cd04473 S1_RecJ_like S1_RecJ_l 97.5 0.00011 2.4E-09 49.0 3.0 35 141-177 13-47 (77)
114 cd04465 S1_RPS1_repeat_ec2_hs2 97.4 0.00011 2.4E-09 47.4 2.8 32 147-179 1-32 (67)
115 cd05686 S1_pNO40 S1_pNO40: pNO 97.4 0.00011 2.3E-09 48.5 2.6 33 146-179 3-37 (73)
116 PRK09521 exosome complex RNA-b 97.4 0.00039 8.4E-09 54.4 6.1 67 103-178 27-106 (189)
117 cd05692 S1_RPS1_repeat_hs4 S1_ 97.4 0.00012 2.7E-09 46.8 2.8 33 147-179 1-33 (69)
118 cd05691 S1_RPS1_repeat_ec6 S1_ 97.4 0.00015 3.3E-09 47.2 3.1 33 147-179 1-33 (73)
119 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.4 0.00017 3.7E-09 48.9 3.2 37 142-178 2-38 (86)
120 cd05685 S1_Tex S1_Tex: The C-t 97.4 0.00016 3.5E-09 46.1 2.9 33 147-179 1-33 (68)
121 PF13509 S1_2: S1 domain; PDB: 97.3 0.00085 1.8E-08 42.8 5.9 48 66-128 14-61 (61)
122 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.3 0.00089 1.9E-08 44.2 5.9 64 59-128 1-72 (72)
123 PRK09202 nusA transcription el 97.3 4.1E-05 8.8E-10 67.6 -0.9 75 103-179 87-166 (470)
124 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.3 0.0021 4.6E-08 44.1 7.8 58 58-121 1-74 (88)
125 cd04472 S1_PNPase S1_PNPase: P 97.2 0.00023 4.9E-09 45.6 2.4 32 147-178 1-32 (68)
126 TIGR02696 pppGpp_PNP guanosine 97.2 0.00042 9E-09 63.9 4.9 63 114-177 611-678 (719)
127 cd04471 S1_RNase_R S1_RNase_R: 97.2 0.00022 4.8E-09 47.6 2.3 32 147-178 2-34 (83)
128 cd05684 S1_DHX8_helicase S1_DH 97.2 0.00028 6.1E-09 47.0 2.8 33 147-179 1-36 (79)
129 cd04452 S1_IF2_alpha S1_IF2_al 97.2 0.00043 9.4E-09 45.5 3.3 34 146-179 3-38 (76)
130 cd05702 S1_Rrp5_repeat_hs11_sc 97.2 0.0004 8.7E-09 45.3 3.0 33 147-179 1-33 (70)
131 cd05687 S1_RPS1_repeat_ec1_hs1 97.1 0.00049 1.1E-08 44.6 3.2 33 147-179 1-33 (70)
132 PRK08059 general stress protei 97.1 0.0004 8.7E-09 50.6 2.8 36 141-178 4-39 (123)
133 PRK12328 nusA transcription el 97.1 0.0023 5E-08 54.9 7.6 63 55-129 135-206 (374)
134 cd05708 S1_Rrp5_repeat_sc12 S1 97.1 0.00063 1.4E-08 44.6 3.2 34 146-179 2-36 (77)
135 cd05693 S1_Rrp5_repeat_hs1_sc1 97.1 0.00052 1.1E-08 48.2 2.9 33 146-178 3-35 (100)
136 smart00316 S1 Ribosomal protei 97.0 0.00079 1.7E-08 42.9 3.2 33 147-179 3-35 (72)
137 PF10447 EXOSC1: Exosome compo 97.0 0.0018 3.9E-08 43.9 4.9 35 82-116 46-82 (82)
138 KOG1856 Transcription elongati 96.9 0.00079 1.7E-08 64.1 3.5 75 54-131 981-1061(1299)
139 cd04454 S1_Rrp4_like S1_Rrp4_l 96.7 0.0018 3.9E-08 43.4 3.4 37 142-178 2-38 (82)
140 COG1107 Archaea-specific RecJ- 96.7 0.0042 9.2E-08 55.7 6.1 68 53-131 117-189 (715)
141 TIGR01953 NusA transcription t 96.5 0.0004 8.7E-09 59.1 -1.2 78 100-179 81-164 (341)
142 cd05688 S1_RPS1_repeat_ec3 S1_ 96.5 0.0021 4.6E-08 40.9 2.4 31 147-178 2-32 (68)
143 COG1185 Pnp Polyribonucleotide 96.4 0.0036 7.7E-08 57.1 4.3 61 115-178 586-651 (692)
144 PHA02945 interferon resistance 96.3 0.0039 8.5E-08 42.5 2.9 34 145-179 10-45 (88)
145 PLN00207 polyribonucleotide nu 96.2 0.0026 5.6E-08 60.0 2.3 34 145-178 752-786 (891)
146 cd04455 S1_NusA S1_NusA: N-uti 96.2 0.0051 1.1E-07 39.7 2.8 33 146-179 3-35 (67)
147 PRK04163 exosome complex RNA-b 96.1 0.025 5.3E-07 45.8 7.1 38 142-179 59-96 (235)
148 PRK10811 rne ribonuclease E; R 96.0 0.021 4.5E-07 54.3 7.1 57 56-117 36-108 (1068)
149 TIGR03591 polynuc_phos polyrib 95.9 0.006 1.3E-07 56.5 3.0 35 145-179 617-651 (684)
150 cd00164 S1_like S1_like: Ribos 95.9 0.0061 1.3E-07 37.9 2.2 30 150-179 1-30 (65)
151 PRK11824 polynucleotide phosph 95.7 0.0076 1.6E-07 56.0 3.0 34 145-178 620-653 (693)
152 PRK12327 nusA transcription el 95.7 0.0016 3.5E-08 55.8 -1.4 76 102-179 86-166 (362)
153 PRK12329 nusA transcription el 95.7 0.057 1.2E-06 47.4 7.9 69 55-129 149-225 (449)
154 PRK11712 ribonuclease G; Provi 95.6 0.064 1.4E-06 47.9 8.0 59 54-117 34-111 (489)
155 COG2183 Tex Transcriptional ac 95.2 0.016 3.4E-07 53.8 3.1 40 140-181 654-693 (780)
156 cd04460 S1_RpoE S1_RpoE: RpoE, 95.0 0.016 3.5E-07 40.2 2.0 28 148-176 1-28 (99)
157 TIGR02063 RNase_R ribonuclease 94.9 0.021 4.5E-07 53.2 2.9 32 145-176 626-658 (709)
158 TIGR00448 rpoE DNA-directed RN 94.4 0.035 7.6E-07 42.9 2.7 31 146-177 81-111 (179)
159 PRK11642 exoribonuclease R; Pr 94.2 0.034 7.4E-07 52.6 2.8 33 145-177 642-675 (813)
160 COG1095 RPB7 DNA-directed RNA 93.7 0.066 1.4E-06 41.5 3.1 37 144-181 79-115 (183)
161 COG1098 VacB Predicted RNA bin 93.7 0.08 1.7E-06 38.5 3.2 25 22-47 52-76 (129)
162 TIGR00358 3_prime_RNase VacB a 93.6 0.064 1.4E-06 49.6 3.3 32 146-177 572-604 (654)
163 TIGR00757 RNaseEG ribonuclease 93.2 0.073 1.6E-06 46.6 2.9 32 147-178 26-59 (414)
164 PRK08563 DNA-directed RNA poly 93.1 0.078 1.7E-06 41.1 2.7 31 146-177 81-111 (187)
165 cd04462 S1_RNAPII_Rpb7 S1_RNAP 93.0 0.099 2.1E-06 35.8 2.7 32 147-179 2-33 (88)
166 KOG1067 Predicted RNA-binding 92.6 0.11 2.3E-06 46.9 3.0 32 146-177 668-699 (760)
167 cd05699 S1_Rrp5_repeat_hs7 S1_ 92.5 0.13 2.7E-06 34.0 2.6 30 147-176 1-31 (72)
168 KOG3298 DNA-directed RNA polym 92.4 1 2.2E-05 34.3 7.6 61 53-119 76-152 (170)
169 COG1107 Archaea-specific RecJ- 90.8 0.1 2.2E-06 47.2 1.0 38 140-179 118-155 (715)
170 PTZ00162 DNA-directed RNA poly 88.6 0.51 1.1E-05 36.5 3.2 34 146-180 81-114 (176)
171 PRK12328 nusA transcription el 88.4 0.064 1.4E-06 46.2 -2.1 77 101-179 89-171 (374)
172 COG1530 CafA Ribonucleases G a 88.2 1 2.2E-05 40.3 5.3 59 54-118 33-103 (487)
173 COG1093 SUI2 Translation initi 87.6 0.5 1.1E-05 38.7 2.7 41 6-46 40-84 (269)
174 PRK07252 hypothetical protein; 87.0 1.2 2.7E-05 32.2 4.3 42 6-47 30-75 (120)
175 PRK05054 exoribonuclease II; P 87.0 0.45 9.7E-06 44.0 2.4 31 147-177 562-593 (644)
176 KOG3409 Exosomal 3'-5' exoribo 87.0 3.8 8.3E-05 31.6 7.0 72 55-128 65-147 (193)
177 PRK08582 hypothetical protein; 86.9 0.67 1.5E-05 34.4 2.9 41 6-47 32-76 (139)
178 COG4044 Uncharacterized protei 86.9 0.3 6.4E-06 38.7 1.0 73 54-127 71-156 (247)
179 cd05790 S1_Rrp40 S1_Rrp40: Rrp 84.9 1.7 3.6E-05 29.7 3.8 39 142-180 2-40 (86)
180 cd05791 S1_CSL4 S1_CSL4: CSL4, 84.7 1.5 3.2E-05 30.1 3.6 34 144-177 4-45 (92)
181 PRK11712 ribonuclease G; Provi 83.8 0.87 1.9E-05 40.8 2.6 32 146-177 38-71 (489)
182 PF08292 RNA_pol_Rbc25: RNA po 83.4 4.4 9.5E-05 29.4 5.7 56 58-118 3-76 (122)
183 TIGR02062 RNase_B exoribonucle 83.3 0.99 2.1E-05 41.8 2.9 32 147-178 558-590 (639)
184 PRK03987 translation initiatio 82.1 0.97 2.1E-05 37.2 2.1 40 6-45 37-80 (262)
185 PHA02858 EIF2a-like PKR inhibi 81.7 2.6 5.7E-05 28.6 3.7 37 8-44 46-85 (86)
186 PF13509 S1_2: S1 domain; PDB: 80.6 1.3 2.8E-05 27.9 1.9 33 147-179 2-34 (61)
187 PF10447 EXOSC1: Exosome compo 80.0 16 0.00034 24.7 7.3 25 104-130 3-27 (82)
188 PRK10811 rne ribonuclease E; R 79.9 1.4 3E-05 42.4 2.5 29 147-175 39-69 (1068)
189 PRK05807 hypothetical protein; 79.1 3 6.5E-05 30.8 3.7 26 21-47 50-75 (136)
190 COG0557 VacB Exoribonuclease R 77.0 2.7 5.8E-05 39.4 3.5 31 146-176 622-653 (706)
191 COG4776 Rnb Exoribonuclease II 75.9 0.11 2.4E-06 45.8 -5.5 110 2-123 498-639 (645)
192 cd05700 S1_Rrp5_repeat_hs9 S1_ 75.3 3.9 8.5E-05 26.0 2.8 27 101-127 39-65 (65)
193 PF10246 MRP-S35: Mitochondria 74.3 13 0.00028 26.2 5.5 48 57-116 22-74 (104)
194 PRK12442 translation initiatio 74.3 21 0.00045 24.4 6.4 50 70-129 23-73 (87)
195 KOG3298 DNA-directed RNA polym 72.3 4.2 9.1E-05 31.0 2.9 28 147-175 82-109 (170)
196 COG1097 RRP4 RNA-binding prote 69.4 30 0.00064 28.1 7.3 67 103-178 30-96 (239)
197 TIGR00008 infA translation ini 67.3 24 0.00051 23.0 5.3 46 70-124 21-66 (68)
198 PRK12329 nusA transcription el 65.2 6.8 0.00015 34.7 3.2 79 100-179 100-190 (449)
199 PF02599 CsrA: Global regulato 61.5 15 0.00032 22.7 3.4 32 98-131 7-38 (54)
200 PRK01712 carbon storage regula 57.4 27 0.00059 22.4 4.1 32 98-131 7-38 (64)
201 COG1096 Predicted RNA-binding 56.0 59 0.0013 25.4 6.6 64 100-168 59-142 (188)
202 PRK15463 cold shock-like prote 54.8 29 0.00063 22.5 4.1 42 66-115 15-57 (70)
203 cd04474 RPA1_DBD_A RPA1_DBD_A: 54.5 41 0.0009 23.2 5.2 41 23-65 34-74 (104)
204 PRK15464 cold shock-like prote 53.8 29 0.00064 22.5 4.0 42 66-115 15-57 (70)
205 PF01835 A2M_N: MG2 domain; I 52.0 25 0.00054 23.7 3.7 32 100-131 8-46 (99)
206 KOG1004 Exosomal 3'-5' exoribo 51.7 69 0.0015 25.7 6.4 58 54-118 61-124 (230)
207 KOG3297 DNA-directed RNA polym 51.4 55 0.0012 25.6 5.7 61 53-118 76-158 (202)
208 cd04480 RPA1_DBD_A_like RPA1_D 51.1 52 0.0011 21.7 5.0 44 22-67 17-60 (86)
209 KOG3409 Exosomal 3'-5' exoribo 49.8 92 0.002 24.2 6.6 64 102-167 65-147 (193)
210 PRK09937 stationary phase/star 48.5 75 0.0016 20.8 6.3 51 70-130 17-67 (74)
211 PRK00568 carbon storage regula 48.3 40 0.00087 22.4 3.9 32 98-131 7-38 (76)
212 PF00313 CSD: 'Cold-shock' DNA 45.9 72 0.0016 19.8 7.6 30 82-115 24-53 (66)
213 PRK09507 cspE cold shock prote 45.6 70 0.0015 20.5 4.8 31 82-116 27-57 (69)
214 PF10246 MRP-S35: Mitochondria 45.4 23 0.00049 25.0 2.5 32 146-177 23-54 (104)
215 PF00970 FAD_binding_6: Oxidor 45.3 73 0.0016 21.2 5.2 46 102-150 29-88 (99)
216 PF11813 DUF3334: Protein of u 45.3 10 0.00022 30.1 0.9 16 159-174 49-64 (229)
217 PRK10943 cold shock-like prote 43.9 70 0.0015 20.5 4.6 30 82-115 27-56 (69)
218 COG1551 CsrA RNA-binding globa 43.9 40 0.00087 22.1 3.3 30 99-130 8-37 (73)
219 PRK10354 RNA chaperone/anti-te 43.0 69 0.0015 20.5 4.5 30 82-115 28-57 (70)
220 TIGR00202 csrA carbon storage 42.3 61 0.0013 21.1 4.0 32 98-131 7-38 (69)
221 PF08845 SymE_toxin: Toxin Sym 42.1 31 0.00066 21.6 2.6 26 94-126 31-56 (57)
222 COG0195 NusA Transcription elo 41.3 54 0.0012 25.7 4.4 42 82-129 2-44 (190)
223 KOG3754 Gamma-glutamylcysteine 40.5 33 0.00072 30.7 3.4 26 22-47 47-72 (640)
224 COG1278 CspC Cold shock protei 39.7 46 0.00099 21.6 3.1 29 82-114 25-53 (67)
225 COG0361 InfA Translation initi 38.6 1.2E+02 0.0025 20.1 6.9 51 69-128 22-72 (75)
226 PRK09890 cold shock protein Cs 38.1 1.1E+02 0.0024 19.6 6.1 30 82-115 28-57 (70)
227 KOG1999 RNA polymerase II tran 36.2 71 0.0015 31.2 5.0 75 103-181 408-498 (1024)
228 PRK14998 cold shock-like prote 35.5 1.3E+02 0.0027 19.6 6.1 41 82-128 25-65 (73)
229 PF06347 SH3_4: Bacterial SH3 35.0 95 0.0021 18.5 4.0 35 54-92 19-54 (55)
230 COG1545 Predicted nucleic-acid 34.0 1.3E+02 0.0028 22.2 5.3 40 69-120 88-127 (140)
231 COG1530 CafA Ribonucleases G a 32.1 27 0.00059 31.4 1.6 31 147-177 38-70 (487)
232 PF07076 DUF1344: Protein of u 31.9 60 0.0013 20.6 2.7 23 148-170 3-25 (61)
233 KOG4078 Putative mitochondrial 31.6 1.5E+02 0.0033 22.2 5.1 51 56-118 80-135 (173)
234 cd04458 CSP_CDS Cold-Shock Pro 30.8 1.3E+02 0.0029 18.4 5.5 31 82-116 24-54 (65)
235 COG1018 Hmp Flavodoxin reducta 30.3 1.7E+02 0.0037 24.0 5.9 56 103-165 35-105 (266)
236 COG4148 ModC ABC-type molybdat 29.5 3.6E+02 0.0078 23.0 7.8 31 82-117 319-349 (352)
237 PF09883 DUF2110: Uncharacteri 29.0 2.7E+02 0.0059 22.4 6.5 58 53-118 67-138 (225)
238 KOG3013 Exosomal 3'-5' exoribo 28.9 59 0.0013 26.9 2.9 71 55-131 82-167 (301)
239 COG1912 Uncharacterized conser 28.0 87 0.0019 25.9 3.7 66 108-174 20-101 (268)
240 cd05793 S1_IF1A S1_IF1A: Trans 26.8 1.8E+02 0.0039 19.2 4.5 41 82-127 23-63 (77)
241 COG1190 LysU Lysyl-tRNA synthe 26.6 3.3E+02 0.0072 24.7 7.3 61 66-128 75-137 (502)
242 COG4110 Uncharacterized protei 26.3 40 0.00087 25.9 1.4 20 159-178 53-72 (200)
243 PF02237 BPL_C: Biotin protein 25.7 1.1E+02 0.0023 18.0 3.0 23 147-169 12-35 (48)
244 TIGR02381 cspD cold shock doma 25.3 1.9E+02 0.004 18.4 5.3 30 82-115 25-54 (68)
245 TIGR00307 S8e ribosomal protei 25.3 2.8E+02 0.006 20.3 5.8 35 147-181 93-127 (127)
246 PTZ00319 NADH-cytochrome B5 re 24.7 3.1E+02 0.0066 22.7 6.6 12 119-130 97-108 (300)
247 PRK13605 endoribonuclease SymE 24.4 92 0.002 22.3 2.8 35 90-131 41-75 (113)
248 COG0425 SirA Predicted redox p 24.3 72 0.0016 21.1 2.2 24 7-30 15-39 (78)
249 PF11061 DUF2862: Protein of u 23.7 1.4E+02 0.0031 19.1 3.4 13 160-172 43-55 (64)
250 PF03293 Pox_RNA_pol: Poxvirus 23.3 1.9E+02 0.0042 21.6 4.4 22 53-74 76-102 (160)
251 PF11580 DUF3239: Protein of u 23.2 2E+02 0.0042 21.1 4.5 38 96-134 4-41 (128)
252 COG0250 NusG Transcription ant 22.7 1.9E+02 0.0042 22.2 4.6 29 101-129 122-160 (178)
253 KOG1856 Transcription elongati 22.7 70 0.0015 31.9 2.5 36 141-178 982-1020(1299)
254 PF02721 DUF223: Domain of unk 22.0 2.6E+02 0.0055 18.7 5.7 39 31-69 3-41 (95)
255 cd06189 flavin_oxioreductase N 21.4 3.5E+02 0.0076 20.8 6.1 56 103-164 26-92 (224)
256 KOG2916 Translation initiation 21.3 90 0.0019 26.0 2.6 38 9-46 48-89 (304)
257 PF09465 LBR_tudor: Lamin-B re 21.1 2.2E+02 0.0048 17.7 4.2 16 110-125 24-39 (55)
258 cd06183 cyt_b5_reduct_like Cyt 20.3 3.3E+02 0.0071 20.9 5.7 29 120-150 59-87 (234)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-35 Score=258.98 Aligned_cols=168 Identities=26% Similarity=0.460 Sum_probs=157.5
Q ss_pred CCCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeE
Q 030172 4 SHSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGA 69 (182)
Q Consensus 4 ~~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~ 69 (182)
+.|+|.|..+.+ +.+..++|.++.++|+++|.+++++.+|++.. ...++..++++|+++.|+ +|||
T Consensus 129 r~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga 208 (541)
T COG0539 129 RAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA 208 (541)
T ss_pred EEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence 358999999998 77888999999999999999999999999963 344567899999999999 9999
Q ss_pred EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCce
Q 030172 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV 149 (182)
Q Consensus 70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~ 149 (182)
||+|+ | ++||||++||||.++.+|.+.|++||.|+|+|+++|++++|++||+|++.++||.....+|++ |+.
T Consensus 209 fVdig---G---vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~--g~~ 280 (541)
T COG0539 209 FVDIG---G---VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPV--GDK 280 (541)
T ss_pred EEEec---C---eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCC--CCE
Confidence 99996 5 999999999999999999999999999999999999999999999999999999999999998 999
Q ss_pred eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
+.|+|+++++|||||++.+|++||||-..+
T Consensus 281 v~G~Vt~i~~~GafVei~~GvEGlvhvSEi 310 (541)
T COG0539 281 VEGKVTNLTDYGAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred EEEEEEEeecCcEEEEecCCccceeechhh
Confidence 999999999999999999999999998765
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-33 Score=246.79 Aligned_cols=167 Identities=31% Similarity=0.487 Sum_probs=155.7
Q ss_pred CCCCCCCccHHHh--hhhc--CCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172 5 HSCKEPQKSIHEI--AKGL--TGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (182)
Q Consensus 5 ~~~p~~e~~~~~~--~~~~--vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (182)
.|+|.+|++|.+. ...+ +|++|+++|+++|+++++++||.|+ .||+....++.+|+.+.|+ +|||||+
T Consensus 217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe 296 (541)
T COG0539 217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE 296 (541)
T ss_pred eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence 3678899999852 3333 8999999999999999999999997 4999999999999999999 9999999
Q ss_pred EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEe
Q 030172 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD 152 (182)
Q Consensus 73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G 152 (182)
+. +| ++||+|+|||||.+...|.+++++||.|.|+|+++|++++||+||+|++..+||..+..++++ |+.++|
T Consensus 297 i~--~G---vEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~--g~~v~g 369 (541)
T COG0539 297 IE--EG---VEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPV--GDVVEG 369 (541)
T ss_pred ec--CC---ccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCC--CCeEEE
Confidence 97 56 999999999999998889999999999999999999999999999999999999999999888 999999
Q ss_pred eEeeecCCeeEEecCCChhhhchhhh
Q 030172 153 SSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 153 ~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.|.++++||+||.+++|++||+|..+
T Consensus 370 ~v~~~t~~g~fv~le~gidG~vh~~d 395 (541)
T COG0539 370 KVKSITDFGAFVELEGGIDGLVHLSD 395 (541)
T ss_pred EEeeecccceEEccCCCccceEEHHh
Confidence 99999999999999999999998765
No 3
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=2.2e-31 Score=233.01 Aligned_cols=166 Identities=23% Similarity=0.412 Sum_probs=152.9
Q ss_pred CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEech-------hHHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172 5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKD-------AVWNKYSSRVNVEDIFVGR-----DYGAF 70 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~-------~~~~~~~~~~~~G~iv~g~-----~~G~f 70 (182)
.|+|.++++++. .++.++|++++|+|+++|++++++.+|+|. .+|+.+..++++|+++.|+ ++|+|
T Consensus 146 gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~F 225 (486)
T PRK07899 146 GFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAF 225 (486)
T ss_pred EEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEE
Confidence 478999988873 456789999999999999999999999884 3567777899999999999 99999
Q ss_pred EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
|+|+ | ++||||+++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.+++.. |+++
T Consensus 226 Vdlg---g---v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~v--G~vv 297 (486)
T PRK07899 226 VDLG---G---VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAI--GQIV 297 (486)
T ss_pred EEEC---C---EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCC--CCEE
Confidence 9995 5 999999999999999999999999999999999999999999999999999999998888877 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.|+|+++.+||+||++.+|++||||...
T Consensus 298 ~G~V~~I~~fGvFVeL~~gieGLvh~Se 325 (486)
T PRK07899 298 PGKVTKLVPFGAFVRVEEGIEGLVHISE 325 (486)
T ss_pred EEEEEEEeccEEEEEeCCCcEEEEEHHH
Confidence 9999999999999999999999999754
No 4
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.97 E-value=1.1e-30 Score=230.15 Aligned_cols=167 Identities=28% Similarity=0.520 Sum_probs=150.6
Q ss_pred CCCCCCCccHHHh--hhhc--CCCeEEEEEEEEeCCC----CEEEEEechh---HHhhhhcCCCCCCEEEEE-----eEe
Q 030172 5 HSCKEPQKSIHEI--AKGL--TGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYG 68 (182)
Q Consensus 5 ~~~p~~e~~~~~~--~~~~--vG~~v~~~v~~~d~~~----~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G 68 (182)
.|+|.+++++... +..+ +|++++|+|+++|.++ +++.+|+|.. +|.....++++|+++.|+ ++|
T Consensus 228 g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G 307 (491)
T PRK13806 228 GMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFG 307 (491)
T ss_pred EEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCce
Confidence 4678888888642 2332 9999999999999876 4799999874 888888899999999999 999
Q ss_pred EEEEEecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCC
Q 030172 69 AFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDG 147 (182)
Q Consensus 69 ~fV~l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g 147 (182)
+||+++ .| ++||+|+++++| .++.++.+.|++||.|+|+|+++|++++++.||+|++..+||..+.+++++ |
T Consensus 308 ~fV~l~--~g---v~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~v--G 380 (491)
T PRK13806 308 AFVEIL--PG---IEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAP--G 380 (491)
T ss_pred EEEEeC--CC---cEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCC--C
Confidence 999996 46 999999999999 467889999999999999999999999999999999999999999999988 9
Q ss_pred ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
++++|+|+++++||+||++++|++||||...
T Consensus 381 ~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se 411 (491)
T PRK13806 381 TTVTGTVEKRAQFGLFVNLAPGVTGLLPASV 411 (491)
T ss_pred CEEEEEEEEEecCceEEEcCCCcEEEEEHHH
Confidence 9999999999999999999999999999765
No 5
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.97 E-value=2.6e-30 Score=238.33 Aligned_cols=167 Identities=26% Similarity=0.449 Sum_probs=152.5
Q ss_pred CCCCCCCccHHHh--hhh--cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172 5 HSCKEPQKSIHEI--AKG--LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (182)
Q Consensus 5 ~~~p~~e~~~~~~--~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (182)
.|+|.++++++.. +.. .+|++++|+|+.+|++++++.+|+|. .+|..+..++++|+++.|+ +||+||+
T Consensus 518 Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe 597 (863)
T PRK12269 518 GLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE 597 (863)
T ss_pred EEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence 4789999988642 222 38999999999999999999999996 5888888899999999999 9999999
Q ss_pred EecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeE
Q 030172 73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS 151 (182)
Q Consensus 73 l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~ 151 (182)
++ +| ++||+|++|++| .+..+|.+.|++||.|+|+|+++|++++++.||+|++.++||..+.++|++ |++++
T Consensus 598 L~--~g---veGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~v--G~~v~ 670 (863)
T PRK12269 598 LA--EG---IEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPV--GARFT 670 (863)
T ss_pred ec--CC---ceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCC--CCEEE
Confidence 96 46 999999999999 578899999999999999999999999999999999999999999889988 99999
Q ss_pred eeEeeecCCeeEEecCCChhhhchhhh
Q 030172 152 DSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 152 G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+|+++++||+||++.+|++||+|...
T Consensus 671 G~V~~i~~~G~fV~l~~gV~GlIh~se 697 (863)
T PRK12269 671 RRIVKVTNAGAFIEMEEGIDGFLHVDD 697 (863)
T ss_pred EEEEEEecceEEEEeCCCcEEEEEhHH
Confidence 999999999999999999999999654
No 6
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.96 E-value=9.8e-30 Score=224.07 Aligned_cols=167 Identities=28% Similarity=0.478 Sum_probs=150.8
Q ss_pred CCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172 5 HSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF 70 (182)
Q Consensus 5 ~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f 70 (182)
.|+|.++++++ +.+..++|++++|+|+.+|++++++.+|++.. .|+.+..++++|+++.|+ ++|+|
T Consensus 140 ~flP~s~~~~~~~~~~~~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~f 219 (491)
T PRK13806 140 AFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAF 219 (491)
T ss_pred EEEEHHHhccccCCChHHcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEE
Confidence 47899998876 34556899999999999999999999999863 456667789999999999 99999
Q ss_pred EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC----CeEEEEEeeccCCchhHHHhhhcCCC
Q 030172 71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQD 146 (182)
Q Consensus 71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~----~ki~lS~k~~~~~p~~~~~~~~~~~~ 146 (182)
|+++ +| ++||||+++++|.++.++.+.|++||.|+|+|+++|.++ .++.||+|++.++||....+++..
T Consensus 220 V~l~--~g---v~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~-- 292 (491)
T PRK13806 220 VELA--PG---VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKA-- 292 (491)
T ss_pred EEcC--CC---cEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCC--
Confidence 9996 45 999999999999999999999999999999999999866 479999999999999999888887
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|+++.+||+||++.+|++||+|...
T Consensus 293 G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~se 324 (491)
T PRK13806 293 GDKVTGKVVRLAPFGAFVEILPGIEGLVHVSE 324 (491)
T ss_pred CCEEEEEEEEEeCceEEEEeCCCcEEEEEHHH
Confidence 99999999999999999999999999999654
No 7
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=2.4e-28 Score=218.66 Aligned_cols=166 Identities=28% Similarity=0.466 Sum_probs=151.8
Q ss_pred CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172 5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF 70 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f 70 (182)
.|||.++++++. .+..++|+++.|+|+.+|++++++.+|+|.+ .|.....++++|+++.|+ ++|+|
T Consensus 139 gfip~s~~~~~~~~~~~~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~ 218 (565)
T PRK06299 139 AFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAF 218 (565)
T ss_pred EEEEHHHccCcCCCChHHhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEE
Confidence 478999998863 3556899999999999999999999999863 356667899999999999 99999
Q ss_pred EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
|+++ | ++||+|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|.+..+||....+.+.+ |+++
T Consensus 219 V~i~---g---~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~--G~~v 290 (565)
T PRK06299 219 VDLG---G---VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPV--GSKV 290 (565)
T ss_pred EEEC---C---EEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCC--CCEE
Confidence 9995 5 999999999999999999999999999999999999999999999999999999998888887 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.|+|+++.++|+||++.+|++||+|...
T Consensus 291 ~g~V~~i~~~G~fV~l~~~v~Glv~~se 318 (565)
T PRK06299 291 KGKVTNITDYGAFVELEEGIEGLVHVSE 318 (565)
T ss_pred EEEEEEEeCCeEEEEeCCCCEEEEEHHH
Confidence 9999999999999999999999998643
No 8
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=3.3e-28 Score=208.96 Aligned_cols=167 Identities=28% Similarity=0.420 Sum_probs=150.7
Q ss_pred CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172 5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF 70 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f 70 (182)
.|+|.++++++. .+..++|+++.|+|+++|++++++.+|++.. .|.....+++.|+++.|+ ++|+|
T Consensus 130 gflp~~el~~~~~~~~~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~f 209 (390)
T PRK06676 130 GFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAF 209 (390)
T ss_pred EEEEHHHcCCccCCChHHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEE
Confidence 478888888763 3556799999999999999999999999863 455566789999999999 99999
Q ss_pred EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
|+++ | ++||||+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++..+||....+.+.+ |+++
T Consensus 210 V~l~---~---v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~--G~~v 281 (390)
T PRK06676 210 VDIG---G---VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPE--GDVI 281 (390)
T ss_pred EEeC---C---eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcC--CcEE
Confidence 9994 5 999999999999999999999999999999999999999999999999999999988888887 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
.|+|+++.++|+||++.+|+.||||....
T Consensus 282 ~g~V~~i~~~G~fV~l~~gi~Glv~~se~ 310 (390)
T PRK06676 282 EGTVKRLTDFGAFVEVLPGVEGLVHISQI 310 (390)
T ss_pred EEEEEEEeCceEEEEECCCCeEEEEhHHc
Confidence 99999999999999999999999996543
No 9
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.96 E-value=2.8e-28 Score=224.94 Aligned_cols=167 Identities=21% Similarity=0.329 Sum_probs=148.3
Q ss_pred CCCCCCCccH-HH--hh-h-hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172 5 HSCKEPQKSI-HE--IA-K-GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~-~~--~~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV 71 (182)
.|+|.+|++| ++ .. . ..+|++++|+|+.+|++++++.+|.|+ .+|+.+..++++|+++.|+ +||+||
T Consensus 604 GLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV 683 (863)
T PRK12269 604 GLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFI 683 (863)
T ss_pred eeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEE
Confidence 4577788887 22 12 2 239999999999999999999999996 4899998899999999999 999999
Q ss_pred EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
++. +| ++||||.++++|.+. .++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.+.+++ |+++
T Consensus 684 ~l~--~g---V~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~v--G~iV 756 (863)
T PRK12269 684 EME--EG---IDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGV--GSTV 756 (863)
T ss_pred EeC--CC---cEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCC--CCEE
Confidence 996 46 999999999999765 445568999999999999999999999999999999999998888877 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
+|+|+++.++|+||+|.+|++||+|...
T Consensus 757 ~GkV~~v~~~GvFVeL~~gVeGlI~~s~ 784 (863)
T PRK12269 757 EGEVSSVTDFGIFVRVPGGVEGLVRKQH 784 (863)
T ss_pred EEEEEEEecCeEEEEcCCCeEEEEEHHH
Confidence 9999999999999999999999998764
No 10
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.94 E-value=1.3e-26 Score=205.39 Aligned_cols=166 Identities=28% Similarity=0.459 Sum_probs=149.5
Q ss_pred CCCCCCCccHH--HhhhhcCCCeEEEEEEEEeCCCCEEEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeEE
Q 030172 5 HSCKEPQKSIH--EIAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAF 70 (182)
Q Consensus 5 ~~~p~~e~~~~--~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~f 70 (182)
.|||.++++.+ +....++|++++|+|+.+|+.++++.+|+|.. .+......+++|+++.|+ ++|+|
T Consensus 125 ~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~ 204 (516)
T TIGR00717 125 AFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAF 204 (516)
T ss_pred EEEeHHHhcCcccCchhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEE
Confidence 47888888765 34556899999999999999999999999864 244556789999999999 99999
Q ss_pred EEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 71 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 71 V~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
|+++ | ++||+|.++++|.+..++.+.|++||.+.|+|+++|++++++.+|+|.+..+||....+.+.+ |+++
T Consensus 205 V~l~---g---~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~--G~i~ 276 (516)
T TIGR00717 205 VDLG---G---VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPV--GDKI 276 (516)
T ss_pred EEEC---C---EEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccC--CCEE
Confidence 9994 5 999999999999999999999999999999999999999999999999999999998878877 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
+|+|+++.++|+||++.+|++||+|...
T Consensus 277 ~g~V~~v~~~G~fV~l~~~v~g~v~~se 304 (516)
T TIGR00717 277 TGRVTNLTDYGVFVEIEEGIEGLVHVSE 304 (516)
T ss_pred EEEEEEeeCCcEEEEeCCCCEEEEEHHH
Confidence 9999999999999999999999999654
No 11
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.94 E-value=1.6e-26 Score=204.87 Aligned_cols=167 Identities=26% Similarity=0.480 Sum_probs=147.1
Q ss_pred CCCCCCCccHHH---hhh--hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172 5 HSCKEPQKSIHE---IAK--GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~~~---~~~--~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV 71 (182)
.|+|.+++++.. ... ..+|+.++|+|+++|++++++.+|++. .+|..+...+++|+++.|+ ++|+||
T Consensus 298 g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV 377 (516)
T TIGR00717 298 GLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFV 377 (516)
T ss_pred EEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEE
Confidence 457777776531 111 249999999999999999999999986 4788887889999999999 999999
Q ss_pred EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
+++ .| ++||+|+++++|.+. .++.+.|++||.|.|+|+++|+++++|.||+|.+..+||..+.+.+.+ |+++
T Consensus 378 ~l~--~~---v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~--G~~v 450 (516)
T TIGR00717 378 ELE--GG---IDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKV--GSVV 450 (516)
T ss_pred ECC--CC---CEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCc--ceEE
Confidence 996 45 999999999999764 567788999999999999999999999999999999999888877877 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
+|+|++++++|+||++.+|+.||||...
T Consensus 451 ~g~V~~v~~~G~fV~l~~~~~Glv~~s~ 478 (516)
T TIGR00717 451 KGKVTEIKDFGAFVELPGGVEGLIRNSE 478 (516)
T ss_pred EEEEEEEecceEEEEcCCCeEEEEEHHH
Confidence 9999999999999999999999999865
No 12
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.94 E-value=1.9e-26 Score=209.10 Aligned_cols=167 Identities=28% Similarity=0.447 Sum_probs=149.8
Q ss_pred CCCCCCCccHHH--hhhhcCCCeEEEEEEEEeCCCCE-EEEEechh-------HHhhhhcCCCCCCEEEEE-----eEeE
Q 030172 5 HSCKEPQKSIHE--IAKGLTGSIISVKVIQANEEMKK-LVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGA 69 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~~vG~~v~~~v~~~d~~~~~-i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~ 69 (182)
.|+|.++++++. .+..++|+++.|+|+++|+++++ +.+|+|.. ++...+.++++|+++.|+ ++|+
T Consensus 414 gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~ 493 (647)
T PRK00087 414 AFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGA 493 (647)
T ss_pred EEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcE
Confidence 368888877652 45557999999999999999888 99999864 345566789999999999 9999
Q ss_pred EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCce
Q 030172 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV 149 (182)
Q Consensus 70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~ 149 (182)
||+++ | ++||+|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++..+||....+++.+ |+.
T Consensus 494 fV~l~---g---v~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~--G~~ 565 (647)
T PRK00087 494 FVDIG---G---VDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPV--GSI 565 (647)
T ss_pred EEEEC---C---EEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccC--CeE
Confidence 99993 5 999999999999999999999999999999999999999999999999999999998888877 999
Q ss_pred eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
+.|+|+++.++|+||++.+|++||||....
T Consensus 566 v~g~V~~i~~~G~fV~l~~~i~Gli~~sel 595 (647)
T PRK00087 566 VLGKVVRIAPFGAFVELEPGVDGLVHISQI 595 (647)
T ss_pred EEEEEEEEECCeEEEEECCCCEEEEEhhhc
Confidence 999999999999999999999999997654
No 13
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.94 E-value=2.9e-26 Score=205.23 Aligned_cols=168 Identities=31% Similarity=0.542 Sum_probs=149.0
Q ss_pred CCCCCCCccHHHh---h-h-hcCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172 5 HSCKEPQKSIHEI---A-K-GLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~~~~---~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~-----~~G~fV 71 (182)
.|+|.+++++... . . ..+|+++.|+|+++|++++++.+|.+. ++|..+...+++|+++.|+ ++|+||
T Consensus 312 Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV 391 (565)
T PRK06299 312 GLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFV 391 (565)
T ss_pred EEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEE
Confidence 3577777775321 1 1 138999999999999999999999986 4788777789999999999 999999
Q ss_pred EEecCCCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 72 HLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 72 ~l~~~~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
+++ +| ++||+|+++++|.+. .++.+.|++||.|+|+|+++|+++++|.||+|.+..+||....+.+.. |+++
T Consensus 392 ~l~--~~---v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~--G~vV 464 (565)
T PRK06299 392 GLE--GG---IDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKK--GSIV 464 (565)
T ss_pred ECC--CC---CEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCC--CCEE
Confidence 996 45 999999999999886 889999999999999999999999999999999999999988888877 9999
Q ss_pred EeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 151 ~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
.|+|+++.++|+||++.+|+.||||....
T Consensus 465 ~G~V~~v~~~G~fV~l~~gi~g~i~~se~ 493 (565)
T PRK06299 465 TGTVTEVKDKGAFVELEDGVEGLIRASEL 493 (565)
T ss_pred EEEEEEEecCceEEecCCCcEEEEEHHHh
Confidence 99999999999999999999999998654
No 14
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.90 E-value=2.1e-23 Score=174.81 Aligned_cols=158 Identities=16% Similarity=0.254 Sum_probs=132.2
Q ss_pred CCCCCCCccHHH--hhhh--cCCCeEEEEEEEEeCCCCEEEEEech----hHHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172 5 HSCKEPQKSIHE--IAKG--LTGSIISVKVIQANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~-----~~G~fV 71 (182)
.|+|.+|+++.. .+.. -+|++++|+|++++++++++.+|+|. .+|+.+......|+++.|+ ++|+||
T Consensus 57 g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V 136 (318)
T PRK07400 57 AFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV 136 (318)
T ss_pred EEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence 478888888763 1222 27999999999999999999999986 3677777777889999998 899999
Q ss_pred EEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeE
Q 030172 72 HLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS 151 (182)
Q Consensus 72 ~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~ 151 (182)
+++ | ++||||+++++|.+.. +.+ +|+.+.++|+++|++++++.||+|.+..+. ..+++.. |+++.
T Consensus 137 ~l~---G---v~gfip~s~ls~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~~k~--G~vv~ 201 (318)
T PRK07400 137 RIE---G---LRGFIPGSHISTRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNRLEV--GEVVV 201 (318)
T ss_pred EEC---C---EEEEEEHHHcCccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhccCCC--CCEEE
Confidence 994 5 9999999999986433 334 999999999999999999999999765432 3456666 99999
Q ss_pred eeEeeecCCeeEEecCCChhhhchhhh
Q 030172 152 DSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 152 G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+|+++.+||+||++ .|++||||...
T Consensus 202 G~V~~I~~~G~fV~i-~gv~Gllhise 227 (318)
T PRK07400 202 GTVRGIKPYGAFIDI-GGVSGLLHISE 227 (318)
T ss_pred EEEEEEECCeEEEEE-CCEEEEEEHHH
Confidence 999999999999999 69999998654
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.90 E-value=3.8e-23 Score=181.22 Aligned_cols=162 Identities=19% Similarity=0.293 Sum_probs=138.4
Q ss_pred CCCCCCCccHHHh--hhh--cCCCeEEEEEEEEeCCCCEEEEEechh----HHhhhhcCCCCCCEEEEE-----eEeEEE
Q 030172 5 HSCKEPQKSIHEI--AKG--LTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~~~~--~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV 71 (182)
.|+|..|+++... +.. -+|++|+|+|+.+++.++++.+|++.. +|..+...++.|+++.|+ ++|+||
T Consensus 61 G~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~V 140 (486)
T PRK07899 61 GVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLIL 140 (486)
T ss_pred EEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEE
Confidence 4678888877532 222 399999999999999999999999963 677766667789999999 889999
Q ss_pred EEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc----CCchhHHHhhhcCCCC
Q 030172 72 HLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE----EDPLLETLEKVIPQDG 147 (182)
Q Consensus 72 ~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~----~~p~~~~~~~~~~~~g 147 (182)
+++ ++||||++++++.++.++.. .+||.|+|+|+++|++++++.||+|.+. .++|..+...+.+ |
T Consensus 141 dlG-------i~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~--G 209 (486)
T PRK07899 141 DIG-------LRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQK--G 209 (486)
T ss_pred EEC-------CEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccC--C
Confidence 994 89999999999988888876 3899999999999999999999999643 3678888888877 9
Q ss_pred ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
++++|+|+++.+||+||++ .|++||+|...
T Consensus 210 ~iv~G~V~~i~~~G~FVdl-ggv~Glv~~Se 239 (486)
T PRK07899 210 QVRKGVVSSIVNFGAFVDL-GGVDGLVHVSE 239 (486)
T ss_pred CEEEEEEEEEECCeEEEEE-CCEEEEEEHHH
Confidence 9999999999999999999 58999999654
No 16
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.90 E-value=4.1e-23 Score=173.02 Aligned_cols=127 Identities=34% Similarity=0.569 Sum_probs=118.3
Q ss_pred CCCCCCCccHHHhhhhcCCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCc
Q 030172 5 HSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL 79 (182)
Q Consensus 5 ~~~p~~e~~~~~~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~ 79 (182)
.|+|.++++++...+.++|+++.|+|+++|++++++.+|+|.+.++....++++|+++.|+ +||+||+++ |
T Consensus 143 gfip~s~ls~~~~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~---g- 218 (318)
T PRK07400 143 GFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG---G- 218 (318)
T ss_pred EEEEHHHcCccCCccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC---C-
Confidence 4799999999866667899999999999999999999999988777778899999999999 999999994 5
Q ss_pred eeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhH
Q 030172 80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 137 (182)
Q Consensus 80 ~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~ 137 (182)
++||+|+++++|.+..++.+.|++||.|+|+|+++|.+++++.||+|.+.++||+.
T Consensus 219 --v~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~ 274 (318)
T PRK07400 219 --VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDM 274 (318)
T ss_pred --EEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhh
Confidence 99999999999999999999999999999999999999999999999999999954
No 17
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.88 E-value=2.3e-22 Score=172.80 Aligned_cols=163 Identities=19% Similarity=0.318 Sum_probs=138.1
Q ss_pred CCCCCCccHHH----hhhhcCCCeEEEEEEEEeCCCCEEEEEech----hHHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172 6 SCKEPQKSIHE----IAKGLTGSIISVKVIQANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (182)
Q Consensus 6 ~~p~~e~~~~~----~~~~~vG~~v~~~v~~~d~~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (182)
|+|..+++... .....+|++++|+|+.++.+++++.+|++. ..|..+...++.|+++.|+ ++|+||+
T Consensus 45 ~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~ 124 (390)
T PRK06676 45 VIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVD 124 (390)
T ss_pred EEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence 46666665521 112349999999999999999999999996 3577777788999999999 8999999
Q ss_pred EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccC----CchhHHHhhhcCCCCc
Q 030172 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGS 148 (182)
Q Consensus 73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~----~p~~~~~~~~~~~~g~ 148 (182)
++ | ++||||++++++.+..++.++ +||.+.|+|+++|.+++++.||+|.+.. ++|......+.. |+
T Consensus 125 ~~---G---~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~--G~ 194 (390)
T PRK06676 125 VE---G---VRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKE--GD 194 (390)
T ss_pred EC---C---EEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCC--CC
Confidence 94 5 899999999999988888764 8999999999999999999999998754 467777777776 99
Q ss_pred eeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 149 VISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 149 ~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
+++|+|+++.++|+||++ +|++||+|....
T Consensus 195 ~v~g~V~~v~~~G~fV~l-~~v~g~v~~sel 224 (390)
T PRK06676 195 VVEGTVARLTDFGAFVDI-GGVDGLVHISEL 224 (390)
T ss_pred EEEEEEEEEecceEEEEe-CCeEEEEEHHHc
Confidence 999999999999999999 689999997643
No 18
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.86 E-value=2.4e-21 Score=160.85 Aligned_cols=119 Identities=22% Similarity=0.316 Sum_probs=108.1
Q ss_pred cCCC-CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 54 ~~~~-~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
.++. +|+++.|+ +||+||+|..++| ++||||+||+||.++.++++.+++||.+.|+|+.+|+++++|.||+
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~g---vEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDD---IEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCCC---cEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 3455 89999998 9999999964445 9999999999999999999999999999999999999999999999
Q ss_pred eeccCCchhHHHhhhcCCCCceeEeeEeeecC-CeeEEe------cCCChhhhchhh
Q 030172 128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSS-NSNTIE------PLPGLGAIFEEL 177 (182)
Q Consensus 128 k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~-~G~fV~------l~~gv~gl~~~~ 177 (182)
|++.++||....++|.. |+.++|+|.++.. +|+|++ ..++++++.|..
T Consensus 89 K~v~~~pw~~~~e~~~~--g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y 143 (319)
T PTZ00248 89 KRVSPEDIEACEEKFSK--SKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHAL 143 (319)
T ss_pred eecccchHHHHHHhCcC--CCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHH
Confidence 99999999999999988 9999999999965 999998 578888777644
No 19
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.83 E-value=2.3e-20 Score=169.46 Aligned_cols=162 Identities=20% Similarity=0.358 Sum_probs=137.3
Q ss_pred CCCCCCccHHH---hhh-hcCCCeEEEEEEEEeCCCCEEEEEechh----HHhhhhcCCCCCCEEEEE-----eEeEEEE
Q 030172 6 SCKEPQKSIHE---IAK-GLTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (182)
Q Consensus 6 ~~p~~e~~~~~---~~~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (182)
|+|..++++.. ... ..+|++++|+|+.+|..++++.+|++.. .|+.+...++.|+++.|+ ++|+||+
T Consensus 329 ~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~ 408 (647)
T PRK00087 329 VIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD 408 (647)
T ss_pred EEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence 45666665432 112 2499999999999999899999999863 577777778999999999 8899999
Q ss_pred EecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCe-EEEEEeeccC----CchhHHHhhhcCCCC
Q 030172 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDG 147 (182)
Q Consensus 73 l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~k-i~lS~k~~~~----~p~~~~~~~~~~~~g 147 (182)
++ | ++||||.+++++.+..++.++ +||.++|+|+++|+++++ +.+|+|.+.. .++....+.+.+ |
T Consensus 409 lg---g---i~gfiP~sel~~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~--G 478 (647)
T PRK00087 409 YG---G---VRAFLPASHVELGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEE--G 478 (647)
T ss_pred EC---C---EEEEEEHHHhCccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCC--C
Confidence 95 4 999999999999988888764 899999999999998888 9999998753 567777777776 9
Q ss_pred ceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
+++.|+|+++.++|+||++ +|++||+|...
T Consensus 479 ~iV~g~V~~v~~~G~fV~l-~gv~Gll~~se 508 (647)
T PRK00087 479 DVVEGEVKRLTDFGAFVDI-GGVDGLLHVSE 508 (647)
T ss_pred CEEEEEEEEEeCCcEEEEE-CCEEEEEEHHH
Confidence 9999999999999999999 89999998754
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=5.5e-18 Score=121.34 Aligned_cols=77 Identities=45% Similarity=0.787 Sum_probs=71.4
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
.+++|++++|+ +|||||+|. +| -.|||||||+.+.|+.++.+++++||.|+|+|+++|. ++++.||+|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~--~g---~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELE--GG---KTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEec--CC---CcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence 57899999999 999999997 56 8999999999999999999999999999999999997 9999999999
Q ss_pred ccCCchhH
Q 030172 130 LEEDPLLE 137 (182)
Q Consensus 130 ~~~~p~~~ 137 (182)
++..|-..
T Consensus 76 ~~e~pe~~ 83 (129)
T COG1098 76 LEEEPEKQ 83 (129)
T ss_pred hhhCcccc
Confidence 98877543
No 21
>PRK08582 hypothetical protein; Provisional
Probab=99.59 E-value=8.5e-15 Score=109.16 Aligned_cols=77 Identities=42% Similarity=0.737 Sum_probs=71.5
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
.+++|++|.|+ ++|+||+|. ++ ++||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~--~~---~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELP--EG---KTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 47899999999 999999996 45 9999999999999999999999999999999999997 5999999999
Q ss_pred ccCCchhH
Q 030172 130 LEEDPLLE 137 (182)
Q Consensus 130 ~~~~p~~~ 137 (182)
+..+||..
T Consensus 76 ~~~~~~~~ 83 (139)
T PRK08582 76 AKDRPKRQ 83 (139)
T ss_pred cccCchhh
Confidence 99999965
No 22
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.58 E-value=5.9e-15 Score=98.63 Aligned_cols=66 Identities=26% Similarity=0.438 Sum_probs=59.9
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc---cccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~---~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
+++|+++.|+ ++|+||+++ .| ++|++|+++++|.++.++ .+.|++||.++|+|+++|++++++.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~--~~---v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLS--SS---IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeC--CC---CEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 5789999999 999999996 45 999999999999997765 588999999999999999999999886
No 23
>PHA02945 interferon resistance protein; Provisional
Probab=99.54 E-value=5.1e-14 Score=95.34 Aligned_cols=74 Identities=30% Similarity=0.366 Sum_probs=67.5
Q ss_pred cCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEEccCc--CCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~~sel--s~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
.-+++|+++.|+ ++|+||.|..++| .+||+|+|+. +..|+++ ++++ .||.+.|+|+.+|+.++.|.||+
T Consensus 7 ~~P~~GelvigtV~~~d~ga~v~L~EY~g---~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl 81 (88)
T PHA02945 7 SLPNVGDVLKGKVYENGYALYIDLFDYPH---SEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY 81 (88)
T ss_pred cCCCCCcEEEEEEEecCceEEEEecccCC---cEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence 346899999999 9999999987666 9999999955 9999999 9999 99999999999999999999999
Q ss_pred eeccC
Q 030172 128 KQLEE 132 (182)
Q Consensus 128 k~~~~ 132 (182)
|....
T Consensus 82 K~V~~ 86 (88)
T PHA02945 82 KRMCR 86 (88)
T ss_pred eEccc
Confidence 98754
No 24
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.54 E-value=2.9e-14 Score=94.67 Aligned_cols=69 Identities=45% Similarity=0.787 Sum_probs=64.5
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
+++.|+++.|+ ++|+||+++ +| ++||||++++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~--~~---~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG--NG---IEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES--TS---SEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC--Cc---EEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 47899999999 899999997 45 99999999999999999999999999999999999999999999986
No 25
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.54 E-value=2.7e-14 Score=97.21 Aligned_cols=70 Identities=33% Similarity=0.464 Sum_probs=65.5
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
+.++++|+++.|+ ++|+||+++ +| ++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+
T Consensus 9 ~~~~~~G~i~~g~V~~v~~~G~fv~l~--~~---~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 9 FSDLKPGMVVHGYVRNITPYGVFVEFL--GG---LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HHhCCCCCEEEEEEEEEeeceEEEEcC--CC---CEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 4679999999999 999999996 45 9999999999999999999999999999999999999999999985
No 26
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.52 E-value=1.1e-13 Score=92.27 Aligned_cols=71 Identities=34% Similarity=0.504 Sum_probs=64.2
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
++.|+++.|+ ++|+||++...+| ++|++|++++++.+..++.+.|++||.|+|+|+++|.+++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~---~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGN---IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCC---eEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 3579999999 9999999963334 999999999999999999999999999999999999989999999974
No 27
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.51 E-value=6.3e-14 Score=129.46 Aligned_cols=86 Identities=29% Similarity=0.474 Sum_probs=77.3
Q ss_pred HhhhhcCCCCCCEEE-EE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCe
Q 030172 49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (182)
Q Consensus 49 ~~~~~~~~~~G~iv~-g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~k 122 (182)
++.+....++|++|. |+ +||+||+|. +| ++||||+|+++|.++.++.+.|++||.|+|+|+++|+ ++|
T Consensus 744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~--~g---~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~gr 817 (891)
T PLN00207 744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIA--PG---REGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ 817 (891)
T ss_pred HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC--CC---CEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence 444556789999996 45 999999996 46 9999999999999999999999999999999999997 899
Q ss_pred EEEEEeeccCCchhHHHh
Q 030172 123 ITLSIKQLEEDPLLETLE 140 (182)
Q Consensus 123 i~lS~k~~~~~p~~~~~~ 140 (182)
|.||+|.+.++||.++.+
T Consensus 818 I~LSlK~l~~~Pw~~~~~ 835 (891)
T PLN00207 818 LRLSRRALLPEANSEKSS 835 (891)
T ss_pred EEEEEeccccCchhhhhh
Confidence 999999999999988765
No 28
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.51 E-value=5.5e-14 Score=93.38 Aligned_cols=66 Identities=21% Similarity=0.297 Sum_probs=60.2
Q ss_pred CCCCCEEEEE-----e-EeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 56 ~~~G~iv~g~-----~-~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
+++|+++.|+ + +|+|+++. .| .+|++|++++++.+..++.+.|++||.|+|+|+++|. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~--~~---~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLP--FG---KTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECC--CC---CEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 4689999999 4 89999996 55 9999999999999999999999999999999999983 89999985
No 29
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.51 E-value=6.9e-14 Score=93.18 Aligned_cols=65 Identities=17% Similarity=0.315 Sum_probs=59.7
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ ++|+||++. ++ ++|+||++++++.. ..++.+.|++||.|+|+|+++|+++++|.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~--~~---i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS--PD---VKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CC---cEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 6788888 999999996 45 99999999999864 889999999999999999999999999999987
No 30
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.50 E-value=8.5e-14 Score=91.51 Aligned_cols=65 Identities=29% Similarity=0.410 Sum_probs=60.2
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ ++|+||++. ++ ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~--~~---~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFY--NN---VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC--CC---CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 6778888 999999996 45 99999999999999999999999999999999999999999999986
No 31
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.50 E-value=2e-13 Score=90.86 Aligned_cols=66 Identities=33% Similarity=0.538 Sum_probs=59.0
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
+.|+++.|+ +||+||++... + .+||+|++++++.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~-~---~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGC-R---KQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCC-C---eEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 579999999 99999999411 2 699999999999999999999999999999999999865 999886
No 32
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.49 E-value=2.2e-13 Score=90.35 Aligned_cols=68 Identities=26% Similarity=0.428 Sum_probs=62.5
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
+++|+++.|+ ++|+||++. ++ ++|++|++++++++..++.+.|++||.++|+|+++|++++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~--~~---~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLG--NK---VTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeC--CC---cEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 4689999999 999999996 45 99999999999998888889999999999999999998999999985
No 33
>PRK07252 hypothetical protein; Provisional
Probab=99.49 E-value=2.1e-13 Score=99.23 Aligned_cols=73 Identities=38% Similarity=0.727 Sum_probs=67.3
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
++|+++.|+ ++|+||+|. ++ ++||+|++++++.++.++.+.|++||.|+|+|+++|++++++.||+|++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~--~~---~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE--NG---TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC--CC---CEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 579999999 999999996 45 99999999999999999999999999999999999999999999999998
Q ss_pred CCc
Q 030172 132 EDP 134 (182)
Q Consensus 132 ~~p 134 (182)
+++
T Consensus 77 ~~~ 79 (120)
T PRK07252 77 EEK 79 (120)
T ss_pred cCc
Confidence 643
No 34
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.47 E-value=4.3e-14 Score=113.34 Aligned_cols=78 Identities=36% Similarity=0.640 Sum_probs=72.6
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
-+..|++|.|+ +||+||.|..++| ++||+|+||++..|+.+.+++++.||.+-|+|+.+|+.++.|.||+|.
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g---~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYPG---KEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccCC---eeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 36789999999 9999999987777 999999999999999999999999999999999999999999999999
Q ss_pred ccCCch
Q 030172 130 LEEDPL 135 (182)
Q Consensus 130 ~~~~p~ 135 (182)
+.++.-
T Consensus 85 V~~~q~ 90 (269)
T COG1093 85 VTEHQR 90 (269)
T ss_pred CCHHHH
Confidence 876553
No 35
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.47 E-value=2.4e-13 Score=89.25 Aligned_cols=64 Identities=22% Similarity=0.438 Sum_probs=59.2
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
|+++.|+ ++|+||++. +| ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~--~~---v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLS--DH---IKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec--CC---cEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 6788888 999999996 45 9999999999999999999999999999999999999999999984
No 36
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.46 E-value=1e-12 Score=123.76 Aligned_cols=151 Identities=19% Similarity=0.189 Sum_probs=126.7
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechh-----------HHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEE
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDA-----------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~-----------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~gl 85 (182)
.++.+.+.++.++..++.+.+|.+.. .-....++++.|+++.|. +.|+|+.+. -+ ++++
T Consensus 1115 ~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls--~~---v~a~ 1189 (1710)
T KOG1070|consen 1115 KIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS--RK---VEAF 1189 (1710)
T ss_pred cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc--cc---eEEE
Confidence 57899999999999888899998731 122335789999999999 999999996 23 9999
Q ss_pred EEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEE
Q 030172 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTI 164 (182)
Q Consensus 86 v~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV 164 (182)
+++++++..+...+++.|++||.+.++|+++++..+++.||+|......-......+.. ..|+...|+|..+.++|.||
T Consensus 1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi 1269 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFI 1269 (1710)
T ss_pred EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEE
Confidence 99999999999999999999999999999999999999999998764333233333321 34999999999999999999
Q ss_pred ecCCCh--hhhchhh
Q 030172 165 EPLPGL--GAIFEEL 177 (182)
Q Consensus 165 ~l~~gv--~gl~~~~ 177 (182)
++++++ .|+||.-
T Consensus 1270 ~l~~tv~~~g~~~~~ 1284 (1710)
T KOG1070|consen 1270 KLDVTVNMVGLCHIS 1284 (1710)
T ss_pred EecCcceecccccce
Confidence 999888 9999853
No 37
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.46 E-value=2.7e-13 Score=89.78 Aligned_cols=57 Identities=30% Similarity=0.493 Sum_probs=53.5
Q ss_pred eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
++|+||++. +| ++||+|++++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus 15 ~~G~~V~l~--~g---v~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 15 DLGAVFELK--DG---LLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CceEEEEeC--CC---CEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 799999996 46 9999999999999999999999999999999999999999999985
No 38
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.45 E-value=9.3e-13 Score=87.99 Aligned_cols=68 Identities=18% Similarity=0.199 Sum_probs=60.6
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
+++.|+++.|. ++|+||+++ .+| ++||+|.+++++. +.+++||.+.|+|+++|++++++.||+|+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g-~~g---v~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIG-IPG---TTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeC-CCC---cEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 46889999999 999999995 345 9999999999986 66899999999999999999999999997
Q ss_pred ccC
Q 030172 130 LEE 132 (182)
Q Consensus 130 ~~~ 132 (182)
..+
T Consensus 71 ~~~ 73 (74)
T cd05694 71 SKV 73 (74)
T ss_pred ccc
Confidence 653
No 39
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.44 E-value=1.3e-12 Score=88.01 Aligned_cols=71 Identities=35% Similarity=0.685 Sum_probs=62.0
Q ss_pred CCEEEEE-----eEeEEEEEecC-CCceeEEEEEEccCcCCccc-cCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 59 EDIFVGR-----DYGAFIHLRFP-DGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~-~g~~~~~glv~~sels~~~~-~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
|+++.|+ ++|+||+|... ++ .+||+|++++++.+. .++.+.|++||.|+|+|+++| ++++.+|+|+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~---~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~ 75 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGR---KEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVD 75 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCC---cEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecc
Confidence 5677777 99999999622 24 899999999999986 899999999999999999999 899999999987
Q ss_pred CCc
Q 030172 132 EDP 134 (182)
Q Consensus 132 ~~p 134 (182)
++.
T Consensus 76 ~~~ 78 (79)
T cd05684 76 QDT 78 (79)
T ss_pred cCC
Confidence 653
No 40
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.43 E-value=1.2e-12 Score=87.27 Aligned_cols=70 Identities=41% Similarity=0.648 Sum_probs=63.4
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
++|+++.|+ ++|+||++.. .+ .+|++|++++++.+..++.+.|++||.|+|+|+++|++++++.+|+|.+
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~-~~---~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDG-TN---VSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECC-CC---eEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 368899998 9999999962 24 9999999999999988999999999999999999999999999999974
No 41
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.43 E-value=9e-13 Score=87.03 Aligned_cols=67 Identities=36% Similarity=0.630 Sum_probs=61.5
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
|+++.|+ ++|+||++. ++ ++|++|++++++.+..++.+.|++||.++|+|+++|++++++.||+|.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~--~~---~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG--DG---VEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC--CC---CEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 6777777 999999996 44 9999999999999999999999999999999999999889999999975
No 42
>PRK08059 general stress protein 13; Validated
Probab=99.43 E-value=1e-12 Score=96.08 Aligned_cols=76 Identities=46% Similarity=0.831 Sum_probs=70.6
Q ss_pred cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
.++++|+++.|+ ++|+||++. ++ ++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.+|+|
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~--~~---~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALD--EE---TQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEEC--CC---CEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 468899999999 999999996 45 99999999999999999999999999999999999999999999999
Q ss_pred eccCCc
Q 030172 129 QLEEDP 134 (182)
Q Consensus 129 ~~~~~p 134 (182)
.+..+|
T Consensus 78 ~~~~~~ 83 (123)
T PRK08059 78 ATEEAP 83 (123)
T ss_pred EcccCc
Confidence 998877
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.42 E-value=5.5e-13 Score=87.29 Aligned_cols=63 Identities=30% Similarity=0.520 Sum_probs=57.9
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
|+++.|+ ++|+||++. ++ ++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~--~~---~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLG--RG---VDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC--CC---CEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 6777787 999999996 45 999999999999999999999999999999999999999999876
No 44
>PRK05807 hypothetical protein; Provisional
Probab=99.40 E-value=2.1e-12 Score=95.98 Aligned_cols=70 Identities=47% Similarity=0.760 Sum_probs=65.3
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
.+++|+++.|+ ++|+||+|. + ..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~---~---~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~ 74 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE---G---KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ 74 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC---C---EEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 46789999999 999999993 4 8999999999999999999999999999999999998 7999999999
Q ss_pred cc
Q 030172 130 LE 131 (182)
Q Consensus 130 ~~ 131 (182)
+.
T Consensus 75 ~~ 76 (136)
T PRK05807 75 AM 76 (136)
T ss_pred cc
Confidence 86
No 45
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.40 E-value=1.2e-12 Score=85.67 Aligned_cols=63 Identities=38% Similarity=0.811 Sum_probs=56.1
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC-ccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~-~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
|+++.|+ ++|+||++. ++ ++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~--~~---~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD--GG---IDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC--CC---CEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 5677777 999999996 45 999999999997 567888999999999999999999999999874
No 46
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.37 E-value=2.5e-12 Score=84.55 Aligned_cols=65 Identities=31% Similarity=0.469 Sum_probs=59.8
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ ++|+||+++ .+ .+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~--~~---~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG--YK---SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--CC---ceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 6788888 889999996 34 99999999999999999999999999999999999988899999985
No 47
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.36 E-value=3.7e-12 Score=82.65 Aligned_cols=64 Identities=45% Similarity=0.893 Sum_probs=58.5
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ ++|+||++. ++ .+||+|.+++++.++.++.+.|++||.++|+|+++|+ ++++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~--~~---~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELG--GG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--CC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 6777777 999999996 45 9999999999999999999999999999999999998 899999986
No 48
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.35 E-value=4.4e-12 Score=103.72 Aligned_cols=85 Identities=35% Similarity=0.597 Sum_probs=73.1
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
-+++|+++.|+ ++|+||+|..++| ++||+|++++++.++.++++.|++||.+.|+|+++|++++++.||+|.
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~g---ieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~ 81 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPG---KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCC---cEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence 36789999999 9999999974445 999999999999999999999999999999999999999999999998
Q ss_pred ccCCchhHHHhhh
Q 030172 130 LEEDPLLETLEKV 142 (182)
Q Consensus 130 ~~~~p~~~~~~~~ 142 (182)
+.++.-....+.+
T Consensus 82 v~~~e~~~~~~~~ 94 (262)
T PRK03987 82 VNEHQRREKIQEW 94 (262)
T ss_pred cccchHHHHHHHH
Confidence 8765533333333
No 49
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.34 E-value=7.1e-12 Score=82.77 Aligned_cols=66 Identities=41% Similarity=0.741 Sum_probs=57.8
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc-cccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~-~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
+.+|+++.|+ ++|+||++. +| ++||+|+++++|. +..++.+.|++||.++|+|+++|.+++++.++
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~--~~---~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE--EG---VEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC--CC---CEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 4678999998 999999996 45 9999999999875 45577788999999999999999988988764
No 50
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.30 E-value=4.4e-12 Score=89.47 Aligned_cols=70 Identities=31% Similarity=0.541 Sum_probs=61.6
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-------------------cCccccccCCCEEEE
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV 111 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-------------------~~~~~~~~~Gd~v~v 111 (182)
+++|+++.|+ ++|+||.+. +| ++|++|++++++.+. .++.+.|++||.|+|
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~--~g---~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~ 75 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLP--NG---LTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC 75 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECC--CC---cEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence 5789999999 999999995 56 999999999998753 347788999999999
Q ss_pred EEEEEeCC---CCeEEEEEeec
Q 030172 112 KVIKIDRE---KSRITLSIKQL 130 (182)
Q Consensus 112 kV~~id~~---~~ki~lS~k~~ 130 (182)
+|+++|++ +++|.||+|..
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHH
Confidence 99999987 78999999864
No 51
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.27 E-value=1.4e-11 Score=79.76 Aligned_cols=63 Identities=38% Similarity=0.652 Sum_probs=56.6
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
|+++.|+ ++|+||++. ++ .+|++|.+++++.++.++.+.|++||.++|+|+++|++++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~--~~---~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG--VK---QDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC--CC---CEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 5677777 999999996 44 999999999999988899999999999999999999988998875
No 52
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.27 E-value=1.8e-11 Score=79.87 Aligned_cols=61 Identities=20% Similarity=0.349 Sum_probs=53.2
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
|+++.|+ ++|+||++. +| ++|++|.++++..+.. .+.|++||.++|+|+++|++++++.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~--~~---v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFL--SS---FTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc--CC---ceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 6788888 999999996 45 9999999999765544 677999999999999999999998876
No 53
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.26 E-value=3.1e-11 Score=78.30 Aligned_cols=63 Identities=46% Similarity=0.907 Sum_probs=57.5
Q ss_pred CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
+|+++.|+ ++|+||+++ + .+|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~---~---~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG---G---VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC---C---eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 47888888 999999995 3 999999999999888899999999999999999999989999875
No 54
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.26 E-value=3.2e-11 Score=78.32 Aligned_cols=63 Identities=46% Similarity=0.838 Sum_probs=56.7
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
|+++.|+ ++|+||++. ++ .+||+|++++++.+..++.+.|++||.++|+|.++|+ ++++.+|+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~--~~---~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEIL--PG---KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC--CC---CEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 5677777 999999996 44 8999999999999988888999999999999999998 89999884
No 55
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.24 E-value=5.6e-11 Score=112.33 Aligned_cols=156 Identities=16% Similarity=0.218 Sum_probs=131.3
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechhHHhh---hhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNK---YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~---~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~ 93 (182)
+|.++.+++..+-.....+.+|..++.... ...++++|++|.|+ +-|+-|.+. +| ++.|++|-+.+++
T Consensus 470 ~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~--~~--ni~g~lp~~hlsd 545 (1710)
T KOG1070|consen 470 VGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVNDIEIGQLVPGVIRKVTPQGVEVLVT--FG--NIKGVLPKEHLSD 545 (1710)
T ss_pred cCCcccCccceecccCcEEEEEEehHhhcccccccccccccceeeeEEEEecCCcEEEEEe--cC--ceeeecChHhhhh
Confidence 788999999999999899999988753221 24579999999999 889999986 34 5999999999999
Q ss_pred ccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEEecCCChhh
Q 030172 94 DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (182)
Q Consensus 94 ~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV~l~~gv~g 172 (182)
....-|...|.+|..++.||+.++.+++++.|++|....+...+..++|.. ..|..+.|++.++.++||||++..|++|
T Consensus 546 ~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsG 625 (1710)
T KOG1070|consen 546 HPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSG 625 (1710)
T ss_pred cccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecCcccc
Confidence 998889889999999999999999999999999997765554444444421 2399999999999999999999999999
Q ss_pred hchhhhhcc
Q 030172 173 IFEELLQED 181 (182)
Q Consensus 173 l~~~~~~~~ 181 (182)
|.|...+-|
T Consensus 626 f~p~s~~sd 634 (1710)
T KOG1070|consen 626 FAPVSEMSD 634 (1710)
T ss_pred ccchhhhhh
Confidence 999987754
No 56
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.23 E-value=3.6e-11 Score=82.17 Aligned_cols=70 Identities=23% Similarity=0.372 Sum_probs=61.4
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCC----ccccCccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~----~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~l 125 (182)
.+++|++|.|+ ++|++|+++ .+ ++|++|++++++ .+..++.+.+++||.++|+|+++|++ +++.|
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~--~~---~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L 76 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDIN--SP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL 76 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECC--CC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence 46899999999 999999996 34 999999999996 45577788899999999999999975 99999
Q ss_pred EEeec
Q 030172 126 SIKQL 130 (182)
Q Consensus 126 S~k~~ 130 (182)
|+|..
T Consensus 77 S~~~~ 81 (86)
T cd05789 77 HTRSL 81 (86)
T ss_pred EeCcc
Confidence 99864
No 57
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.22 E-value=6.7e-11 Score=92.54 Aligned_cols=101 Identities=23% Similarity=0.318 Sum_probs=80.9
Q ss_pred CCCeEEEEEE---EEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCC--C---ceeEEEEEEc
Q 030172 22 TGSIISVKVI---QANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV 88 (182)
Q Consensus 22 vG~~v~~~v~---~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~--g---~~~~~glv~~ 88 (182)
.+..+.+.+. ++|.+++++.+ .+|......+++|++|.|+ ++|+||+|...+ + ..+.+|++|+
T Consensus 29 ~~~~i~as~~G~~~id~~~~~Isv----~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~ 104 (189)
T PRK09521 29 DNGEVYASVVGKVFIDDINRKISV----IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI 104 (189)
T ss_pred eCCEEEEEeeEEEEEcCCCCEEEE----ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence 4666666554 44667778877 4666656778999999999 999999996321 0 0028999999
Q ss_pred cCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 89 sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
+++++.+..++.+.|++||.|.|+|++++ +++.||+|+
T Consensus 105 s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 105 SQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred hHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 99999988899999999999999999997 789999985
No 58
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.21 E-value=6.7e-11 Score=77.13 Aligned_cols=62 Identities=29% Similarity=0.584 Sum_probs=55.0
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ ++|+||+++ | ++||+|.+++++.+..++.+ .+||.++|+|+++|.+++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~---g---~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIE---G---VRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEEC---C---EEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 6788887 999999993 5 99999999999988777766 3899999999999998999999975
No 59
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.21 E-value=9.8e-11 Score=107.42 Aligned_cols=91 Identities=35% Similarity=0.647 Sum_probs=76.1
Q ss_pred EeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc
Q 030172 33 ANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 99 (182)
Q Consensus 33 ~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~ 99 (182)
+++ ++.+.++... ...+.....+++|+++.|+ +||+||+|. +| .+||+|++++++.++.++
T Consensus 589 i~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~--~~---~~GllhiSels~~~v~~~ 662 (693)
T PRK11824 589 IED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL--PG---KDGLVHISEIADERVEKV 662 (693)
T ss_pred cCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeeccCccccCc
Confidence 443 4676666542 1233445678999999999 999999996 45 999999999999999999
Q ss_pred cccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 100 ~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
.+.|++||.|+|+|+++|++ +++.||+|.+
T Consensus 663 ~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 663 EDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred cceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 99999999999999999986 9999999975
No 60
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.21 E-value=8.5e-11 Score=106.92 Aligned_cols=89 Identities=25% Similarity=0.545 Sum_probs=71.3
Q ss_pred EEEeCCCCEEEEEechh--------HHhhhhc--CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC---
Q 030172 31 IQANEEMKKLVFSEKDA--------VWNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--- 92 (182)
Q Consensus 31 ~~~d~~~~~i~lS~k~~--------~~~~~~~--~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels--- 92 (182)
+++++ ++.+.++-... ..+.+.. .+++|++|.|+ +||+||+|. .| ++||||+|+++
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~--~G---~eGLvHISeisdls 684 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL--PG---KDGLLHISQIRKLA 684 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec--CC---ceEEEEhhhccccc
Confidence 35665 57777765431 2223333 47899999999 999999996 45 99999999996
Q ss_pred -CccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 93 -~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
+.++.++.+.|++||.|+|+|+++|. ++|+.|+
T Consensus 685 ~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 685 GGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 45789999999999999999999995 8899886
No 61
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.20 E-value=1.1e-10 Score=75.74 Aligned_cols=67 Identities=45% Similarity=0.783 Sum_probs=60.6
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
++|+++.|+ ++|+||+++ ++ +.|++|.+++++.+..++.+.|++||.+.|+|++++++++++.+|++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG--NG---VEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeC--CC---CEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 368999998 899999996 35 99999999999988888888999999999999999998899999975
No 62
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.18 E-value=1.2e-10 Score=80.34 Aligned_cols=70 Identities=27% Similarity=0.423 Sum_probs=59.2
Q ss_pred cCCCCCCEEEEE-----eE--eEEEEEecCCCceeEEEEEEccCcCC---ccccCccccccCCCEEEEEEEEEeCCCCeE
Q 030172 54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRI 123 (182)
Q Consensus 54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~~~~glv~~sels~---~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki 123 (182)
.+++.|++|.|+ ++ ||||+++ +| .+||||+++++| .++.++.+.+++||.|.|+|++.....+-.
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~--~g---~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIG--LG---KNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeC--CC---CEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence 357899999999 64 9999997 46 999999999999 668888999999999999999987655555
Q ss_pred EEEEe
Q 030172 124 TLSIK 128 (182)
Q Consensus 124 ~lS~k 128 (182)
.||.+
T Consensus 78 ~lt~~ 82 (88)
T cd04453 78 RLTTN 82 (88)
T ss_pred eEEEE
Confidence 55554
No 63
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.14 E-value=4.9e-10 Score=75.61 Aligned_cols=65 Identities=29% Similarity=0.577 Sum_probs=54.8
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeCCCCe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKSR 122 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~~~~k 122 (182)
|+++.|. ++|+||++.. .| ++|++|++++++.++. +..+.|++||.|+|+|.++|.++++
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~-~~---~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~ 77 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDN-LT---VEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRK 77 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecC-CC---EEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCE
Confidence 7788888 9999999962 15 9999999999876422 3457899999999999999998999
Q ss_pred EEEEE
Q 030172 123 ITLSI 127 (182)
Q Consensus 123 i~lS~ 127 (182)
+.+++
T Consensus 78 i~~~l 82 (83)
T cd04471 78 IDFEL 82 (83)
T ss_pred EEEEE
Confidence 99986
No 64
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.09 E-value=5e-10 Score=75.89 Aligned_cols=69 Identities=22% Similarity=0.216 Sum_probs=62.7
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
.+++|+++.|+ +.+++|+++ .+ .+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDIL--SR---GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeC--CC---ceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 35899999999 899999996 33 99999999999888888999999999999999999985 899999986
No 65
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.06 E-value=2.8e-10 Score=103.39 Aligned_cols=75 Identities=36% Similarity=0.607 Sum_probs=69.4
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
..++++|.++.|+ +||+||+|+ -+ .+|+||+|+++..++.+|.+.+++||.|+|+|+++|..+++|.|||
T Consensus 653 i~dLk~Gm~leg~Vrnv~~fgafVdIg--v~---qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm 727 (780)
T COG2183 653 ITDLKPGMILEGTVRNVVDFGAFVDIG--VH---QDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM 727 (780)
T ss_pred HhhccCCCEEEEEEEEeeeccceEEec--cc---cceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence 3579999999999 999999997 23 8999999999999999999999999999999999999999999999
Q ss_pred eeccC
Q 030172 128 KQLEE 132 (182)
Q Consensus 128 k~~~~ 132 (182)
+....
T Consensus 728 r~~~~ 732 (780)
T COG2183 728 RLDEE 732 (780)
T ss_pred eccCC
Confidence 97644
No 66
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=99.06 E-value=1e-10 Score=107.82 Aligned_cols=120 Identities=23% Similarity=0.341 Sum_probs=80.7
Q ss_pred CCCCCCCCCCccHHHhhhhcCCCe--EE-EEEEEEeCCC-CEE--EEEec--hh---------HHhhhhcCCCCCCEEEE
Q 030172 2 SPSHSCKEPQKSIHEIAKGLTGSI--IS-VKVIQANEEM-KKL--VFSEK--DA---------VWNKYSSRVNVEDIFVG 64 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~vG~~--v~-~~v~~~d~~~-~~i--~lS~k--~~---------~~~~~~~~~~~G~iv~g 64 (182)
||+| +|+|+-.|+.++.++... .. ..-....... ..+ .++.+ .+ .|...+...++|+++.|
T Consensus 556 SPIR--RY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g 633 (709)
T TIGR02063 556 SPIR--RYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEG 633 (709)
T ss_pred Cccc--cchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEEE
Confidence 8999 999999999888775322 11 0000000000 000 00000 00 12223445678999999
Q ss_pred E-----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 65 R-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 65 ~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
+ +||+||++.. .| ++|+||++++++.+. .+..+.|++||.|+|+|.++|..+++|.+++
T Consensus 634 ~V~~v~~fGifV~L~~-~~---~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l 708 (709)
T TIGR02063 634 VISGVTSFGLFVELEN-NT---IEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFEL 708 (709)
T ss_pred EEEEEEeCCEEEEecC-Cc---eEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence 9 9999999962 15 999999999987643 2345679999999999999999999999986
No 67
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=6.4e-10 Score=99.72 Aligned_cols=93 Identities=37% Similarity=0.659 Sum_probs=78.0
Q ss_pred EEeCCCCEEEEEech--------hHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172 32 QANEEMKKLVFSEKD--------AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD 98 (182)
Q Consensus 32 ~~d~~~~~i~lS~k~--------~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~ 98 (182)
+++ +++.+..+-.. .........+++|++|.|+ +||+||++. +| .+|+||+|++++.++.+
T Consensus 586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~--~g---kdgl~hiS~~~~~rv~k 659 (692)
T COG1185 586 DIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL--PG---KDGLVHISQLAKERVEK 659 (692)
T ss_pred Eec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec--CC---cceeEEehhhhhhhhhc
Confidence 455 45666555443 1344556789999999999 999999996 45 89999999999999999
Q ss_pred ccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 99 ~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
..+.+++||.+.||++.+|. .+++.||+|...
T Consensus 660 v~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~ 691 (692)
T COG1185 660 VEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL 691 (692)
T ss_pred ccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence 99999999999999999996 899999998653
No 68
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.99 E-value=1.4e-09 Score=71.56 Aligned_cols=57 Identities=23% Similarity=0.295 Sum_probs=50.5
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCC
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK 120 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~ 120 (182)
|+++.|+ ++|+||+++ +| ++|++|++++++.+ ..++.+.|++||.|+|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~--~~---i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA--DN---VHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC--CC---cEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 6778888 889999996 55 99999999999885 7888899999999999999999743
No 69
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.99 E-value=1.7e-09 Score=99.13 Aligned_cols=87 Identities=34% Similarity=0.679 Sum_probs=70.6
Q ss_pred EEeCCCCEEEEEech-h-------HHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccC
Q 030172 32 QANEEMKKLVFSEKD-A-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD 98 (182)
Q Consensus 32 ~~d~~~~~i~lS~k~-~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~ 98 (182)
+++. ++.+.++... + ..+.....+++|++|.|+ +||+||++. +| .+||||+|++++.++.+
T Consensus 585 ~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~--~g---~~GllHiSei~~~~v~~ 658 (684)
T TIGR03591 585 DIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL--PG---KDGLVHISEIANERVEK 658 (684)
T ss_pred EEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC--CC---cEEEEEHHHcCCCcccC
Confidence 4554 4777666532 1 233345568999999999 999999996 45 99999999999999999
Q ss_pred ccccccCCCEEEEEEEEEeCCCCeEEE
Q 030172 99 IRDILNEGDEVRVKVIKIDREKSRITL 125 (182)
Q Consensus 99 ~~~~~~~Gd~v~vkV~~id~~~~ki~l 125 (182)
+.+.|++||.|+|+|+++|. ++++.|
T Consensus 659 ~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 659 VEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred hhhccCCCCEEEEEEEEECC-CCCccC
Confidence 99999999999999999997 677754
No 70
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.99 E-value=1.5e-09 Score=68.96 Aligned_cols=56 Identities=48% Similarity=0.873 Sum_probs=51.3
Q ss_pred eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
++|+||+++ ++ .+|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
T Consensus 10 ~~g~~v~l~--~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 10 KFGVFVELE--DG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred eeeEEEEec--CC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 899999996 45 999999999999988888999999999999999999988888875
No 71
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.97 E-value=5.6e-09 Score=70.02 Aligned_cols=61 Identities=34% Similarity=0.579 Sum_probs=53.8
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
.++++.|+.+.|+ ++|+||++. ++ .+||+|.+++. +.|++||.++++|.++ .+++++.+|+
T Consensus 11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~--~~---~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 11 MEDLEVGKLYKGKVNGVAKYGVFVDLN--DH---VRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hhhCCCCCEEEEEEEeEecceEEEEEC--CC---cEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 3568999999999 999999996 44 99999999964 4599999999999999 7899999986
No 72
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.95 E-value=6.4e-09 Score=73.02 Aligned_cols=68 Identities=29% Similarity=0.518 Sum_probs=57.7
Q ss_pred eEeEEEEEecCCCceeEEEEEEccCcCCccccC-----------ccccccCCCEEEEEEEEEeCCC-----CeEEEEEee
Q 030172 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ 129 (182)
Q Consensus 66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~-----------~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k~ 129 (182)
++|+||++. + ++|++|++++++.+... ..+.|++||.|+|+|.++|.+. .++.||+|+
T Consensus 12 ~~GifV~l~---~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~ 85 (99)
T cd04460 12 DFGAFVRIG---P---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ 85 (99)
T ss_pred eccEEEEEc---C---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence 999999995 3 99999999999876543 3477999999999999999753 589999999
Q ss_pred ccCCchhHHH
Q 030172 130 LEEDPLLETL 139 (182)
Q Consensus 130 ~~~~p~~~~~ 139 (182)
....||....
T Consensus 86 ~~~g~~~~~~ 95 (99)
T cd04460 86 PGLGKLEWIE 95 (99)
T ss_pred CCCCcHHHhh
Confidence 9888887654
No 73
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.92 E-value=1.5e-08 Score=82.16 Aligned_cols=137 Identities=16% Similarity=0.158 Sum_probs=102.7
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE------eEeEEEEEecCCCceeEEEEEEccCcCCcc
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL 95 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~------~~G~fV~l~~~~g~~~~~glv~~sels~~~ 95 (182)
+|++|++.| +-..++++.+|.++ +..++|+.-.++ +-|+|++.+-+ .+.+||++++...+
T Consensus 46 vGdev~vFi--Y~D~~~rl~aTt~~-------p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~-----KDl~vp~~elp~~~ 111 (287)
T COG2996 46 VGDEVTVFI--YVDSEDRLIATTRE-------PKATVGEYGWLKVVEVNKDLGAFLDWGLP-----KDLLVPLDELPTLK 111 (287)
T ss_pred cCcEEEEEE--EECCCCceeheeec-------ceEeecceeEEEEEEEcCCcceEEecCCC-----cceeeehhhccccc
Confidence 899999999 65567889988877 566677765554 88999999743 79999999987531
Q ss_pred ccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcC-CCCceeEeeEeeecCCeeEEecCCChhhhc
Q 030172 96 IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP-QDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174 (182)
Q Consensus 96 ~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~-~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~ 174 (182)
.--+++||.+-|.+ .+|. ++|+.-+++. ....+..+..... -.++.+.|+|++....|.||-+++++-||+
T Consensus 112 ----~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~--~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI 183 (287)
T COG2996 112 ----SLWPQKGDKLLVYL-YVDK-KGRIWGTLAI--EKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI 183 (287)
T ss_pred ----ccCCCCCCEEEEEE-EEcc-CCcEEEEecc--hhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence 00168999999997 8997 6688888763 2222222222111 128999999999999999999999999999
Q ss_pred hhhhhc
Q 030172 175 EELLQE 180 (182)
Q Consensus 175 ~~~~~~ 180 (182)
|..++.
T Consensus 184 h~sEr~ 189 (287)
T COG2996 184 HKSERF 189 (287)
T ss_pred cchhhc
Confidence 987753
No 74
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.92 E-value=1.7e-10 Score=105.40 Aligned_cols=119 Identities=22% Similarity=0.353 Sum_probs=80.2
Q ss_pred CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCC-CEE--EEEec--hh---------HHhhhhcCCCCCCEEEEE-
Q 030172 2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEM-KKL--VFSEK--DA---------VWNKYSSRVNVEDIFVGR- 65 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~-~~i--~lS~k--~~---------~~~~~~~~~~~G~iv~g~- 65 (182)
||+| +|+|+-.|+.++.++ |......- ..+.+. ..+ .+|.+ .+ .|...+..-++|+++.|+
T Consensus 504 SPIR--RY~DLivHr~L~a~l~~~~~~~~~-~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I 580 (654)
T TIGR00358 504 SPIR--RYPDLTNHRLIKAVLAKEQTDTER-YQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEI 580 (654)
T ss_pred Cccc--cchHHHHHHHHHHHHcCCCCcccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEE
Confidence 9999 999999999888775 33211000 000000 000 00000 00 122223445689999999
Q ss_pred ----eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 66 ----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 66 ----~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
++|+||+|.. .| ++|+||++++.+.+. .+....|++||.|+|+|.++|.++++|.+++
T Consensus 581 ~~v~~~GifV~L~~-~~---veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l 653 (654)
T TIGR00358 581 SSVTRFGMFVRLDD-NG---IDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFEL 653 (654)
T ss_pred EeEEcCcEEEEecC-Cc---eEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence 9999999963 24 999999999988742 2334679999999999999999999999986
No 75
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.87 E-value=1.2e-08 Score=79.16 Aligned_cols=131 Identities=23% Similarity=0.480 Sum_probs=85.9
Q ss_pred CCCCCCCCCCCccHH-HhhhhcCCCe-----EEEEEEEEeC-CCCEEEEEec----hhHHhhhhcCCCCCCEEEEE----
Q 030172 1 MSPSHSCKEPQKSIH-EIAKGLTGSI-----ISVKVIQANE-EMKKLVFSEK----DAVWNKYSSRVNVEDIFVGR---- 65 (182)
Q Consensus 1 ~~p~~~~p~~e~~~~-~~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k----~~~~~~~~~~~~~G~iv~g~---- 65 (182)
++|+.|.+...-.+. ++.+.+.|.. +-..|.++.. ..+++.-..- .........+...|+++.|+
T Consensus 13 i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v 92 (179)
T TIGR00448 13 IPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEI 92 (179)
T ss_pred ECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence 467777654444443 3444455543 2333333332 2344431111 11233344567889999999
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEe-----CCCCeEEEEEe
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK 128 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id-----~~~~ki~lS~k 128 (182)
++|+||+++ + ++|++|.+++.+.+.. +....|+.||.|++||+++| ++..++.+|+|
T Consensus 93 ~~~GifV~lg-~-----~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k 166 (179)
T TIGR00448 93 VEFGAFVSLG-P-----FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMR 166 (179)
T ss_pred EeeEEEEEeC-C-----ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEec
Confidence 999999995 2 8999999998865432 23467999999999999998 56789999999
Q ss_pred eccCCchhH
Q 030172 129 QLEEDPLLE 137 (182)
Q Consensus 129 ~~~~~p~~~ 137 (182)
+.-..+++.
T Consensus 167 ~~~LG~~~w 175 (179)
T TIGR00448 167 QPLLGKLEW 175 (179)
T ss_pred cCcCCcccc
Confidence 876555443
No 76
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.87 E-value=4.8e-09 Score=92.23 Aligned_cols=108 Identities=19% Similarity=0.271 Sum_probs=82.1
Q ss_pred CCCCccHHHh----hhhcCCCeEEEEEEEEeCCCCEEEEEe-ch--------hHHhhhhcCCC--CCCEEEEE-----eE
Q 030172 8 KEPQKSIHEI----AKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRVN--VEDIFVGR-----DY 67 (182)
Q Consensus 8 p~~e~~~~~~----~~~~vG~~v~~~v~~~d~~~~~i~lS~-k~--------~~~~~~~~~~~--~G~iv~g~-----~~ 67 (182)
|..++++.+. ....+|+.+.+.|...+ .+++.++. |+ +.++..+..++ .|+++.|+ ++
T Consensus 71 ~~~eI~L~eAk~~~~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~ 148 (470)
T PRK09202 71 PTKEISLEEARKIDPDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERG 148 (470)
T ss_pred CcceeeHHHHhhhCccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecC
Confidence 3445555532 33459999999997776 34443332 22 12335566776 99999999 89
Q ss_pred eEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEEEee
Q 030172 68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (182)
Q Consensus 68 G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS~k~ 129 (182)
|+||+++ | ++||+|.++++ |++.|++||.++|.|++++++++ +|.||++.
T Consensus 149 giiVDLg---g---vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 149 NIIVDLG---R---AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred CEEEEEC---C---eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 9999995 5 99999999986 77889999999999999998777 89999975
No 77
>PRK11642 exoribonuclease R; Provisional
Probab=98.86 E-value=5.8e-10 Score=103.77 Aligned_cols=73 Identities=29% Similarity=0.432 Sum_probs=60.8
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeC
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR 118 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~ 118 (182)
.-++|+++.|+ +||+||+|.. .+ ++|+||++++++.|.. +..+.|++||.|+|+|.++|.
T Consensus 640 ~~~iGe~f~G~Is~V~~fGifVeL~~-~~---vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~ 715 (813)
T PRK11642 640 LDQVGNVFKGVISSVTGFGFFVRLDD-LF---IDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNM 715 (813)
T ss_pred hccCCcEEEEEEEEeecCceEEEECC-CC---eeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeec
Confidence 44789999999 9999999962 24 9999999999876432 234679999999999999999
Q ss_pred CCCeEEEEEeecc
Q 030172 119 EKSRITLSIKQLE 131 (182)
Q Consensus 119 ~~~ki~lS~k~~~ 131 (182)
++++|.+++....
T Consensus 716 ~~rkI~f~l~~~~ 728 (813)
T PRK11642 716 DERKIDFSLISSE 728 (813)
T ss_pred CCCeEEEEEeccc
Confidence 9999999996443
No 78
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.77 E-value=3.2e-08 Score=76.13 Aligned_cols=126 Identities=25% Similarity=0.433 Sum_probs=83.0
Q ss_pred CCCCCC-CCCCCccHHHhhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172 1 MSPSHS-CKEPQKSIHEIAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (182)
Q Consensus 1 ~~p~~~-~p~~e~~~~~~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~---- 65 (182)
++|+.| -|..+.-.+.+.+.+.|.- +-..|.++.. ..+++....-. .....+..++..|+++.|.
T Consensus 13 ipP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~ 92 (183)
T COG1095 13 IPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEV 92 (183)
T ss_pred eCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEE
Confidence 467766 3344444444555565543 3334444433 23444432211 2334445678889999998
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCCccc----------cC-ccccccCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK-----SRITLSIK 128 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~----------~~-~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k 128 (182)
++|+||.++ | .+||+|++++.+.++ .+ ....+++||.|++||++.+... .+|.+|+|
T Consensus 93 ~~~G~fV~ig-p-----~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmr 166 (183)
T COG1095 93 VEFGAFVRIG-P-----LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR 166 (183)
T ss_pred eecceEEEec-c-----ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEec
Confidence 999999997 3 899999999988743 22 3346999999999999998654 67899999
Q ss_pred eccC
Q 030172 129 QLEE 132 (182)
Q Consensus 129 ~~~~ 132 (182)
+.-.
T Consensus 167 q~~L 170 (183)
T COG1095 167 QPGL 170 (183)
T ss_pred cccC
Confidence 8654
No 79
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.77 E-value=2.4e-08 Score=80.71 Aligned_cols=71 Identities=27% Similarity=0.364 Sum_probs=62.7
Q ss_pred cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccc----cCccccccCCCEEEEEEEEEeCCCCeEE
Q 030172 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT 124 (182)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~----~~~~~~~~~Gd~v~vkV~~id~~~~ki~ 124 (182)
..+++||+|.|+ ++|+||+|+ .+ .+|++|++++++.++ .++++.|++||.|.|+|+++++ .+++.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~--~~---~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~ 132 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDIN--SP---YKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV 132 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeC--CC---ceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence 457899999999 899999996 23 899999999999887 7889999999999999999996 55699
Q ss_pred EEEeec
Q 030172 125 LSIKQL 130 (182)
Q Consensus 125 lS~k~~ 130 (182)
||+|+.
T Consensus 133 LS~k~~ 138 (235)
T PRK04163 133 LTLKGK 138 (235)
T ss_pred EEEcCC
Confidence 999863
No 80
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.66 E-value=1.6e-08 Score=88.91 Aligned_cols=82 Identities=27% Similarity=0.423 Sum_probs=71.4
Q ss_pred cCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
.++..|.+|.|+ ++|+||++. .| ..|++|+++|+..++.+|.+.+.+||.|.|+.++.|+ ++.+.+|.|
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~--p~---~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~r 737 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELY--PM---QQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSR 737 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEec--CC---chhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhh
Confidence 356777788888 999999996 36 9999999999999999999999999999999999998 888888889
Q ss_pred eccCCchhHHHhh
Q 030172 129 QLEEDPLLETLEK 141 (182)
Q Consensus 129 ~~~~~p~~~~~~~ 141 (182)
.+.++|.......
T Consensus 738 alLp~p~~~~~st 750 (760)
T KOG1067|consen 738 ALLPDPATKESST 750 (760)
T ss_pred hhcCCcccCCccc
Confidence 8888886554433
No 81
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.65 E-value=2.2e-07 Score=72.48 Aligned_cols=128 Identities=23% Similarity=0.465 Sum_probs=84.0
Q ss_pred CCCCCCCCCCCccHHH-hhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172 1 MSPSHSCKEPQKSIHE-IAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (182)
Q Consensus 1 ~~p~~~~p~~e~~~~~-~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~---- 65 (182)
++|++|.+..+-.+.+ +.+.+.|.. +-..|.+++. ..+++.-.... +.......++..|+++.|+
T Consensus 13 i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v 92 (187)
T PRK08563 13 IPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEV 92 (187)
T ss_pred ECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence 3677776644444443 333344443 3444444443 33444322111 2233444568899999999
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------CccccccCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK-----SRITLSIK 128 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------~~~~~~~~Gd~v~vkV~~id~~~-----~ki~lS~k 128 (182)
++|+||+++ + ++|++|.+++.+.+.. +....+++||.|+++|.+++.+. .++.+|++
T Consensus 93 ~~~Gi~V~lg-~-----~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~ 166 (187)
T PRK08563 93 VEFGAFVRIG-P-----VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMR 166 (187)
T ss_pred EccEEEEEEe-C-----ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEec
Confidence 999999996 2 8999999999876432 34567999999999999998754 38999999
Q ss_pred eccCCc
Q 030172 129 QLEEDP 134 (182)
Q Consensus 129 ~~~~~p 134 (182)
+.-.-+
T Consensus 167 ~~~LG~ 172 (187)
T PRK08563 167 QPGLGK 172 (187)
T ss_pred CCCCCc
Confidence 765433
No 82
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.62 E-value=2.1e-07 Score=60.70 Aligned_cols=59 Identities=17% Similarity=0.285 Sum_probs=48.8
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC--CeEEEEE
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI 127 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~--~ki~lS~ 127 (182)
..|+++.|+ +.|+||+++ + .+|++|.+|++ +.+.|++||.++|.|.+++.++ .+|.+|.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig---~---~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG---K---VEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC---C---eEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 468999999 889999995 4 89999999987 3456899999999999998643 4677773
No 83
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.55 E-value=2.5e-07 Score=64.25 Aligned_cols=74 Identities=22% Similarity=0.262 Sum_probs=57.9
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCC---ceeEEEEEEccCcCCcccc--CccccccCCCEEEEEEEEEeCCCCeEE
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRIT 124 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g---~~~~~glv~~sels~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~ki~ 124 (182)
.+++|++|.|+ ...+.|+|...++ .....|++|++++...+.. ++.+.|++||.|+|+|++++. .+.+.
T Consensus 3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~ 81 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYY 81 (92)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcE
Confidence 35899999999 5568888821111 0027899999999877766 788999999999999999985 56789
Q ss_pred EEEee
Q 030172 125 LSIKQ 129 (182)
Q Consensus 125 lS~k~ 129 (182)
||+++
T Consensus 82 Lst~~ 86 (92)
T cd05791 82 LSTAE 86 (92)
T ss_pred EEecC
Confidence 99975
No 84
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.47 E-value=4.4e-07 Score=61.08 Aligned_cols=69 Identities=23% Similarity=0.288 Sum_probs=62.5
Q ss_pred cCCCCCCEEEEE----eEeEEEEEecCCCceeEEEEEE-ccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~~~~glv~-~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
.-+++|+++.|. +.|+||.|... +++|++. .+|++.+++.+..+.+ +|..+.|+|+.+|+++|.|.||.
T Consensus 12 ~~P~v~dvv~~Vv~i~d~~~YV~LleY----~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 12 VFPNINEVTKGIVFVKDNIFYVKLIDY----GLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred ecCCCCeEEEEEEEEeccEEEEEEecC----ccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 457899999987 99999999744 3999998 9999999999999999 99999999999999999999985
No 85
>PRK05054 exoribonuclease II; Provisional
Probab=98.47 E-value=7.4e-08 Score=88.00 Aligned_cols=117 Identities=16% Similarity=0.136 Sum_probs=75.4
Q ss_pred CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCCCEEEEEechh---------HHhhhhcCCCCC--CEEEEE----
Q 030172 2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEMKKLVFSEKDA---------VWNKYSSRVNVE--DIFVGR---- 65 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G--~iv~g~---- 65 (182)
|||| +|+|+-.|+.++.++ |+... . ..+.-..++....+.+ .+...+.+-++| +.+.|.
T Consensus 498 SPIR--RY~DLivHR~L~a~l~~~~~~-~--~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v 572 (644)
T PRK05054 498 SPIR--KYGDMINHRLLKAVIKGETAE-R--PQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDI 572 (644)
T ss_pred Chhh--hhHHHHHHHHHHHHHcCCCCC-c--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEee
Confidence 8999 999999999887765 33211 0 0000000011000111 111112334565 488887
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCCcc--c---c-------CccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I---Q-------DIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~--~---~-------~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
++|+||+|.. .| ++||||++.+...+ . . .-+..|+.||.|+|+|.++|..+++|.+++
T Consensus 573 ~~~G~fV~l~~-~~---veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~ 643 (644)
T PRK05054 573 SRGGMRVRLLE-NG---AVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARP 643 (644)
T ss_pred ecCcEEEEEeC-Cc---eEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEE
Confidence 9999999973 45 99999999986531 1 1 112469999999999999999999999875
No 86
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.42 E-value=8.3e-07 Score=75.29 Aligned_cols=109 Identities=16% Similarity=0.237 Sum_probs=76.7
Q ss_pred CCCCccHHH----hhhhcCCCeEEEEEEEEeCCCCEEEEEe-ch--------hHHhhhhcCC--CCCCEEEEE-----eE
Q 030172 8 KEPQKSIHE----IAKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DY 67 (182)
Q Consensus 8 p~~e~~~~~----~~~~~vG~~v~~~v~~~d~~~~~i~lS~-k~--------~~~~~~~~~~--~~G~iv~g~-----~~ 67 (182)
|..++++.+ .....+|+.+.+.+...+ -++..++. +. +.++..+..+ +.|+++.|+ +.
T Consensus 68 ~~~ei~l~~A~~~d~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~ 145 (341)
T TIGR01953 68 PSLEISLEDAREIDPDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRR 145 (341)
T ss_pred CcccccHHHHHhhccccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecC
Confidence 344566653 233459999998884333 23433332 22 2344455566 599999999 44
Q ss_pred e-EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCC--CCeEEEEEeec
Q 030172 68 G-AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQL 130 (182)
Q Consensus 68 G-~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~--~~ki~lS~k~~ 130 (182)
| +||+++ | ++|++|.++.. +.+.|++||.++|.|++++.. ..++.||++..
T Consensus 146 g~v~VdiG---~---~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 146 GNLYVELG---K---TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred CcEEEEEC---C---eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 6 699995 4 99999999987 456699999999999999954 36799999853
No 87
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.40 E-value=5.1e-07 Score=77.06 Aligned_cols=109 Identities=17% Similarity=0.247 Sum_probs=76.2
Q ss_pred CCCCccHHHh----hhhcCCCeEEEEEEEEeCCCCEEEEEech--------hHHhhhhcCC--CCCCEEEEE-----eEe
Q 030172 8 KEPQKSIHEI----AKGLTGSIISVKVIQANEEMKKLVFSEKD--------AVWNKYSSRV--NVEDIFVGR-----DYG 68 (182)
Q Consensus 8 p~~e~~~~~~----~~~~vG~~v~~~v~~~d~~~~~i~lS~k~--------~~~~~~~~~~--~~G~iv~g~-----~~G 68 (182)
|..++++.+. ....+|+.+.+.+...+.. +....+.++ +..+..+..+ +.|+++.|+ +.|
T Consensus 71 ~~~eisL~eAk~i~~~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~ 149 (362)
T PRK12327 71 SRLEISLEDALAINPAYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRF 149 (362)
T ss_pred CcccccHHHHhhhCccccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCc
Confidence 4455666532 3335899999988654432 222222222 2334455666 899999999 889
Q ss_pred EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC--eEEEEEee
Q 030172 69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (182)
Q Consensus 69 ~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~--ki~lS~k~ 129 (182)
+||+++ | ++|++|.+++. +++.|++||.++|.|++++.+++ +|.||+..
T Consensus 150 ~~Vdlg---~---vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 150 VYVNLG---K---IEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred EEEEeC---C---eEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 999995 4 99999988875 36779999999999999996443 57777753
No 88
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.29 E-value=9.5e-06 Score=66.04 Aligned_cols=94 Identities=15% Similarity=0.269 Sum_probs=73.0
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechh-HHhhhhcCCCC---CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDA-VWNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~-~~~~~~~~~~~---G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels 92 (182)
+|+++-+.+ .+|+. +++..+.+.. ..+........ ++.+.|+ ..|.||-++ ++ .-||||-||..
T Consensus 117 ~Gd~l~v~l-~~Dkk-~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e--~~---~~GfIh~sEr~ 189 (287)
T COG2996 117 KGDKLLVYL-YVDKK-GRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE--NG---YLGFIHKSERF 189 (287)
T ss_pred CCCEEEEEE-EEccC-CcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc--CC---eEEEEcchhhc
Confidence 799999998 56664 5777777653 33344444444 7777777 889999885 55 99999999865
Q ss_pred CccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 93 ~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
-. ++.|+.++++|+.+.+ +++|.||++...
T Consensus 190 ~~--------prlG~~l~~rVi~~re-Dg~lnLSl~p~~ 219 (287)
T COG2996 190 AE--------PRLGERLTARVIGVRE-DGKLNLSLRPRA 219 (287)
T ss_pred cc--------ccCCceEEEEEEEEcc-CCeeeccccccc
Confidence 33 6799999999999997 999999998654
No 89
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.20 E-value=7.5e-07 Score=82.32 Aligned_cols=121 Identities=28% Similarity=0.415 Sum_probs=82.1
Q ss_pred CCCCCCCCCCccHHHhhhhcCCC-eEEEEEE---EEeCCCCEEEEEechh---------HHhhhhcCCCCCCEEEEE---
Q 030172 2 SPSHSCKEPQKSIHEIAKGLTGS-IISVKVI---QANEEMKKLVFSEKDA---------VWNKYSSRVNVEDIFVGR--- 65 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~vG~-~v~~~v~---~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G~iv~g~--- 65 (182)
||+| +|+|+-.|+.++.++.. .....-. .++.....+.-..+.+ .|...+.+-.+|+.+.|.
T Consensus 555 SPIR--RY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~ 632 (706)
T COG0557 555 SPIR--RYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTG 632 (706)
T ss_pred Cchh--hchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEE
Confidence 8999 99999999988776543 3222211 1111111111111111 233334567789888888
Q ss_pred --eEeEEEEEecCCCceeEEEEEEccCcCCccc-----------cCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 66 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 66 --~~G~fV~l~~~~g~~~~~glv~~sels~~~~-----------~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
.+|+||.+.. .+ ++|++|++.+...+. ......|+.||.|+|++.+++...+++.+++.
T Consensus 633 v~~~g~~V~l~~-~~---ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v 704 (706)
T COG0557 633 VTSFGFFVELPE-LG---LEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELV 704 (706)
T ss_pred EEeccEEEEecc-cc---cccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceEEEec
Confidence 8999999973 24 899999999996542 12344599999999999999999999998875
No 90
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.20 E-value=1.1e-06 Score=70.99 Aligned_cols=85 Identities=26% Similarity=0.441 Sum_probs=74.5
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
+.++++|.+. +.|+||.|-.++ +++|++-++|||..++...++.+++|..=.|.|+.+|++++.|.||.+.+
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV 90 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV 90 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence 5688888887 999999997665 49999999999999999999999999999999999999999999999998
Q ss_pred cCCchhHHHhhhc
Q 030172 131 EEDPLLETLEKVI 143 (182)
Q Consensus 131 ~~~p~~~~~~~~~ 143 (182)
.++.-....++|.
T Consensus 91 s~ed~~kC~Er~~ 103 (304)
T KOG2916|consen 91 SPEDKEKCEERFA 103 (304)
T ss_pred CHHHHHHHHHHHH
Confidence 8766655555553
No 91
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.18 E-value=2e-07 Score=78.06 Aligned_cols=108 Identities=11% Similarity=0.096 Sum_probs=84.4
Q ss_pred CCCCCCCccHHH--hhhh--cCCCeEEEEEEEEeCCCCEEEEEech---hHHhhhhcCCCCCCEEEEE------eEeEEE
Q 030172 5 HSCKEPQKSIHE--IAKG--LTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR------DYGAFI 71 (182)
Q Consensus 5 ~~~p~~e~~~~~--~~~~--~vG~~v~~~v~~~d~~~~~i~lS~k~---~~~~~~~~~~~~G~iv~g~------~~G~fV 71 (182)
.|+|.||+++.+ ..+. -+|+++.|+|+.+|++++++.||.|+ .+|......++.|+++.|+ ++|+++
T Consensus 45 GlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~ 124 (319)
T PTZ00248 45 GMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSV 124 (319)
T ss_pred EEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCH
Confidence 357888888874 2333 28999999999999999999999996 4899999999999999999 699999
Q ss_pred E-----EecCCCceeEEEEEEccCcCCccccCcccccc---CCCEEEEEEEEE
Q 030172 72 H-----LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EGDEVRVKVIKI 116 (182)
Q Consensus 72 ~-----l~~~~g~~~~~glv~~sels~~~~~~~~~~~~---~Gd~v~vkV~~i 116 (182)
+ +.-+ + .++|.|+.+.....+.++.+.|. +++.+...++.+
T Consensus 125 eely~~i~~p-l---~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~~ 173 (319)
T PTZ00248 125 EELYTKIIWP-L---YKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQD 173 (319)
T ss_pred HHHHHHHHHH-H---HHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHHH
Confidence 7 1112 2 78899999887777777776665 666665555443
No 92
>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=98.18 E-value=5.9e-07 Score=82.09 Aligned_cols=116 Identities=15% Similarity=0.145 Sum_probs=73.2
Q ss_pred CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCCCEEEEEechh---------HHhhhhcCCCCC--CEEEEE----
Q 030172 2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEMKKLVFSEKDA---------VWNKYSSRVNVE--DIFVGR---- 65 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~~~i~lS~k~~---------~~~~~~~~~~~G--~iv~g~---- 65 (182)
|||| +|+|+-.|+.++.++ |+.... ..+.-..+++-..+.+ .+...+.+-++| +.+.|.
T Consensus 494 SPIR--RY~DLivHR~L~~~l~~~~~~~---~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v 568 (639)
T TIGR02062 494 SPIR--KYGDMINHRLLKAVIKGETATR---PQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDI 568 (639)
T ss_pred Chhh--hhHHHHHHHHHHHHHcCCCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEee
Confidence 8999 999999999887775 332111 0110000011001111 111112333564 477777
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCC--ccc---cCc-------cccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QDI-------RDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~--~~~---~~~-------~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
++|+||+|. .+| ++|+||++.+.. .+. .+. +..|+.||.|+|+|.++|.++++|.+.
T Consensus 569 ~~~g~~v~l~-~~~---~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 569 SRGGMRVRLL-ENG---AIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR 638 (639)
T ss_pred eCCcEEEEEe-cCc---eEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence 899999996 345 999999999965 211 111 226999999999999999999988764
No 93
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.15 E-value=2e-06 Score=57.19 Aligned_cols=34 Identities=6% Similarity=-0.077 Sum_probs=31.3
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
.|+.+.|+|+++.++|+||++.+|++|++|....
T Consensus 3 ~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~l 36 (74)
T cd05705 3 EGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNV 36 (74)
T ss_pred CCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHc
Confidence 3999999999999999999999999999996654
No 94
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=98.13 E-value=2e-05 Score=60.90 Aligned_cols=75 Identities=28% Similarity=0.335 Sum_probs=58.6
Q ss_pred hhcCCCCCCEEEEE-----eEeEEEEEecCCC-----ceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC
Q 030172 52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS 121 (182)
Q Consensus 52 ~~~~~~~G~iv~g~-----~~G~fV~l~~~~g-----~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ 121 (182)
..+.++.|++|.|+ ...+.|++...++ .....|-+|+|+.+..+..+..+.|++||.|+|+|++.- .
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~ 134 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---D 134 (188)
T ss_pred CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---C
Confidence 45678999999999 5557777643222 002578899999999999999999999999999999983 4
Q ss_pred eEEEEEee
Q 030172 122 RITLSIKQ 129 (182)
Q Consensus 122 ki~lS~k~ 129 (182)
.+.||.+.
T Consensus 135 ~~~Lst~~ 142 (188)
T COG1096 135 PIQLSTKG 142 (188)
T ss_pred CeEEEecC
Confidence 56777764
No 95
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=98.00 E-value=4.7e-05 Score=61.12 Aligned_cols=99 Identities=24% Similarity=0.332 Sum_probs=73.8
Q ss_pred cCCCeEEEEEEEEe-CCCCEEEEEechhHHhhhhcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCc
Q 030172 21 LTGSIISVKVIQAN-EEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD 94 (182)
Q Consensus 21 ~vG~~v~~~v~~~d-~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~ 94 (182)
+.|+++...+...= ..++.+.+ -+... ...++.||+|.|+ ..++.|+|+.+ ..+++|++++.+.
T Consensus 31 ~~~~~iyssv~G~~~~~~~~v~V----Ipl~g-~YiP~~gD~VIG~I~~v~~~~W~VDI~sp-----~~A~L~ls~~~~r 100 (239)
T COG1097 31 FEGGKIYSSVVGLLDVKGKLVRV----IPLEG-RYIPEVGDVVIGKIIEVGPSGWKVDIGSP-----YPALLSLSDFLRR 100 (239)
T ss_pred ecCCEEEEEEEeEEEEeCCEEEE----EeCCC-cccCCCCCEEEEEEEEEcccceEEEcCCc-----cceEeehhhhhcc
Confidence 46777777764432 22223322 12323 3568899999999 88999999754 8999999999665
Q ss_pred c----ccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 95 L----IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 95 ~----~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
. ..+++.+|++||.|.|+|..+|+ .+.+.|++|..
T Consensus 101 ~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~ 139 (239)
T COG1097 101 KFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDE 139 (239)
T ss_pred cccccccccccccccCCEEEEEEEEccC-CCceEEEeecC
Confidence 5 35788899999999999999997 88999999754
No 96
>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=97.88 E-value=1e-05 Score=53.00 Aligned_cols=31 Identities=10% Similarity=0.088 Sum_probs=29.2
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
|+.+.|+|+++.++|+||++.+|++||+|--
T Consensus 4 g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~ 34 (72)
T cd05689 4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVS 34 (72)
T ss_pred CCEEEEEEEEEEeeEEEEEcCCCCEEEEEEE
Confidence 8999999999999999999999999999843
No 97
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.87 E-value=1.3e-05 Score=52.23 Aligned_cols=32 Identities=6% Similarity=0.094 Sum_probs=29.4
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|++++|+|+++.++|+||++.+|++||+|...
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~ 32 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMH 32 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHH
Confidence 68899999999999999999999999998644
No 98
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.87 E-value=1.3e-05 Score=53.12 Aligned_cols=32 Identities=13% Similarity=0.007 Sum_probs=29.9
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|+++.++|+||+|.+|++|+||.+.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ 32 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLD 32 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHH
Confidence 68899999999999999999999999998764
No 99
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.86 E-value=1.6e-05 Score=52.91 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=31.1
Q ss_pred CCceeEeeEeeecCCeeEEecC-CChhhhchhhhhc
Q 030172 146 DGSVISDSSSMSSSNSNTIEPL-PGLGAIFEELLQE 180 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~~~~ 180 (182)
.|++++|+|.+++++|+||++. +|++||+|.....
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~ 39 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG 39 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC
Confidence 3899999999999999999996 6999999976543
No 100
>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=97.85 E-value=1.1e-05 Score=52.28 Aligned_cols=32 Identities=13% Similarity=0.058 Sum_probs=29.4
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|+++.+||+||++.+|++||+|...
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~ 32 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISD 32 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHH
Confidence 67899999999999999999999999998654
No 101
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.80 E-value=1.6e-05 Score=51.69 Aligned_cols=33 Identities=6% Similarity=-0.017 Sum_probs=30.2
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||++.+++.||+|....
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l 33 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSEL 33 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHc
Confidence 688999999999999999999999999997653
No 102
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=97.80 E-value=2.5e-05 Score=51.34 Aligned_cols=35 Identities=6% Similarity=0.078 Sum_probs=31.9
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE 180 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~ 180 (182)
.|+++.|+|+++.++|+||++..|++||||.-...
T Consensus 4 ~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~ 38 (74)
T PF00575_consen 4 EGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELS 38 (74)
T ss_dssp TTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSS
T ss_pred CCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhc
Confidence 39999999999999999999999999999986543
No 103
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.78 E-value=2.9e-05 Score=52.40 Aligned_cols=39 Identities=18% Similarity=0.203 Sum_probs=33.8
Q ss_pred HhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 139 LEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 139 ~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
.+++.. |+++.|+|+++.++|+||++.+|++||+|....
T Consensus 9 ~~~~~~--G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el 47 (83)
T cd04461 9 FSDLKP--GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYI 47 (83)
T ss_pred HHhCCC--CCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHC
Confidence 344555 999999999999999999999999999997543
No 104
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.75 E-value=2.5e-05 Score=50.69 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=29.6
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+.++|+|+++.++|+||++.++++||+|...
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~ 32 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLH 32 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHH
Confidence 68899999999999999999999999998764
No 105
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.74 E-value=0.00019 Score=49.10 Aligned_cols=69 Identities=19% Similarity=0.065 Sum_probs=55.3
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
.+++||+|.|+ ....+|+|+.+ ..|++|..++... .++.+..+++||.|.|+|..+|+ .....||...
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~-----~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~ 75 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIGGS-----EPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD 75 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcCCC-----cceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence 46789999999 55689999743 7899999876543 44456779999999999999997 5678999986
Q ss_pred c
Q 030172 130 L 130 (182)
Q Consensus 130 ~ 130 (182)
.
T Consensus 76 ~ 76 (86)
T cd05790 76 S 76 (86)
T ss_pred C
Confidence 3
No 106
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.72 E-value=0.00016 Score=55.94 Aligned_cols=123 Identities=17% Similarity=0.211 Sum_probs=74.8
Q ss_pred CCCCCCCCCCCccHHH-hhhhcCCCe-----EEEEEEEEeC-CCCEEEEEech----hHHhhhhcCCCCCCEEEEE----
Q 030172 1 MSPSHSCKEPQKSIHE-IAKGLTGSI-----ISVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (182)
Q Consensus 1 ~~p~~~~p~~e~~~~~-~~~~~vG~~-----v~~~v~~~d~-~~~~i~lS~k~----~~~~~~~~~~~~G~iv~g~---- 65 (182)
+.|+.|.+..+-.+.+ +.+.+.|.. +-..|.+++. ..+++.-..-. ........++-.|+++.|.
T Consensus 13 i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v 92 (176)
T PTZ00162 13 LKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDV 92 (176)
T ss_pred ECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEE
Confidence 3577775544444443 333455542 2233333332 22444321111 1233445678899999999
Q ss_pred -eEeEEEEEecCCCceeEEEEEEccCcCCcc-----------c-cCccccccCCCEEEEEEEEEeCCC--CeEEEEEee
Q 030172 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-----------I-QDIRDILNEGDEVRVKVIKIDREK--SRITLSIKQ 129 (182)
Q Consensus 66 -~~G~fV~l~~~~g~~~~~glv~~sels~~~-----------~-~~~~~~~~~Gd~v~vkV~~id~~~--~ki~lS~k~ 129 (182)
++|+|+.++ + .++|+|.+.|.... . .+.+..++.|+.|++||.++..+. .++..|+|+
T Consensus 93 ~~~G~~v~~G-p-----~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~ 165 (176)
T PTZ00162 93 NKLGFFAQAG-P-----LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS 165 (176)
T ss_pred ecceEEEEee-C-----eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence 999999996 3 78999999986431 1 122456899999999998886533 345567765
No 107
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.71 E-value=2.8e-05 Score=50.40 Aligned_cols=32 Identities=16% Similarity=0.057 Sum_probs=29.5
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|+++.++|+||++.++++||+|-..
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~ 32 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSE 32 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHH
Confidence 67899999999999999999999999998654
No 108
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=97.67 E-value=3.6e-05 Score=52.88 Aligned_cols=33 Identities=6% Similarity=-0.043 Sum_probs=30.3
Q ss_pred CCceeEeeEeeecCC--eeEEecCCChhhhchhhh
Q 030172 146 DGSVISDSSSMSSSN--SNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~--G~fV~l~~gv~gl~~~~~ 178 (182)
.|+++.|+|+++.++ |+||++.+|.+||+|-..
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~se 41 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSD 41 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHH
Confidence 399999999999996 999999999999999654
No 109
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.65 E-value=4.2e-05 Score=50.28 Aligned_cols=32 Identities=16% Similarity=0.096 Sum_probs=28.5
Q ss_pred CceeE-eeEeee-cCCeeEEecCCChhhhchhhh
Q 030172 147 GSVIS-DSSSMS-SSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~-G~V~~v-~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++. |+|+++ .++|+||++.+|++||+|...
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~ 34 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISH 34 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHH
Confidence 57788 899999 699999999999999999754
No 110
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.62 E-value=5.5e-05 Score=49.63 Aligned_cols=33 Identities=3% Similarity=-0.150 Sum_probs=30.6
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.|+++.|+|+++.++|+||+|+++++|++|...
T Consensus 3 ~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~ 35 (73)
T cd05706 3 VGDILPGRVTKVNDRYVLVQLGNKVTGPSFITD 35 (73)
T ss_pred CCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhh
Confidence 499999999999999999999999999998654
No 111
>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=97.49 E-value=0.00012 Score=48.19 Aligned_cols=35 Identities=11% Similarity=0.066 Sum_probs=31.2
Q ss_pred CCceeEeeEeeecC-CeeEEecCCChhhhchhhhhc
Q 030172 146 DGSVISDSSSMSSS-NSNTIEPLPGLGAIFEELLQE 180 (182)
Q Consensus 146 ~g~~v~G~V~~v~~-~G~fV~l~~gv~gl~~~~~~~ 180 (182)
.|+++.|+|+++.+ +|+||++.+|.+|++|-....
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s 38 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLS 38 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhc
Confidence 39999999999986 899999999999999976553
No 112
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.49 E-value=0.00034 Score=61.01 Aligned_cols=58 Identities=29% Similarity=0.447 Sum_probs=46.9
Q ss_pred cCCCCCCEEEEE-----eE--eEEEEEecCCCceeEEEEEEccCcCCc------------cccCccccccCCCEEEEEEE
Q 030172 54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 114 (182)
Q Consensus 54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~~~~glv~~sels~~------------~~~~~~~~~~~Gd~v~vkV~ 114 (182)
....+|++|.|+ ++ ||||+|+ .| ..||+|++|+.+. ...++.+.+++||.|.|.|.
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG--~~---k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~ 95 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIG--LE---KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV 95 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcC--CC---ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence 456799999999 65 8999997 45 8999999998753 23345667999999999998
Q ss_pred EE
Q 030172 115 KI 116 (182)
Q Consensus 115 ~i 116 (182)
+-
T Consensus 96 Ke 97 (414)
T TIGR00757 96 KE 97 (414)
T ss_pred eC
Confidence 83
No 113
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=97.47 E-value=0.00011 Score=49.04 Aligned_cols=35 Identities=3% Similarity=-0.004 Sum_probs=31.4
Q ss_pred hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
+++. |+.+.|+|+++.++|+||++.++++||+|..
T Consensus 13 ~~~~--G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~s 47 (77)
T cd04473 13 DLEV--GKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS 47 (77)
T ss_pred hCCC--CCEEEEEEEeEecceEEEEECCCcEEEEEch
Confidence 4555 9999999999999999999999999999854
No 114
>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=97.45 E-value=0.00011 Score=47.44 Aligned_cols=32 Identities=9% Similarity=0.191 Sum_probs=29.3
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|++++|+|+++.++|+||++ +|++||+|....
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~ 32 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQV 32 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHC
Confidence 67899999999999999999 899999997654
No 115
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=97.44 E-value=0.00011 Score=48.52 Aligned_cols=33 Identities=6% Similarity=0.057 Sum_probs=28.7
Q ss_pred CCceeEeeEeeecCCeeEEecCCC--hhhhchhhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPG--LGAIFEELLQ 179 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~g--v~gl~~~~~~ 179 (182)
.|+++.|+|+++.+||+||++ +| .+||||....
T Consensus 3 ~g~~~~g~V~~i~~fG~fv~l-~~~~~eGlvh~sel 37 (73)
T cd05686 3 LYQIFKGEVASVTEYGAFVKI-PGCRKQGLVHKSHM 37 (73)
T ss_pred CCCEEEEEEEEEEeeeEEEEE-CCCCeEEEEEchhh
Confidence 499999999999999999999 56 6999996543
No 116
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.43 E-value=0.00039 Score=54.36 Aligned_cols=67 Identities=13% Similarity=0.130 Sum_probs=49.4
Q ss_pred ccCCCEEEEEEEEE---eCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecC----------CC
Q 030172 103 LNEGDEVRVKVIKI---DREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL----------PG 169 (182)
Q Consensus 103 ~~~Gd~v~vkV~~i---d~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~----------~g 169 (182)
|..++.+.+.+.+. |.+++++.+ +||......+. .|+++.|+|+++.++|+||++. ++
T Consensus 27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~~~~~--~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~ 97 (189)
T PRK09521 27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTPPLLK--KGDIVYGRVVDVKEQRALVRIVSIEGSERELATS 97 (189)
T ss_pred EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCCCCCC--CCCEEEEEEEEEcCCeEEEEEEEecccccccCCC
Confidence 55667777766555 666667766 47765433334 4999999999999999999984 47
Q ss_pred hhhhchhhh
Q 030172 170 LGAIFEELL 178 (182)
Q Consensus 170 v~gl~~~~~ 178 (182)
+.|++|...
T Consensus 98 ~~G~l~~s~ 106 (189)
T PRK09521 98 KLAYIHISQ 106 (189)
T ss_pred ceeeEEhhH
Confidence 889998654
No 117
>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=97.43 E-value=0.00012 Score=46.76 Aligned_cols=33 Identities=15% Similarity=0.131 Sum_probs=29.8
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||++.+++.||+|....
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l 33 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQI 33 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHc
Confidence 678999999999999999999999999996543
No 118
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.41 E-value=0.00015 Score=47.23 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=30.1
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||++.++++|+||....
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~ 33 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAEL 33 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHC
Confidence 678999999999999999999999999987653
No 119
>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=97.39 E-value=0.00017 Score=48.87 Aligned_cols=37 Identities=14% Similarity=0.107 Sum_probs=32.8
Q ss_pred hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|.+..|+++.|+|+++.++|++|++.++++|++|...
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se 38 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSE 38 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHH
Confidence 3445699999999999999999999999999999754
No 120
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=97.38 E-value=0.00016 Score=46.12 Aligned_cols=33 Identities=6% Similarity=-0.038 Sum_probs=29.7
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+.+.|+|+++.++|+||++.++..||||--..
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l 33 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKM 33 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHC
Confidence 578999999999999999999999999986544
No 121
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.34 E-value=0.00085 Score=42.83 Aligned_cols=48 Identities=35% Similarity=0.515 Sum_probs=32.0
Q ss_pred eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 66 ~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
++|+|++.+ .+ -+.++|.+++... +++||.|.|-| ..|. ++++..|+|
T Consensus 14 ~~g~fL~~~--~~---~~vlLp~~e~~~~--------~~~Gd~v~VFv-Y~D~-~~rl~AT~k 61 (61)
T PF13509_consen 14 EFGYFLDDG--EG---KEVLLPKSEVPEP--------LKVGDEVEVFV-YLDK-EGRLVATTK 61 (61)
T ss_dssp SSEEEEEET--T----EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred CCEEEEECC--CC---CEEEechHHcCCC--------CCCCCEEEEEE-EECC-CCCEEEecC
Confidence 899999975 33 8999999987643 88999999887 7786 668888875
No 122
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.33 E-value=0.00089 Score=44.19 Aligned_cols=64 Identities=19% Similarity=0.240 Sum_probs=49.0
Q ss_pred CCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc--CccccccCCCEE-EEEEEEEeCCCCeEEEEEe
Q 030172 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEV-RVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~--~~~~~~~~Gd~v-~vkV~~id~~~~ki~lS~k 128 (182)
|+++.|+ +-+++|++.. .| +.|++|..++++..-+ ..-..+++||.+ .+.|+ +...+.+.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~-~~---l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILP-EE---IRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecC-CC---cEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 5677777 6679999973 34 9999999999993322 234458999999 99998 777788888865
No 123
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.30 E-value=4.1e-05 Score=67.64 Aligned_cols=75 Identities=15% Similarity=0.123 Sum_probs=56.1
Q ss_pred ccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchh-----HHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL-----ETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 103 ~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~-----~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
+.+||.+.+.|...+. .+....+.|+.....|. .....|....|++++|+|.++.++|+||++ .|++||+|+.
T Consensus 87 ~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP~s 164 (470)
T PRK09202 87 AEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRK 164 (470)
T ss_pred ccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEecHH
Confidence 7899999999988773 22223333444333343 566777644599999999999999999999 6999999986
Q ss_pred hh
Q 030172 178 LQ 179 (182)
Q Consensus 178 ~~ 179 (182)
.+
T Consensus 165 E~ 166 (470)
T PRK09202 165 EQ 166 (470)
T ss_pred Hc
Confidence 54
No 124
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.29 E-value=0.0021 Score=44.09 Aligned_cols=58 Identities=19% Similarity=0.285 Sum_probs=44.0
Q ss_pred CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCc-----------cccccCCCEEEEEEEEEeCCCC
Q 030172 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS 121 (182)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~-----------~~~~~~Gd~v~vkV~~id~~~~ 121 (182)
.|+++.|+ +.|+|+.++ | +++|+|...+......++ ...+..|+.|++||+++..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-p-----l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-P-----LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-C-----ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 47888888 999999996 2 889999888755433222 3458899999999999876443
No 125
>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=97.23 E-value=0.00023 Score=45.59 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=28.8
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|+++.++|+||++.++.+||+|-..
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~ 32 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISE 32 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHH
Confidence 57899999999999999999999999998543
No 126
>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=97.23 E-value=0.00042 Score=63.91 Aligned_cols=63 Identities=11% Similarity=0.195 Sum_probs=42.7
Q ss_pred EEEeCCCCeEEEEEeeccC-CchhH----HHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 114 IKIDREKSRITLSIKQLEE-DPLLE----TLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 114 ~~id~~~~ki~lS~k~~~~-~p~~~----~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
++++. ++++.++-..... +.... ....+.+..|+++.|+|+++.+||+||++.+|++||+|-.
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHIS 678 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHIS 678 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhh
Confidence 36664 6777776643211 00111 1111123469999999999999999999999999999965
No 127
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=97.22 E-value=0.00022 Score=47.61 Aligned_cols=32 Identities=13% Similarity=-0.048 Sum_probs=29.1
Q ss_pred CceeEeeEeeecCCeeEEecCC-Chhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLP-GLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~ 178 (182)
|+++.|+|+++.++|+||++.+ |++|++|-..
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~ 34 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVST 34 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEe
Confidence 7899999999999999999998 8999997543
No 128
>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=97.22 E-value=0.00028 Score=47.03 Aligned_cols=33 Identities=3% Similarity=-0.107 Sum_probs=28.9
Q ss_pred CceeEeeEeeecCCeeEEecC---CChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPL---PGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~---~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.+||+||+++ ++++||+|-...
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l 36 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQL 36 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhc
Confidence 578999999999999999998 479999986544
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=97.17 E-value=0.00043 Score=45.48 Aligned_cols=34 Identities=6% Similarity=0.034 Sum_probs=29.9
Q ss_pred CCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ 179 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~ 179 (182)
.|+++.|+|+++.++|+||++. +|++||+|....
T Consensus 3 ~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l 38 (76)
T cd04452 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSEL 38 (76)
T ss_pred CCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHc
Confidence 3899999999999999999997 469999997643
No 130
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.16 E-value=0.0004 Score=45.25 Aligned_cols=33 Identities=3% Similarity=0.002 Sum_probs=30.1
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||++.+|++|++|....
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i 33 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEV 33 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHh
Confidence 688999999999999999999999999987643
No 131
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.13 E-value=0.00049 Score=44.62 Aligned_cols=33 Identities=6% Similarity=-0.028 Sum_probs=30.3
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|.++.++|+||++..+++|++|....
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~ 33 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEF 33 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHh
Confidence 688999999999999999999999999997654
No 132
>PRK08059 general stress protein 13; Validated
Probab=97.10 E-value=0.0004 Score=50.58 Aligned_cols=36 Identities=8% Similarity=-0.047 Sum_probs=32.1
Q ss_pred hhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 141 KVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 141 ~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
++.+ |+++.|+|+++.++|+||++.++++||+|...
T Consensus 4 ~~k~--G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~se 39 (123)
T PRK08059 4 QYEV--GSVVTGKVTGIQPYGAFVALDEETQGLVHISE 39 (123)
T ss_pred cCCC--CCEEEEEEEEEecceEEEEECCCCEEEEEHHH
Confidence 3455 99999999999999999999999999998654
No 133
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.08 E-value=0.0023 Score=54.88 Aligned_cols=63 Identities=21% Similarity=0.343 Sum_probs=51.7
Q ss_pred CCCCCCEEEEE----e--EeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCC---eEEE
Q 030172 55 RVNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITL 125 (182)
Q Consensus 55 ~~~~G~iv~g~----~--~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~---ki~l 125 (182)
.-+.|+++.|+ + .++||+++ + .+|++|.++.. |++.|++||.++|.|.+++...+ +|.|
T Consensus 135 ~~~~Geiv~g~V~r~~~~~~i~vdlg---~---~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Iil 202 (374)
T PRK12328 135 KKKVGKIVFGTVVRVDNEENTFIEID---E---IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIEL 202 (374)
T ss_pred HHhcCcEEEEEEEEEecCCCEEEEcC---C---eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEE
Confidence 35799999999 3 34899995 4 99999988765 66889999999999999987654 7888
Q ss_pred EEee
Q 030172 126 SIKQ 129 (182)
Q Consensus 126 S~k~ 129 (182)
|+..
T Consensus 203 SRt~ 206 (374)
T PRK12328 203 SRTS 206 (374)
T ss_pred EcCC
Confidence 8854
No 134
>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=97.06 E-value=0.00063 Score=44.65 Aligned_cols=34 Identities=9% Similarity=-0.016 Sum_probs=29.9
Q ss_pred CCceeEeeEeeecCCeeEEecCC-Chhhhchhhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLP-GLGAIFEELLQ 179 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~~~~ 179 (182)
.|+++.|+|+++.++|+||++.+ +++|++|....
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l 36 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEI 36 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHC
Confidence 38999999999999999999985 89999986543
No 135
>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=97.05 E-value=0.00052 Score=48.23 Aligned_cols=33 Identities=12% Similarity=0.033 Sum_probs=30.3
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.|+++.|+|+++.++|+||+|.+|+.|++|-..
T Consensus 3 ~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~se 35 (100)
T cd05693 3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITN 35 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHH
Confidence 499999999999999999999999999998644
No 136
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.00 E-value=0.00079 Score=42.86 Aligned_cols=33 Identities=9% Similarity=0.095 Sum_probs=30.5
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||++.+++.|++|....
T Consensus 3 G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~ 35 (72)
T smart00316 3 GDVVEGTVTEITPFGAFVDLGNGVEGLIPISEL 35 (72)
T ss_pred CCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHC
Confidence 899999999999999999999999999987654
No 137
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.98 E-value=0.0018 Score=43.90 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=23.7
Q ss_pred EEEEEEccCcCCcccc--CccccccCCCEEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI 116 (182)
Q Consensus 82 ~~glv~~sels~~~~~--~~~~~~~~Gd~v~vkV~~i 116 (182)
..|.+|.+++...... ++.+-|++||.|+|+|++.
T Consensus 46 f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 46 FQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp S-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred cEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 7899999998766544 4578899999999999974
No 138
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.90 E-value=0.00079 Score=64.08 Aligned_cols=75 Identities=24% Similarity=0.328 Sum_probs=60.5
Q ss_pred cCCCCCCEEEEE------eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 54 SRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 54 ~~~~~G~iv~g~------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
+.+..|.+|.++ ..|+-|.+-..+| ++|+|+.+++|...+.+|.+.+++||.|.+||+++|.++-.+.||.
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G---~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~ 1057 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCG---VTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSC 1057 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCC---CceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhh
Confidence 347788888866 3343333332367 9999999999999999999999999999999999999888888888
Q ss_pred eecc
Q 030172 128 KQLE 131 (182)
Q Consensus 128 k~~~ 131 (182)
|...
T Consensus 1058 r~sd 1061 (1299)
T KOG1856|consen 1058 RTSD 1061 (1299)
T ss_pred hhHH
Confidence 7553
No 139
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.74 E-value=0.0018 Score=43.43 Aligned_cols=37 Identities=16% Similarity=0.154 Sum_probs=33.2
Q ss_pred hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|.|..|+++.|+|+++.+.+++|++..+++|++|...
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~ 38 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSS 38 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechh
Confidence 4456799999999999999999999999999998764
No 140
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.66 E-value=0.0042 Score=55.74 Aligned_cols=68 Identities=29% Similarity=0.508 Sum_probs=57.1
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
.++++.|.+|.|+ .||+||++. . .+.|++|-++++.. .-|.+|+.+-|++..+.+.++.+.+..
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln--~---~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~ 185 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELN--S---HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP 185 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecC--h---hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence 4678999999999 999999996 3 39999999998862 227899999999999998878888877
Q ss_pred eecc
Q 030172 128 KQLE 131 (182)
Q Consensus 128 k~~~ 131 (182)
..+.
T Consensus 186 ~~~~ 189 (715)
T COG1107 186 VGLD 189 (715)
T ss_pred cCCc
Confidence 6554
No 141
>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=96.52 E-value=0.0004 Score=59.09 Aligned_cols=78 Identities=17% Similarity=0.139 Sum_probs=54.8
Q ss_pred cccccCCCEEEEEEEEEeCCCCeEEEEEeecc-----CCchhHHHhhhcCCCCceeEeeEeeecCCe-eEEecCCChhhh
Q 030172 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE-----EDPLLETLEKVIPQDGSVISDSSSMSSSNS-NTIEPLPGLGAI 173 (182)
Q Consensus 100 ~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~-----~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G-~fV~l~~gv~gl 173 (182)
...+++||.+.+.+...+. .+....+.|+.. ...++...+.|....|++++|+|.++.+.| +||++ +|++|+
T Consensus 81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~ 158 (341)
T TIGR01953 81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVEL-GKTEGI 158 (341)
T ss_pred ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEE-CCeEEE
Confidence 3448899999988854443 232333334421 234556667775445999999999999988 69999 699999
Q ss_pred chhhhh
Q 030172 174 FEELLQ 179 (182)
Q Consensus 174 ~~~~~~ 179 (182)
+|...+
T Consensus 159 LP~~E~ 164 (341)
T TIGR01953 159 LPKKEQ 164 (341)
T ss_pred ecHHHc
Confidence 998654
No 142
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=96.51 E-value=0.0021 Score=40.92 Aligned_cols=31 Identities=10% Similarity=0.138 Sum_probs=27.9
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|+.+.|+|+++.++|+||++. +++|++|...
T Consensus 2 g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e 32 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDLG-GVDGLLHISD 32 (68)
T ss_pred CCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHH
Confidence 889999999999999999996 7999998643
No 143
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.44 E-value=0.0036 Score=57.11 Aligned_cols=61 Identities=15% Similarity=0.183 Sum_probs=43.1
Q ss_pred EEeCCCCeEEEEEeeccC--Cc--h-hHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 115 KIDREKSRITLSIKQLEE--DP--L-LETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 115 ~id~~~~ki~lS~k~~~~--~p--~-~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
.++ +++.+.++-..... .+ | ......+ .+|+++.|+|+++.+||+||++.+|-+||||-..
T Consensus 586 die-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~--evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~ 651 (692)
T COG1185 586 DIE-DDGTVKIAASDGESAKKAKERIEAITREV--EVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQ 651 (692)
T ss_pred Eec-CCCcEEEEecchHHHHHHHHHHHHHHhhc--ccccEEEEEEEEEeecceEEEecCCcceeEEehh
Confidence 555 57777776654321 11 1 1112233 4599999999999999999999999999998643
No 144
>PHA02945 interferon resistance protein; Provisional
Probab=96.32 E-value=0.0039 Score=42.51 Aligned_cols=34 Identities=24% Similarity=0.263 Sum_probs=30.1
Q ss_pred CCCceeEeeEeeecCCeeEEecC--CChhhhchhhhh
Q 030172 145 QDGSVISDSSSMSSSNSNTIEPL--PGLGAIFEELLQ 179 (182)
Q Consensus 145 ~~g~~v~G~V~~v~~~G~fV~l~--~gv~gl~~~~~~ 179 (182)
..|+.+-|+|.. .+||+||.|+ +|.+||+|....
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev 45 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ 45 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh
Confidence 359999999999 9999999995 799999998743
No 145
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.24 E-value=0.0026 Score=60.05 Aligned_cols=34 Identities=12% Similarity=0.060 Sum_probs=30.5
Q ss_pred CCCceeE-eeEeeecCCeeEEecCCChhhhchhhh
Q 030172 145 QDGSVIS-DSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 145 ~~g~~v~-G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
..|+++. |+|++|.+||+||++.+|++||||-..
T Consensus 752 ~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISe 786 (891)
T PLN00207 752 TVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISE 786 (891)
T ss_pred CCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhh
Confidence 4699995 699999999999999999999999654
No 146
>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=96.18 E-value=0.0051 Score=39.74 Aligned_cols=33 Identities=12% Similarity=0.170 Sum_probs=29.0
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
.|++++|+|.++.++|+||++. +++|++|.-..
T Consensus 3 ~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~ 35 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQ 35 (67)
T ss_pred CCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHC
Confidence 3899999999999999999995 59999997543
No 147
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.10 E-value=0.025 Score=45.77 Aligned_cols=38 Identities=11% Similarity=0.047 Sum_probs=34.1
Q ss_pred hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|.|..|++|.|+|+++.++|+||++..+++|++|-...
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i 96 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEV 96 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHc
Confidence 66667999999999999999999999999999997653
No 148
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.04 E-value=0.021 Score=54.30 Aligned_cols=57 Identities=26% Similarity=0.490 Sum_probs=44.6
Q ss_pred CCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCcccc---------CccccccCCCEEEEEEEEEe
Q 030172 56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKID 117 (182)
Q Consensus 56 ~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~---------~~~~~~~~Gd~v~vkV~~id 117 (182)
..+|.||.|+ =.++||+|+ .| ..||+|+++....+.. +....+++||.|.|.|.+-.
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG--~g---knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEec--CC---cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 3589999999 557999998 55 8999999999644322 23456899999999998754
No 149
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=95.90 E-value=0.006 Score=56.54 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=31.9
Q ss_pred CCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
..|+++.|+|+++.+||+||++.+|++||+|-...
T Consensus 617 ~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 617 EVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred ccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHc
Confidence 45999999999999999999999999999997643
No 150
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=95.89 E-value=0.0061 Score=37.85 Aligned_cols=30 Identities=7% Similarity=-0.028 Sum_probs=26.5
Q ss_pred eEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 150 v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
+.|+|+++.++|+||++.++++|++|....
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~ 30 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISEL 30 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHC
Confidence 368999999999999999999999987554
No 151
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.74 E-value=0.0076 Score=55.95 Aligned_cols=34 Identities=15% Similarity=0.137 Sum_probs=31.0
Q ss_pred CCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 145 QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 145 ~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
..|+++.|+|+++.+||+||++.+|.+||+|-..
T Consensus 620 ~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSe 653 (693)
T PRK11824 620 EVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISE 653 (693)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEeee
Confidence 3599999999999999999999999999998543
No 152
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.71 E-value=0.0016 Score=55.80 Aligned_cols=76 Identities=12% Similarity=0.098 Sum_probs=51.1
Q ss_pred cccCCCEEEEEEEEEeCCCCeEEEEEeeccC-----CchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172 102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEE-----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE 176 (182)
Q Consensus 102 ~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~-----~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~ 176 (182)
..++||.+...+...+.. +....+.|+... -..+.....|....|++++|+|.++.++|+||++ +|++|++|+
T Consensus 86 ~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~ 163 (362)
T PRK12327 86 AYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPP 163 (362)
T ss_pred cccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecH
Confidence 378999999887655432 222222222211 1123445566444599999999999999999999 579999997
Q ss_pred hhh
Q 030172 177 LLQ 179 (182)
Q Consensus 177 ~~~ 179 (182)
..+
T Consensus 164 ~E~ 166 (362)
T PRK12327 164 AEQ 166 (362)
T ss_pred HHc
Confidence 544
No 153
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.68 E-value=0.057 Score=47.38 Aligned_cols=69 Identities=9% Similarity=0.059 Sum_probs=51.3
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC---CeEEEE
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLS 126 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~---~ki~lS 126 (182)
.-+.|+++.|+ ..+++|+++..-|-.+++|++|.++.. |++.|++||.++|.|.++.... -+|.||
T Consensus 149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilS 222 (449)
T PRK12329 149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVS 222 (449)
T ss_pred HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEE
Confidence 35689999999 557899983100100289999988755 5688999999999999997642 468888
Q ss_pred Eee
Q 030172 127 IKQ 129 (182)
Q Consensus 127 ~k~ 129 (182)
+..
T Consensus 223 Rt~ 225 (449)
T PRK12329 223 RAN 225 (449)
T ss_pred cCC
Confidence 753
No 154
>PRK11712 ribonuclease G; Provisional
Probab=95.56 E-value=0.064 Score=47.87 Aligned_cols=59 Identities=25% Similarity=0.487 Sum_probs=43.9
Q ss_pred cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCc------------cccCccccccCCCEEEEEEE
Q 030172 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 114 (182)
Q Consensus 54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~------------~~~~~~~~~~~Gd~v~vkV~ 114 (182)
....+|.+|.|+ =.+|||+|+ .+ ..||+|++|+... ...+..+.+++||.|-|.|.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG--~~---k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG--LD---KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeC--CC---ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence 345689999999 446999998 44 8999999997321 01123456899999999997
Q ss_pred EEe
Q 030172 115 KID 117 (182)
Q Consensus 115 ~id 117 (182)
+-.
T Consensus 109 Ke~ 111 (489)
T PRK11712 109 KDP 111 (489)
T ss_pred eCC
Confidence 753
No 155
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=95.22 E-value=0.016 Score=53.80 Aligned_cols=40 Identities=8% Similarity=0.047 Sum_probs=34.5
Q ss_pred hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172 140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED 181 (182)
Q Consensus 140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~ 181 (182)
..+++ |++..|+|+++.+||+||.+.-..+||+|-.-..|
T Consensus 654 ~dLk~--Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~ 693 (780)
T COG2183 654 TDLKP--GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSD 693 (780)
T ss_pred hhccC--CCEEEEEEEEeeeccceEEeccccceeeeHHHhhh
Confidence 34455 99999999999999999999999999999766543
No 156
>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=95.00 E-value=0.016 Score=40.25 Aligned_cols=28 Identities=4% Similarity=-0.041 Sum_probs=24.7
Q ss_pred ceeEeeEeeecCCeeEEecCCChhhhchh
Q 030172 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEE 176 (182)
Q Consensus 148 ~~v~G~V~~v~~~G~fV~l~~gv~gl~~~ 176 (182)
+++.|+|+++.++|+||++. +++|++|-
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~ 28 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHI 28 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEE
Confidence 36889999999999999997 59999973
No 157
>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=94.87 E-value=0.021 Score=53.21 Aligned_cols=32 Identities=13% Similarity=-0.025 Sum_probs=29.4
Q ss_pred CCCceeEeeEeeecCCeeEEecCC-Chhhhchh
Q 030172 145 QDGSVISDSSSMSSSNSNTIEPLP-GLGAIFEE 176 (182)
Q Consensus 145 ~~g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~ 176 (182)
..|+++.|+|+++.+||+||++.+ |++||+|-
T Consensus 626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhi 658 (709)
T TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHI 658 (709)
T ss_pred cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEe
Confidence 359999999999999999999988 89999974
No 158
>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=94.37 E-value=0.035 Score=42.91 Aligned_cols=31 Identities=6% Similarity=0.010 Sum_probs=26.9
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
.|+++.|+|+++.++|+||++. .++|+++-.
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~ 111 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVS 111 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeC-CceEEEEcH
Confidence 3999999999999999999995 489887643
No 159
>PRK11642 exoribonuclease R; Provisional
Probab=94.25 E-value=0.034 Score=52.57 Aligned_cols=33 Identities=12% Similarity=-0.022 Sum_probs=29.4
Q ss_pred CCCceeEeeEeeecCCeeEEecCCC-hhhhchhh
Q 030172 145 QDGSVISDSSSMSSSNSNTIEPLPG-LGAIFEEL 177 (182)
Q Consensus 145 ~~g~~v~G~V~~v~~~G~fV~l~~g-v~gl~~~~ 177 (182)
..|+++.|+|+++.+||+||+|.++ ++||+|-.
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs 675 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVS 675 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEe
Confidence 3599999999999999999999875 99999854
No 160
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=93.74 E-value=0.066 Score=41.54 Aligned_cols=37 Identities=14% Similarity=0.052 Sum_probs=31.3
Q ss_pred CCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172 144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED 181 (182)
Q Consensus 144 ~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~ 181 (182)
|-.|.++.|.|+++.++|+||.+. =++||+|..+.-|
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~d 115 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMD 115 (183)
T ss_pred eccccEEEEEEEEEeecceEEEec-cccccccHhhccC
Confidence 334899999999999999999996 7999999876433
No 161
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=93.67 E-value=0.08 Score=38.51 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=23.3
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechh
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDA 47 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~ 47 (182)
+|++|.++|+.+|+ ++++.||.|.+
T Consensus 52 vG~eV~vKVl~ide-~GKisLSIr~~ 76 (129)
T COG1098 52 VGQEVKVKVLDIDE-NGKISLSIRKL 76 (129)
T ss_pred CCCEEEEEEEeecc-CCCcceehHHh
Confidence 89999999999998 89999998863
No 162
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=93.58 E-value=0.064 Score=49.58 Aligned_cols=32 Identities=13% Similarity=0.051 Sum_probs=29.3
Q ss_pred CCceeEeeEeeecCCeeEEecC-CChhhhchhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPL-PGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~ 177 (182)
.|+++.|+|+++.++|+||+|+ .|++||+|-.
T Consensus 572 iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s 604 (654)
T TIGR00358 572 VGTEFSGEISSVTRFGMFVRLDDNGIDGLIHIS 604 (654)
T ss_pred CCcEEEEEEEeEEcCcEEEEecCCceEEEEEeE
Confidence 5999999999999999999997 8899998753
No 163
>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=93.22 E-value=0.073 Score=46.58 Aligned_cols=32 Identities=3% Similarity=-0.034 Sum_probs=29.9
Q ss_pred CceeEeeEeeecCC--eeEEecCCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSN--SNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~--G~fV~l~~gv~gl~~~~~ 178 (182)
|+++.|+|.++.++ ||||++..|-+||+|-..
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d 59 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASD 59 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCCCceEEEEHHH
Confidence 99999999999997 999999999999998664
No 164
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=93.13 E-value=0.078 Score=41.14 Aligned_cols=31 Identities=3% Similarity=-0.116 Sum_probs=27.4
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
.|+++.|+|+++.++|+||++. .++|+++..
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~ 111 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIG-PVDGLLHIS 111 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEe-CceEEEEcH
Confidence 3999999999999999999996 499988754
No 165
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=92.97 E-value=0.099 Score=35.77 Aligned_cols=32 Identities=16% Similarity=0.113 Sum_probs=27.3
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|+++.|+|+++.++|+||.+ ..+++|+++...
T Consensus 2 gEVi~g~V~~v~~~G~~v~~-Gpl~~f~~~~~i 33 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEV-GPLSIFISRHLI 33 (88)
T ss_pred CcEEEEEEEEEeccEEEEEE-cCceEEEEeeec
Confidence 78999999999999999999 567888776543
No 166
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.60 E-value=0.11 Score=46.95 Aligned_cols=32 Identities=13% Similarity=0.133 Sum_probs=29.2
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
.|-+++++|+.+.++|+||+++|+-.||||..
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~s 699 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNS 699 (760)
T ss_pred eeeEEEEEEeeecccceEEEecCCchhhccch
Confidence 37788999999999999999999999999864
No 167
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.51 E-value=0.13 Score=34.00 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=27.2
Q ss_pred CceeEeeEeeecCCeeEEecCC-Chhhhchh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLP-GLGAIFEE 176 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~-gv~gl~~~ 176 (182)
|+.++|+|...++.+++|++.+ |+.|++|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~ 31 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPT 31 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEc
Confidence 5789999999999999999987 99998874
No 168
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=92.43 E-value=1 Score=34.35 Aligned_cols=61 Identities=20% Similarity=0.288 Sum_probs=41.5
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcC----CccccC-------ccccccCCCEEEEEEEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQD-------IRDILNEGDEVRVKVIKI 116 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels----~~~~~~-------~~~~~~~Gd~v~vkV~~i 116 (182)
..+.-.|+++.|+ ..|+|++++ | ++.++.---+. ...-++ -...+++|..|+++|++.
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~G-P-----l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigt 149 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSG-P-----LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGT 149 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEecc-c-----eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEE
Confidence 3466789999999 899999996 2 77776432222 221122 122589999999999988
Q ss_pred eCC
Q 030172 117 DRE 119 (182)
Q Consensus 117 d~~ 119 (182)
.-+
T Consensus 150 r~~ 152 (170)
T KOG3298|consen 150 RVD 152 (170)
T ss_pred EEe
Confidence 543
No 169
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=90.83 E-value=0.1 Score=47.18 Aligned_cols=38 Identities=13% Similarity=0.005 Sum_probs=33.4
Q ss_pred hhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 140 EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 140 ~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
..+.. |..+.|+|.++..||+||+|..-+.||+++..+
T Consensus 118 ~Dve~--g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~ 155 (715)
T COG1107 118 EDVEA--GKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDL 155 (715)
T ss_pred hhccc--ceeeeccccchhhhcceeecChhhhcccccccc
Confidence 34555 999999999999999999999999999998743
No 170
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=88.58 E-value=0.51 Score=36.51 Aligned_cols=34 Identities=9% Similarity=-0.080 Sum_probs=29.0
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE 180 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~ 180 (182)
.|+++.|.|+++.++|+||.+. =+++|+|.....
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~ 114 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIP 114 (176)
T ss_pred CCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCC
Confidence 4999999999999999999995 455898887654
No 171
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=88.36 E-value=0.064 Score=46.16 Aligned_cols=77 Identities=13% Similarity=0.055 Sum_probs=49.0
Q ss_pred ccccCCCEEEEEEEEEeCCCCeEEEEEeeccC-----CchhHHHhhhcCCCCceeEeeEeeecCC-eeEEecCCChhhhc
Q 030172 101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEE-----DPLLETLEKVIPQDGSVISDSSSMSSSN-SNTIEPLPGLGAIF 174 (182)
Q Consensus 101 ~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~-----~p~~~~~~~~~~~~g~~v~G~V~~v~~~-G~fV~l~~gv~gl~ 174 (182)
..+++||.+...+--.+. .+...-+.|+... -..+.....|....|++++|+|.++... ++||++ +++.|++
T Consensus 89 ~~~~vGd~i~~~i~~~~f-gRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~L 166 (374)
T PRK12328 89 PSVEIGDELTYELSLENM-GRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVL 166 (374)
T ss_pred CCCCCCCEEEEecChhhC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEe
Confidence 348899999876533322 2212222232221 0112344566556799999999999874 599999 4899999
Q ss_pred hhhhh
Q 030172 175 EELLQ 179 (182)
Q Consensus 175 ~~~~~ 179 (182)
|+-.+
T Consensus 167 P~~eq 171 (374)
T PRK12328 167 PMKNR 171 (374)
T ss_pred CHHHc
Confidence 98765
No 172
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=88.17 E-value=1 Score=40.30 Aligned_cols=59 Identities=27% Similarity=0.432 Sum_probs=46.1
Q ss_pred cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCccccCc-----cccccCCCEEEEEEEEEeC
Q 030172 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKIDR 118 (182)
Q Consensus 54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~-----~~~~~~Gd~v~vkV~~id~ 118 (182)
....+|.+|.|+ =-.+||+++. + -.||+|++++.+ +...+ ...++.||.+-|.|+.-..
T Consensus 33 ~~~~~gniy~grv~~i~p~~~aafvdig~--~---r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~ 103 (487)
T COG1530 33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGL--E---RNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR 103 (487)
T ss_pred cEeeecCceEEEecccCccchhheeeccC--C---ccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence 456689999999 2348999983 3 789999999998 54433 3479999999999987654
No 173
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=87.64 E-value=0.5 Score=38.69 Aligned_cols=41 Identities=12% Similarity=0.127 Sum_probs=31.8
Q ss_pred CCCCCCccHH--Hhhhhc--CCCeEEEEEEEEeCCCCEEEEEech
Q 030172 6 SCKEPQKSIH--EIAKGL--TGSIISVKVIQANEEMKKLVFSEKD 46 (182)
Q Consensus 6 ~~p~~e~~~~--~~~~~~--vG~~v~~~v~~~d~~~~~i~lS~k~ 46 (182)
|++.||++-. ++.+.+ +|+++=|+|+.+|+..+.+.+|+|+
T Consensus 40 ~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 40 FIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred eEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 4555665544 334444 8999999999999999999999874
No 174
>PRK07252 hypothetical protein; Provisional
Probab=87.04 E-value=1.2 Score=32.17 Aligned_cols=42 Identities=14% Similarity=0.008 Sum_probs=30.9
Q ss_pred CCCCCCccHHH--hh-h-hcCCCeEEEEEEEEeCCCCEEEEEechh
Q 030172 6 SCKEPQKSIHE--IA-K-GLTGSIISVKVIQANEEMKKLVFSEKDA 47 (182)
Q Consensus 6 ~~p~~e~~~~~--~~-~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~ 47 (182)
|+|.++++... .. . ..+||.|.++|+++|.+.+++.+|.++.
T Consensus 30 llhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 30 LIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred EEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 45555555331 11 1 2489999999999999999999999874
No 175
>PRK05054 exoribonuclease II; Provisional
Probab=86.99 E-value=0.45 Score=44.02 Aligned_cols=31 Identities=13% Similarity=0.022 Sum_probs=26.5
Q ss_pred CceeEeeEeeecCCeeEEecC-CChhhhchhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPL-PGLGAIFEEL 177 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~-~gv~gl~~~~ 177 (182)
|+.+.|.|+++.+||.||+|. .|+.||+|-.
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~ 593 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPAS 593 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEcc
Confidence 459999999999999999995 5799997754
No 176
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=86.98 E-value=3.8 Score=31.62 Aligned_cols=72 Identities=21% Similarity=0.201 Sum_probs=45.5
Q ss_pred CCCCCCEEEEE------eEeEEEEEecCCC-c--eeEEEEEEccCcCCcc--ccCccccccCCCEEEEEEEEEeCCCCeE
Q 030172 55 RVNVEDIFVGR------DYGAFIHLRFPDG-L--YHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRI 123 (182)
Q Consensus 55 ~~~~G~iv~g~------~~G~fV~l~~~~g-~--~~~~glv~~sels~~~--~~~~~~~~~~Gd~v~vkV~~id~~~~ki 123 (182)
-+..|+||.++ .| +-|+|...+. . ....|++|..++.... .-++-+-|++||.|.|+|++.+. ....
T Consensus 65 LP~~G~IVtarV~~i~~rf-Akv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y 142 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRF-AKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNY 142 (193)
T ss_pred CCccCcEEEEEEEeeccce-eeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcE
Confidence 35789999999 22 3333321110 0 0378999988875431 23455669999999999999654 4555
Q ss_pred EEEEe
Q 030172 124 TLSIK 128 (182)
Q Consensus 124 ~lS~k 128 (182)
.||.-
T Consensus 143 ~LTtA 147 (193)
T KOG3409|consen 143 LLTTA 147 (193)
T ss_pred EEEEe
Confidence 55553
No 177
>PRK08582 hypothetical protein; Provisional
Probab=86.91 E-value=0.67 Score=34.42 Aligned_cols=41 Identities=22% Similarity=0.171 Sum_probs=29.6
Q ss_pred CCCCCCccHHH---hhh-hcCCCeEEEEEEEEeCCCCEEEEEechh
Q 030172 6 SCKEPQKSIHE---IAK-GLTGSIISVKVIQANEEMKKLVFSEKDA 47 (182)
Q Consensus 6 ~~p~~e~~~~~---~~~-~~vG~~v~~~v~~~d~~~~~i~lS~k~~ 47 (182)
|++.++++... ... ..+|+.|+|+|+.+|. .+++.+|.++.
T Consensus 32 lVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~ 76 (139)
T PRK08582 32 LVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKA 76 (139)
T ss_pred EEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEec
Confidence 45666665432 111 2389999999999997 48999999874
No 178
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.91 E-value=0.3 Score=38.73 Aligned_cols=73 Identities=23% Similarity=0.352 Sum_probs=50.8
Q ss_pred cCCCCCCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCccccCc----cccc--cCCCEEEEEEEEEeCCC
Q 030172 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----RDIL--NEGDEVRVKVIKIDREK 120 (182)
Q Consensus 54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~----~~~~--~~Gd~v~vkV~~id~~~ 120 (182)
.+++.|+++.|+ -||+||+++- .|.-..++++|.-+|....-..| ...| -.-..++|-|.+++...
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV-~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~ 149 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGV-LGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLA 149 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccc-cCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchh
Confidence 688999999999 8899999852 22223789999988876654444 2223 23456777888888766
Q ss_pred CeEEEEE
Q 030172 121 SRITLSI 127 (182)
Q Consensus 121 ~ki~lS~ 127 (182)
+.|...+
T Consensus 150 ~EIea~l 156 (247)
T COG4044 150 QEIEARL 156 (247)
T ss_pred hhhhhhh
Confidence 6665444
No 179
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=84.88 E-value=1.7 Score=29.68 Aligned_cols=39 Identities=13% Similarity=0.062 Sum_probs=33.4
Q ss_pred hcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhhhc
Q 030172 142 VIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE 180 (182)
Q Consensus 142 ~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~ 180 (182)
|.|..||.|=|+|+.+.....+|++..-..|++|-+.-|
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ 40 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFE 40 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcc
Confidence 556679999999999999999999988888998876544
No 180
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=84.75 E-value=1.5 Score=30.12 Aligned_cols=34 Identities=9% Similarity=0.197 Sum_probs=29.2
Q ss_pred CCCCceeEeeEeeecCCeeEEec--------CCChhhhchhh
Q 030172 144 PQDGSVISDSSSMSSSNSNTIEP--------LPGLGAIFEEL 177 (182)
Q Consensus 144 ~~~g~~v~G~V~~v~~~G~fV~l--------~~gv~gl~~~~ 177 (182)
|..|++|-|+|+++....+.|++ .....|++|-.
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~ 45 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKE 45 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHH
Confidence 45699999999999999999999 77788888743
No 181
>PRK11712 ribonuclease G; Provisional
Probab=83.84 E-value=0.87 Score=40.77 Aligned_cols=32 Identities=9% Similarity=0.021 Sum_probs=29.2
Q ss_pred CCceeEeeEeeecC--CeeEEecCCChhhhchhh
Q 030172 146 DGSVISDSSSMSSS--NSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~--~G~fV~l~~gv~gl~~~~ 177 (182)
+|.++.|+|.++.| .+|||++..+-.||+|--
T Consensus 38 vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~ 71 (489)
T PRK11712 38 VGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHAS 71 (489)
T ss_pred cccEEEEEEeecCCCCceeEEeeCCCccEEEEhh
Confidence 49999999999998 789999999999999754
No 182
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=83.36 E-value=4.4 Score=29.43 Aligned_cols=56 Identities=18% Similarity=0.192 Sum_probs=37.3
Q ss_pred CCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcc------------c-cCccccccCCCEEEEEEEEEeC
Q 030172 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL------------I-QDIRDILNEGDEVRVKVIKIDR 118 (182)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~------------~-~~~~~~~~~Gd~v~vkV~~id~ 118 (182)
+|+++.|+ ..|+.|.|+.. -+.+||.+.|...- . .+.+-++..|+.|+.||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFF-----ddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFF-----DDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCE-----EEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEeccc-----ccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 68888888 77899988632 57888888775321 1 3334457899999999998864
No 183
>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=83.35 E-value=0.99 Score=41.77 Aligned_cols=32 Identities=9% Similarity=-0.020 Sum_probs=26.9
Q ss_pred CceeEeeEeeecCCeeEEec-CCChhhhchhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEP-LPGLGAIFEELL 178 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l-~~gv~gl~~~~~ 178 (182)
++.+.|.|+.+..+|+||+| ..|++||+|..-
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~ 590 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAF 590 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhh
Confidence 45899999999999999999 577999987543
No 184
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=82.14 E-value=0.97 Score=37.18 Aligned_cols=40 Identities=15% Similarity=0.062 Sum_probs=29.6
Q ss_pred CCCCCCccHHH--hhh-h-cCCCeEEEEEEEEeCCCCEEEEEec
Q 030172 6 SCKEPQKSIHE--IAK-G-LTGSIISVKVIQANEEMKKLVFSEK 45 (182)
Q Consensus 6 ~~p~~e~~~~~--~~~-~-~vG~~v~~~v~~~d~~~~~i~lS~k 45 (182)
|+|.++++... .+. . -+|+.+.|+|+.+|..++++.+|.+
T Consensus 37 lI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 37 FIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred EEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence 45556655331 111 2 3899999999999999999999987
No 185
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=81.75 E-value=2.6 Score=28.59 Aligned_cols=37 Identities=19% Similarity=0.239 Sum_probs=29.0
Q ss_pred CCCCccHHH---hhhhcCCCeEEEEEEEEeCCCCEEEEEe
Q 030172 8 KEPQKSIHE---IAKGLTGSIISVKVIQANEEMKKLVFSE 44 (182)
Q Consensus 8 p~~e~~~~~---~~~~~vG~~v~~~v~~~d~~~~~i~lS~ 44 (182)
+++|++-++ .-+.++|....+.|+.+|+.+|-+.+|.
T Consensus 46 ~~selsr~rirsi~kllVGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 46 NYVNVNADRAEKLKKKLVGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred cHHHHhHHHHHhhhhhhcCCeeEEEEEEECCCCCEEEeEc
Confidence 466666664 2334599999999999999999999874
No 186
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=80.57 E-value=1.3 Score=27.93 Aligned_cols=33 Identities=6% Similarity=-0.024 Sum_probs=20.2
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhh
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~ 179 (182)
|++...+|..+.++|+|++-..+-+-|+|....
T Consensus 2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~ 34 (61)
T PF13509_consen 2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV 34 (61)
T ss_dssp -------EEEE-SSEEEEEETT-EEEEEEGGG-
T ss_pred CCCcceEEEEEeCCEEEEECCCCCEEEechHHc
Confidence 778889999999999999977778888887654
No 187
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=80.01 E-value=16 Score=24.66 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=16.9
Q ss_pred cCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 104 NEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 104 ~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
++|+.|.++|..+. .++..+.+-.+
T Consensus 3 ~vGdiV~~rVtrv~--~~~a~v~Il~v 27 (82)
T PF10447_consen 3 KVGDIVIARVTRVN--PRQAKVEILCV 27 (82)
T ss_dssp -TT-EEEEEEEEE---SSEEEEEEEES
T ss_pred CCCCEEEEEEEEEe--ccEEEEEEEEE
Confidence 58999999999996 56666666555
No 188
>PRK10811 rne ribonuclease E; Reviewed
Probab=79.85 E-value=1.4 Score=42.43 Aligned_cols=29 Identities=0% Similarity=-0.025 Sum_probs=27.8
Q ss_pred CceeEeeEeeecC--CeeEEecCCChhhhch
Q 030172 147 GSVISDSSSMSSS--NSNTIEPLPGLGAIFE 175 (182)
Q Consensus 147 g~~v~G~V~~v~~--~G~fV~l~~gv~gl~~ 175 (182)
|.++.|+|.+|.+ .++||++..|-.||++
T Consensus 39 GnIYkGkVenIvPGInAAFVDIG~gknGFL~ 69 (1068)
T PRK10811 39 ANIYKGKITRIEPSLEAAFVDYGAERHGFLP 69 (1068)
T ss_pred cceEEEEEecccCCcceeEEEecCCcceEEE
Confidence 9999999999998 7899999999999997
No 189
>PRK05807 hypothetical protein; Provisional
Probab=79.14 E-value=3 Score=30.78 Aligned_cols=26 Identities=31% Similarity=0.340 Sum_probs=23.4
Q ss_pred cCCCeEEEEEEEEeCCCCEEEEEechh
Q 030172 21 LTGSIISVKVIQANEEMKKLVFSEKDA 47 (182)
Q Consensus 21 ~vG~~v~~~v~~~d~~~~~i~lS~k~~ 47 (182)
-+|+.|.++|+.+|. ++++.+|.+..
T Consensus 50 kvGd~V~VkV~~id~-~gkI~LSlk~~ 75 (136)
T PRK05807 50 KEQDKVKVKVISIDD-NGKISLSIKQA 75 (136)
T ss_pred CCCCEEEEEEEEECC-CCcEEEEEEec
Confidence 389999999999998 69999999874
No 190
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=77.05 E-value=2.7 Score=39.37 Aligned_cols=31 Identities=13% Similarity=-0.042 Sum_probs=27.7
Q ss_pred CCceeEeeEeeecCCeeEEecCCC-hhhhchh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPG-LGAIFEE 176 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~g-v~gl~~~ 176 (182)
.|....|+|+++..+|+||.+.+- ++|+++-
T Consensus 622 vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~ 653 (706)
T COG0557 622 VGEEFDGVVTGVTSFGFFVELPELGLEGLVHI 653 (706)
T ss_pred cCCEEEEEEEEEEeccEEEEecccccccceEc
Confidence 599999999999999999999654 9999874
No 191
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=75.85 E-value=0.11 Score=45.84 Aligned_cols=110 Identities=15% Similarity=0.232 Sum_probs=62.2
Q ss_pred CCCCCCCCCCccHHHhhhhcC-CCeEEEEEEEEeCCCC-EEEEE--ech--------hHHhh---hhcCCCCCCEEEEE-
Q 030172 2 SPSHSCKEPQKSIHEIAKGLT-GSIISVKVIQANEEMK-KLVFS--EKD--------AVWNK---YSSRVNVEDIFVGR- 65 (182)
Q Consensus 2 ~p~~~~p~~e~~~~~~~~~~v-G~~v~~~v~~~d~~~~-~i~lS--~k~--------~~~~~---~~~~~~~G~iv~g~- 65 (182)
|||| -|+++--|++++..+ |++-. .+.+. .+.++ ++. +.|.- +..+..-...+.+.
T Consensus 498 SPIR--KY~DMiNHRLlKavi~~~~~~------kPqedi~v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~~~~F~AEI 569 (645)
T COG4776 498 SPIR--KYGDMINHRLLKAVIKGETAE------KPQEDITVQLAERRRLNRMAERDVADWLYARFLADKAGTNTRFAAEI 569 (645)
T ss_pred chhh--hhhhHHHHHHHHHHHcCCCcC------CCchHHHHHHHHHHHhhhhhhhhhHHHHHHHHhccccccCchhhhhh
Confidence 8999 999999999988764 44311 11110 11111 111 12221 11122222233333
Q ss_pred ----eEeEEEEEecCCCceeEEEEEEccCcCCccc------------cCccccccCCCEEEEEEEEEeCCCCeE
Q 030172 66 ----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREKSRI 123 (182)
Q Consensus 66 ----~~G~fV~l~~~~g~~~~~glv~~sels~~~~------------~~~~~~~~~Gd~v~vkV~~id~~~~ki 123 (182)
..|+-|.+- .+| ..+|+|..-+-..+- -+-+..|++||.++|++.++..+++.|
T Consensus 570 ~Di~R~G~RvrLl-eNG---A~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRsi 639 (645)
T COG4776 570 QDISRGGMRVRLL-ENG---AIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRSI 639 (645)
T ss_pred hhhccCceEEEec-cCC---cceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhhhh
Confidence 778888885 356 788888665543321 133556899999999998887655443
No 192
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=75.26 E-value=3.9 Score=25.96 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=22.2
Q ss_pred ccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 101 DILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 101 ~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
..+.+||.+++.|+.+|.-+.++.+|+
T Consensus 39 ~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 39 VNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred eecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 337799999999999998777777664
No 193
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=74.27 E-value=13 Score=26.18 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=35.7
Q ss_pred CCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEE
Q 030172 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (182)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~i 116 (182)
..|.++.|+ +--+|++++ | +..+.|+..+... +.|+.|..|.+++.+.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG---~--KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFG---G--KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeC---C--ceeEEEecccccc-------cccccCCEEEEEECCH
Confidence 467788888 557999997 3 5899998665432 3488999999888654
No 194
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=74.26 E-value=21 Score=24.40 Aligned_cols=50 Identities=24% Similarity=0.239 Sum_probs=36.2
Q ss_pred EEEEecCCCceeEEEEEEccCc-CCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEee
Q 030172 70 FIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 70 fV~l~~~~g~~~~~glv~~sel-s~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~ 129 (182)
-|.+. +| ...+.|++-- ...++ .+.+||.|.|.+-..|.++++|..-.|.
T Consensus 23 rV~Le--nG---~~vla~isGKmR~~rI-----rIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 23 RVTLE--NG---VEVGAYASGRMRKHRI-----RILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEeC--CC---CEEEEEeccceeeeeE-----EecCCCEEEEEECcccCCceeEEEEecC
Confidence 34664 56 7777777641 11122 2679999999999999999999988874
No 195
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=72.27 E-value=4.2 Score=31.02 Aligned_cols=28 Identities=14% Similarity=0.223 Sum_probs=22.8
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhch
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFE 175 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~ 175 (182)
|++++|+|+.+...|+|++..| ++.++.
T Consensus 82 GEVvdgvV~~Vnk~G~F~~~GP-l~~f~s 109 (170)
T KOG3298|consen 82 GEVVDGVVTKVNKMGVFARSGP-LEVFYS 109 (170)
T ss_pred CcEEEEEEEEEeeeeEEEeccc-eEeeee
Confidence 9999999999999999999743 444443
No 196
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=69.40 E-value=30 Score=28.14 Aligned_cols=67 Identities=16% Similarity=0.197 Sum_probs=45.3
Q ss_pred ccCCCEEEEEEEEEeCCCCeEEEEEeeccCCchhHHHhhhcCCCCceeEeeEeeecCCeeEEecCCChhhhchhhh
Q 030172 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 103 ~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~ 178 (182)
|..|+.+.+.+.+.-..+++. ++. -|... +|.|..||.|=|+|..+.+.+-.|++..-+.+++|-..
T Consensus 30 y~~~~~iyssv~G~~~~~~~~-v~V-----Ipl~g---~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~ 96 (239)
T COG1097 30 YFEGGKIYSSVVGLLDVKGKL-VRV-----IPLEG---RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSD 96 (239)
T ss_pred EecCCEEEEEEEeEEEEeCCE-EEE-----EeCCC---cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhh
Confidence 336677777665542222222 222 23333 67777899999999999999999999877888887654
No 197
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=67.27 E-value=24 Score=22.96 Aligned_cols=46 Identities=28% Similarity=0.309 Sum_probs=31.1
Q ss_pred EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEE
Q 030172 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (182)
Q Consensus 70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~ 124 (182)
-|.+. +| .+-+.|++---. .-+-.+.+||.|.|.+-..|.++++|.
T Consensus 21 ~V~l~--ng---~~vla~i~GKmr----~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 21 RVELE--NG---HEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEC--CC---CEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEE
Confidence 34554 56 788888764211 112227799999999988988888775
No 198
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=65.23 E-value=6.8 Score=34.67 Aligned_cols=79 Identities=16% Similarity=0.109 Sum_probs=48.6
Q ss_pred cccccCCCEEEEEEEEEe-CCCCeEE-EEEeeccC-----CchhHHHhhhcCCCCceeEeeEeeecCCeeEEecC---C-
Q 030172 100 RDILNEGDEVRVKVIKID-REKSRIT-LSIKQLEE-----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL---P- 168 (182)
Q Consensus 100 ~~~~~~Gd~v~vkV~~id-~~~~ki~-lS~k~~~~-----~p~~~~~~~~~~~~g~~v~G~V~~v~~~G~fV~l~---~- 168 (182)
...+++||.+...+- .+ .+=+|+. .+.|+... -........|....|++++|+|.++...+++|++. .
T Consensus 100 ~~~~~iGD~v~~~v~-~~~~~fgRiAAq~aKQvi~Qkire~ER~~i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~ 178 (449)
T PRK12329 100 ADEAQLGDTVVLDVT-PEQEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQ 178 (449)
T ss_pred CCCCcCCCEEEEecC-ccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCC
Confidence 344889999986552 11 0112222 11222111 11223445666567999999999999999999984 2
Q ss_pred -Chhhhchhhhh
Q 030172 169 -GLGAIFEELLQ 179 (182)
Q Consensus 169 -gv~gl~~~~~~ 179 (182)
++.|++|+-.+
T Consensus 179 ~~~EaiLP~~Eq 190 (449)
T PRK12329 179 PEVEAELPKREQ 190 (449)
T ss_pred cceEEEecHHHc
Confidence 48999998654
No 199
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=61.46 E-value=15 Score=22.74 Aligned_cols=32 Identities=19% Similarity=0.476 Sum_probs=25.8
Q ss_pred CccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 98 ~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
++.+.+.+|+.+.++|++++ .+++.|.+....
T Consensus 7 k~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~ 38 (54)
T PF02599_consen 7 KVGESIVIGDDIEITVLEIS--GGQVKLGIDAPK 38 (54)
T ss_dssp ETT-EEEETTTEEEEEEEEE--TTEEEEEEEECT
T ss_pred cCCCEEEECCCEEEEEEEEc--CCEEEEEEECCC
Confidence 34566888999999999998 788999988654
No 200
>PRK01712 carbon storage regulator; Provisional
Probab=57.36 E-value=27 Score=22.44 Aligned_cols=32 Identities=19% Similarity=0.451 Sum_probs=26.1
Q ss_pred CccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 98 ~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
.+.+.+.+|+.+.++|+++. .+++.|.+....
T Consensus 7 k~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~ 38 (64)
T PRK01712 7 KVGESLMIGDDIEVTVLGVK--GNQVRIGINAPK 38 (64)
T ss_pred cCCCEEEeCCCEEEEEEEEe--CCEEEEEEECCC
Confidence 34566889999999999997 788999987654
No 201
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=56.03 E-value=59 Score=25.43 Aligned_cols=64 Identities=13% Similarity=0.138 Sum_probs=39.3
Q ss_pred cccccCCCEEEEEEEEEeCCCCeEEEEEeeccC--------------------CchhHHHhhhcCCCCceeEeeEeeecC
Q 030172 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEE--------------------DPLLETLEKVIPQDGSVISDSSSMSSS 159 (182)
Q Consensus 100 ~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~--------------------~p~~~~~~~~~~~~g~~v~G~V~~v~~ 159 (182)
....+.|+.|-++|.++.. ++..+.+-..+. .......+.|.+ ||++.++|.+..
T Consensus 59 ~~~~K~GdiV~grV~~v~~--~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~--GDivrA~Vis~~- 133 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVRE--QRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRI--GDIVRARVISTG- 133 (188)
T ss_pred CCCCCCCCEEEEEEeeccc--eEEEEEEEEEecccccCCCCceeeEEEEeccccccccccccccc--ccEEEEEEEecC-
Confidence 3447889999999988863 333333322111 122233345566 999999999987
Q ss_pred CeeEEecCC
Q 030172 160 NSNTIEPLP 168 (182)
Q Consensus 160 ~G~fV~l~~ 168 (182)
...++.+..
T Consensus 134 ~~~~Lst~~ 142 (188)
T COG1096 134 DPIQLSTKG 142 (188)
T ss_pred CCeEEEecC
Confidence 466666643
No 202
>PRK15463 cold shock-like protein CspF; Provisional
Probab=54.76 E-value=29 Score=22.47 Aligned_cols=42 Identities=26% Similarity=0.286 Sum_probs=28.4
Q ss_pred eEeE-EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 66 DYGA-FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 66 ~~G~-fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
+.|. |++-. +| +-+.|+|++.+...-. ..+++||.|...+..
T Consensus 15 ~kGfGFI~~~--~g--~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 15 KSGKGLITPS--DG--RKDVQVHISALNLRDA----EELTTGLRVEFCRIN 57 (70)
T ss_pred CCceEEEecC--CC--CccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence 3444 66654 23 2799999999975422 237799999997644
No 203
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=54.53 E-value=41 Score=23.22 Aligned_cols=41 Identities=12% Similarity=0.216 Sum_probs=30.3
Q ss_pred CCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEE
Q 030172 23 GSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR 65 (182)
Q Consensus 23 G~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~ 65 (182)
|....+.+ .|.+.+.+.++.-....+.+...+++|++|.=.
T Consensus 34 g~~~~~~l--~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 34 GKLFSFDL--LDEDGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred cEEEEEEE--EECCCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 33344444 777788888888777777788899999988755
No 204
>PRK15464 cold shock-like protein CspH; Provisional
Probab=53.83 E-value=29 Score=22.50 Aligned_cols=42 Identities=26% Similarity=0.276 Sum_probs=28.7
Q ss_pred eEeE-EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 66 DYGA-FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 66 ~~G~-fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
+.|. |+.-. +| +-+.|+|++.+...-. +.+.+||.|...+..
T Consensus 15 ~KGfGFI~~~--~g--~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 15 KSGKGFIIPS--DG--RKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN 57 (70)
T ss_pred CCCeEEEccC--CC--CccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence 4444 66654 33 2799999999864422 337799999988744
No 205
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=51.97 E-value=25 Score=23.69 Aligned_cols=32 Identities=31% Similarity=0.480 Sum_probs=21.6
Q ss_pred cccccCCCEEEEEEEEEeCC-------CCeEEEEEeecc
Q 030172 100 RDILNEGDEVRVKVIKIDRE-------KSRITLSIKQLE 131 (182)
Q Consensus 100 ~~~~~~Gd~v~vkV~~id~~-------~~ki~lS~k~~~ 131 (182)
+..|++||.|.++++-.+.+ ...+.++++...
T Consensus 8 r~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~ 46 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPS 46 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETT
T ss_pred ccCcCCCCEEEEEEEEeccccccccccCCceEEEEECCC
Confidence 45699999999999955443 246677776543
No 206
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=51.71 E-value=69 Score=25.69 Aligned_cols=58 Identities=14% Similarity=0.060 Sum_probs=37.2
Q ss_pred cCCCCCCEEEEE---eEe--EEEEEecCCCceeEEEEEEccCcCCc-cccCccccccCCCEEEEEEEEEeC
Q 030172 54 SRVNVEDIFVGR---DYG--AFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDR 118 (182)
Q Consensus 54 ~~~~~G~iv~g~---~~G--~fV~l~~~~g~~~~~glv~~sels~~-~~~~~~~~~~~Gd~v~vkV~~id~ 118 (182)
.-+.+||.|.|. .+| .-|+|+++ ..+.++.-..... +-..|+ +++||.|.++|...++
T Consensus 61 YiP~~~D~VIGiV~~~~gd~ykVDigg~-----~~a~L~~laFe~AtkrNrPn--l~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 61 YIPVKGDHVIGIVTSKSGDIYKVDIGGS-----EPASLSYLAFEGATKRNRPN--LQVGDLIYAKVVDANK 124 (230)
T ss_pred ecCCCCCEEEEEEEeccCceEEEecCCC-----CeeeeeeccccCccccCCCc--cccccEEEEEEEecCC
Confidence 346789999999 333 56777522 4555554333222 223333 8999999999998864
No 207
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=51.41 E-value=55 Score=25.61 Aligned_cols=61 Identities=16% Similarity=0.183 Sum_probs=40.3
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc-----------------CccccccCCCEEE
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------------DIRDILNEGDEVR 110 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~-----------------~~~~~~~~Gd~v~ 110 (182)
..++-.|+++.|+ .-|+-|.|+.- -+.|+|..-|...... ...=++.+|..|+
T Consensus 76 VFrPF~gEVi~gki~~cs~eG~rvtl~FF-----dDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IR 150 (202)
T KOG3297|consen 76 VFRPFVGEVITGKIKECSEEGLRVTLGFF-----DDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIR 150 (202)
T ss_pred EEecccceEEEEEeecCCccceEEEEEee-----eceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEE
Confidence 4567899999999 77888888632 3567776655432111 1222477888899
Q ss_pred EEEEEEeC
Q 030172 111 VKVIKIDR 118 (182)
Q Consensus 111 vkV~~id~ 118 (182)
.||.+.+.
T Consensus 151 FRV~~e~f 158 (202)
T KOG3297|consen 151 FRVEDESF 158 (202)
T ss_pred EEEeeecc
Confidence 88877743
No 208
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=51.06 E-value=52 Score=21.69 Aligned_cols=44 Identities=7% Similarity=0.194 Sum_probs=33.8
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEEeE
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDY 67 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~~~ 67 (182)
.|..++..+ +|+...++.++......+.+.+.+++|.++.=.+|
T Consensus 17 ~~~~~~miL--~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f 60 (86)
T cd04480 17 SGESLEMVL--VDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNF 60 (86)
T ss_pred CCcEEEEEE--EcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeE
Confidence 455556555 88887899999988778888889999988775443
No 209
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=49.78 E-value=92 Score=24.21 Aligned_cols=64 Identities=13% Similarity=0.159 Sum_probs=39.9
Q ss_pred cccCCCEEEEEEEEEeCCCCeEEEEEee------------------ccCCchhHHHhhhcCCCCceeEeeEeeecCCe-e
Q 030172 102 ILNEGDEVRVKVIKIDREKSRITLSIKQ------------------LEEDPLLETLEKVIPQDGSVISDSSSMSSSNS-N 162 (182)
Q Consensus 102 ~~~~Gd~v~vkV~~id~~~~ki~lS~k~------------------~~~~p~~~~~~~~~~~~g~~v~G~V~~v~~~G-~ 162 (182)
....|+.|.+||..++....++.+.-.. +.+...-+..+.|.| ||++-.+|.+..+.- .
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrP--gDiVlAkVis~~~~~~y 142 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRP--GDIVLAKVISLGDGSNY 142 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCC--CcEEEEEEeecCCCCcE
Confidence 3568999999999998655555433211 011122344567788 999999999955432 3
Q ss_pred EEecC
Q 030172 163 TIEPL 167 (182)
Q Consensus 163 fV~l~ 167 (182)
|+..+
T Consensus 143 ~LTtA 147 (193)
T KOG3409|consen 143 LLTTA 147 (193)
T ss_pred EEEEe
Confidence 44443
No 210
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=48.49 E-value=75 Score=20.77 Aligned_cols=51 Identities=24% Similarity=0.219 Sum_probs=32.8
Q ss_pred EEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 70 fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
|+.-. .+| -+.|+|++.+...- ...++.||.|...+..-. +++-...+..+
T Consensus 17 FI~~~-~gg---~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~~~ 67 (74)
T PRK09937 17 FICPE-GGG---EDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGP--KGNHASVIVPV 67 (74)
T ss_pred EEeeC-CCC---ccEEEEEeeccccC----CCCCCCCCEEEEEEEECC--CCceeeEEEEC
Confidence 56554 133 89999999987442 234789999999875433 55544444443
No 211
>PRK00568 carbon storage regulator; Provisional
Probab=48.29 E-value=40 Score=22.43 Aligned_cols=32 Identities=25% Similarity=0.474 Sum_probs=25.7
Q ss_pred CccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 98 ~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
+..+.+.+||.+.++|+++. .+++.+.+....
T Consensus 7 K~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~ 38 (76)
T PRK00568 7 KVNEGIVIDDNIHIKVISID--RGSVRLGFEAPE 38 (76)
T ss_pred eCCCeEEeCCCeEEEEEEEc--CCEEEEEEECCC
Confidence 34566889999999999996 788999887543
No 212
>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=45.87 E-value=72 Score=19.78 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=22.8
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
-+.|+|++++.... -..++.|+.|+..+..
T Consensus 24 ~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 24 EDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp SEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred eeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 58999999988764 2347899999999876
No 213
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=45.55 E-value=70 Score=20.48 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=23.1
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~i 116 (182)
-+.|+|++.+..... ..+.+||.|...+..-
T Consensus 27 ~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 27 KDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG 57 (69)
T ss_pred eeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence 799999999875422 3367899999877443
No 214
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=45.40 E-value=23 Score=25.00 Aligned_cols=32 Identities=6% Similarity=0.033 Sum_probs=28.8
Q ss_pred CCceeEeeEeeecCCeeEEecCCChhhhchhh
Q 030172 146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 146 ~g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~ 177 (182)
.|..+.|+|..+.+.-+||++.....|.|++-
T Consensus 23 ~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp 54 (104)
T PF10246_consen 23 EGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRP 54 (104)
T ss_pred cCCEEEEEEEEEecCceEEEeCCceeEEEecc
Confidence 38899999999999999999999999999764
No 215
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=45.31 E-value=73 Score=21.16 Aligned_cols=46 Identities=24% Similarity=0.389 Sum_probs=30.6
Q ss_pred cccCCCEEEEEEEEE--------------eCCCCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 102 ILNEGDEVRVKVIKI--------------DREKSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 102 ~~~~Gd~v~vkV~~i--------------d~~~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
.+++||.+.+++- . +.+++.+.+.+|..........+.+.++ |+.+
T Consensus 29 ~~~pGQ~v~v~~~-~~~~~~~R~yS~~s~~~~~~~~~~~ik~~~~G~~S~~L~~l~~--Gd~v 88 (99)
T PF00970_consen 29 DFKPGQFVSVRVP-INGKQVSRPYSPASSPDDKGYLEFAIKRYPNGRVSRYLHQLKP--GDEV 88 (99)
T ss_dssp SSTTT-EEEEEEE-ETTEEEEEEEEBCSSTTSSSEEEEEEEECTTSHHHHHHHTSCT--TSEE
T ss_pred ccCcceEEEEEEc-cCCcceecceeEeeecCCCCcEEEEEEeccCCHHHHHHHhCCC--CCEE
Confidence 4788999998886 2 1235578899988755555555666666 7755
No 216
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=45.25 E-value=10 Score=30.14 Aligned_cols=16 Identities=6% Similarity=-0.051 Sum_probs=14.8
Q ss_pred CCeeEEecCCChhhhc
Q 030172 159 SNSNTIEPLPGLGAIF 174 (182)
Q Consensus 159 ~~G~fV~l~~gv~gl~ 174 (182)
+.|+||-++.|.+||+
T Consensus 49 DiGCFvlFDGGFsGLV 64 (229)
T PF11813_consen 49 DIGCFVLFDGGFSGLV 64 (229)
T ss_pred CcceEEEecCCcceEE
Confidence 4999999999999997
No 217
>PRK10943 cold shock-like protein CspC; Provisional
Probab=43.94 E-value=70 Score=20.50 Aligned_cols=30 Identities=23% Similarity=0.321 Sum_probs=23.1
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
-+.|+|++.+..... ..+..||.|...+..
T Consensus 27 ~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 27 KDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred eeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 799999999875422 346789999988744
No 218
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=43.91 E-value=40 Score=22.13 Aligned_cols=30 Identities=17% Similarity=0.472 Sum_probs=24.0
Q ss_pred ccccccCCCEEEEEEEEEeCCCCeEEEEEeec
Q 030172 99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (182)
Q Consensus 99 ~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~ 130 (182)
.++.+.+||.|.+.|++++ .+++.+-+...
T Consensus 8 ~~Esi~IgddI~itVl~i~--gnqVkiGi~AP 37 (73)
T COG1551 8 VGESIMIGDDIEITVLSIK--GNQVKIGINAP 37 (73)
T ss_pred cCceEEecCCeEEEEEEEc--CCeEEEeecCC
Confidence 4556889999999999997 67788777653
No 219
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=43.01 E-value=69 Score=20.53 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=22.9
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
-+.|+|++.+...- ...+++||.|...+..
T Consensus 28 ~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 28 KDVFVHFSAIQNDG----YKSLDEGQKVSFTIES 57 (70)
T ss_pred ccEEEEEeeccccC----CCCCCCCCEEEEEEEE
Confidence 79999999987542 2347799999987644
No 220
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=42.28 E-value=61 Score=21.15 Aligned_cols=32 Identities=22% Similarity=0.542 Sum_probs=25.8
Q ss_pred CccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 98 ~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
++.+.+.+|+.++++|+++. .+++.+.+....
T Consensus 7 k~gE~I~Igd~I~I~Vl~i~--g~~VrlGI~AP~ 38 (69)
T TIGR00202 7 KVNESIQIGDDIEVKVLSVK--GDQVKLGIEAPK 38 (69)
T ss_pred cCCCEEEeCCCEEEEEEEEc--CCeEEEEEECCC
Confidence 45566889999999999996 788888887543
No 221
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=42.11 E-value=31 Score=21.55 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=17.5
Q ss_pred ccccCccccccCCCEEEEEEEEEeCCCCeEEEE
Q 030172 94 DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (182)
Q Consensus 94 ~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS 126 (182)
.|++.+. |.+|+.|+++| ..++|.++
T Consensus 31 ~WL~~aG--F~~G~~v~V~v-----~~g~lvIt 56 (57)
T PF08845_consen 31 KWLEEAG--FTIGDPVKVRV-----MPGCLVIT 56 (57)
T ss_pred hhhHHhC--CCCCCEEEEEE-----ECCEEEEe
Confidence 3444333 89999999888 35666554
No 222
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=41.35 E-value=54 Score=25.70 Aligned_cols=42 Identities=21% Similarity=0.338 Sum_probs=32.0
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCC-CCeEEEEEee
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE-KSRITLSIKQ 129 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~-~~ki~lS~k~ 129 (182)
++|+++..++. +.+.|++|+.+++.+.++... ++++.+|+..
T Consensus 2 ~~~~l~~~~~~------~~e~~~~g~ri~~~~~~v~~~~~g~~~~srt~ 44 (190)
T COG0195 2 VEAILPKREQI------PGENFKVGDRIRALLYEVQKEAKGQIELSRTI 44 (190)
T ss_pred ceeEcchhhcC------CCcccccCcEEEEEEeeeeecCcccEEEEecc
Confidence 67888877765 557799999999999999753 3457777653
No 223
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=40.46 E-value=33 Score=30.66 Aligned_cols=26 Identities=23% Similarity=0.224 Sum_probs=23.6
Q ss_pred CCCeEEEEEEEEeCCCCEEEEEechh
Q 030172 22 TGSIISVKVIQANEEMKKLVFSEKDA 47 (182)
Q Consensus 22 vG~~v~~~v~~~d~~~~~i~lS~k~~ 47 (182)
=|+++++.|+++|.+++++.++.+..
T Consensus 47 WGDEiEy~vV~fDd~~kk~rv~l~~e 72 (640)
T KOG3754|consen 47 WGDEIEYMVVKFDDKNKKARVSLRAE 72 (640)
T ss_pred ccceeEEEEEecccccceeeeeeeHH
Confidence 49999999999999999999998864
No 224
>COG1278 CspC Cold shock proteins [Transcription]
Probab=39.75 E-value=46 Score=21.58 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=22.1
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~ 114 (182)
-+.|+|+|.+...-.. .+..||.|...+.
T Consensus 25 ~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~ 53 (67)
T COG1278 25 KDVFVHISAIQRAGFR----TLREGQKVEFEVE 53 (67)
T ss_pred cCEEEEeeeeccCCCc----ccCCCCEEEEEEe
Confidence 7999999998654333 3678999998773
No 225
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.61 E-value=1.2e+02 Score=20.14 Aligned_cols=51 Identities=29% Similarity=0.292 Sum_probs=34.0
Q ss_pred EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 69 ~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
+.|.+. +| ..-+-|++---.. .+-.+.+||.|.|..-..|.++++|..-.+
T Consensus 22 f~v~~e--dg---~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 22 FRVELE--NG---HERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EEEEec--CC---cEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 456664 56 7777776642211 112277999999999999977887776554
No 226
>PRK09890 cold shock protein CspG; Provisional
Probab=38.07 E-value=1.1e+02 Score=19.64 Aligned_cols=30 Identities=20% Similarity=0.300 Sum_probs=22.7
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
-+.|+|++.+...-. ..+++||.|...+..
T Consensus 28 ~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 28 KDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 799999999875522 236789999987643
No 227
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=36.21 E-value=71 Score=31.16 Aligned_cols=75 Identities=20% Similarity=0.228 Sum_probs=43.9
Q ss_pred ccCCCEEEEEEEEEeCCCCe---------EEEEEeeccCCchh----HHHhhhcCCCCceeEeeEeee-c--CCeeEEec
Q 030172 103 LNEGDEVRVKVIKIDREKSR---------ITLSIKQLEEDPLL----ETLEKVIPQDGSVISDSSSMS-S--SNSNTIEP 166 (182)
Q Consensus 103 ~~~Gd~v~vkV~~id~~~~k---------i~lS~k~~~~~p~~----~~~~~~~~~~g~~v~G~V~~v-~--~~G~fV~l 166 (182)
|++||.|.|..-+.--.+++ +.++-++-+.+|++ +.-+.|.+ |+.| +|.+- . +.|+.|.+
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~--GDhV--KVi~G~~eG~tGlVvrV 483 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEP--GDHV--KVIAGRYEGDTGLVVRV 483 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccC--CCeE--EEEeccccCCcceEEEE
Confidence 99999988754333211221 12222233455543 33344455 7766 44433 2 47889999
Q ss_pred CCChhhhchhhhhcc
Q 030172 167 LPGLGAIFEELLQED 181 (182)
Q Consensus 167 ~~gv~gl~~~~~~~~ 181 (182)
+.+.-=|+.++.+|+
T Consensus 484 e~~~vi~~Sd~t~ee 498 (1024)
T KOG1999|consen 484 EQGDVILLSDLTMEE 498 (1024)
T ss_pred eCCeEEEEecCccce
Confidence 888888888888776
No 228
>PRK14998 cold shock-like protein CspD; Provisional
Probab=35.48 E-value=1.3e+02 Score=19.61 Aligned_cols=41 Identities=24% Similarity=0.180 Sum_probs=28.0
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
-+.|+|++.+...- ...+..||.|...+..-+ ++.-...+.
T Consensus 25 ~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~ 65 (73)
T PRK14998 25 EDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGP--KGNHASVIV 65 (73)
T ss_pred ccEEEEeeeecccC----CCCCCCCCEEEEEEEECC--CCceeEEEE
Confidence 79999999987442 234789999999875543 454443333
No 229
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=35.03 E-value=95 Score=18.46 Aligned_cols=35 Identities=29% Similarity=0.267 Sum_probs=25.0
Q ss_pred cCCCCCCEEEEE-eEeEEEEEecCCCceeEEEEEEccCcC
Q 030172 54 SRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (182)
Q Consensus 54 ~~~~~G~iv~g~-~~G~fV~l~~~~g~~~~~glv~~sels 92 (182)
..++.|..+.-. ..+-++.+. .+| ..|.|+.+.|+
T Consensus 19 ~~l~~g~~v~v~~~~~~W~~V~-~~g---~~GWv~~~~lw 54 (55)
T PF06347_consen 19 ARLEPGVPVRVIECRGGWCKVR-ADG---RTGWVHKSLLW 54 (55)
T ss_pred EEECCCCEEEEEEccCCeEEEE-ECC---eEEeEEeeecc
Confidence 467788887777 555555555 466 99999988765
No 230
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.96 E-value=1.3e+02 Score=22.16 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=24.5
Q ss_pred EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCC
Q 030172 69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK 120 (182)
Q Consensus 69 ~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~ 120 (182)
+.|+|+ ++ -.++.|+.+ .++. .+++|+.|++.+.......
T Consensus 88 aiV~l~--~~---~~i~~~i~~------~~p~-~v~iGm~V~~v~~~~~~~~ 127 (140)
T COG1545 88 AIVELE--EG---GRILGQLVD------VDPD-DVEIGMKVEAVFRKREEDG 127 (140)
T ss_pred EEEEeC--CC---CceEEEEEe------cCcc-cccCCCEEEEEEEEccccC
Confidence 466664 23 345655554 1232 3789999999988776433
No 231
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=32.08 E-value=27 Score=31.36 Aligned_cols=31 Identities=3% Similarity=-0.015 Sum_probs=27.9
Q ss_pred CceeEeeEeeecC--CeeEEecCCChhhhchhh
Q 030172 147 GSVISDSSSMSSS--NSNTIEPLPGLGAIFEEL 177 (182)
Q Consensus 147 g~~v~G~V~~v~~--~G~fV~l~~gv~gl~~~~ 177 (182)
|.++.|+|+++.+ -.+||++..+=.||+|..
T Consensus 38 gniy~grv~~i~p~~~aafvdig~~r~gfl~~~ 70 (487)
T COG1530 38 GNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLS 70 (487)
T ss_pred cCceEEEecccCccchhheeeccCCccceEEec
Confidence 9999999999998 569999999999998754
No 232
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=31.90 E-value=60 Score=20.63 Aligned_cols=23 Identities=13% Similarity=0.049 Sum_probs=19.1
Q ss_pred ceeEeeEeeecCCeeEEecCCCh
Q 030172 148 SVISDSSSMSSSNSNTIEPLPGL 170 (182)
Q Consensus 148 ~~v~G~V~~v~~~G~fV~l~~gv 170 (182)
..++|+|++|.+...-+.|++|=
T Consensus 3 ~~veG~I~~id~~~~titLdDGk 25 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDDGK 25 (61)
T ss_pred ccceEEEEEEcCCceEEEecCCC
Confidence 45789999999999988887763
No 233
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=31.57 E-value=1.5e+02 Score=22.22 Aligned_cols=51 Identities=14% Similarity=0.384 Sum_probs=37.0
Q ss_pred CCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeC
Q 030172 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDR 118 (182)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~ 118 (182)
.-.|..|.|+ ..-+|++++ + +..+.|...++.. +.|+.|-.|..++++...
T Consensus 80 ~a~gklV~GkIfhiV~~DlYIDFG---~--KFhcVC~rP~~n~-------e~Y~~GaRVrlRl~DlEL 135 (173)
T KOG4078|consen 80 DAKGKLVIGKIFHIVEEDLYIDFG---G--KFHCVCKRPALNG-------EAYQKGARVRLRLIDLEL 135 (173)
T ss_pred CcCCcEEEeeeeeeeccceEEecC---C--eEEEEEcCcCcCH-------HHhhcCceEEEEEcChhH
Confidence 3467788888 566899986 3 4788887666543 448899999998877643
No 234
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=30.81 E-value=1.3e+02 Score=18.44 Aligned_cols=31 Identities=29% Similarity=0.267 Sum_probs=23.9
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~i 116 (182)
-+.|+|.+++...- ...+++||.|...+..-
T Consensus 24 ~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 24 EDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 78999999987642 24478999999987544
No 235
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=30.30 E-value=1.7e+02 Score=23.98 Aligned_cols=56 Identities=14% Similarity=0.183 Sum_probs=33.4
Q ss_pred ccCCCEEEEEEEEEe-------------CCC-CeEEEEEeeccCCchhHHHh-hhcCCCCceeEeeEeeecCCeeEEe
Q 030172 103 LNEGDEVRVKVIKID-------------REK-SRITLSIKQLEEDPLLETLE-KVIPQDGSVISDSSSMSSSNSNTIE 165 (182)
Q Consensus 103 ~~~Gd~v~vkV~~id-------------~~~-~ki~lS~k~~~~~p~~~~~~-~~~~~~g~~v~G~V~~v~~~G~fV~ 165 (182)
|++||.|.+.+ .++ +.+ ..+.+|+|....-+...... ..++ |+.+ .| ..+.|-|+-
T Consensus 35 f~pGQ~i~v~l-~~~~~~~~R~YSl~s~p~~~~~~~isVk~~~~G~~S~~Lh~~lk~--Gd~l--~v--~~P~G~F~l 105 (266)
T COG1018 35 FEPGQYITVGL-PNGGEPLLRAYSLSSAPDEDSLYRISVKREDGGGGSNWLHDHLKV--GDTL--EV--SAPAGDFVL 105 (266)
T ss_pred cCCCCeEEEEe-cCCCceeeEEEEeccCCCCCceEEEEEEEeCCCcccHHHHhcCCC--CCEE--EE--ecCCCCccC
Confidence 78888888776 332 222 36778888764334333333 5565 8866 33 566787753
No 236
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=29.50 E-value=3.6e+02 Score=23.03 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=21.1
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEEe
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id 117 (182)
..-.-.+++++.+.. .+++||.|.|.|.++.
T Consensus 319 ~~l~Arit~~srd~L-----~l~~G~~v~AqIKsVs 349 (352)
T COG4148 319 KTLWARITPWARDEL-----ALKPGQWVYAQIKSVS 349 (352)
T ss_pred cEEEEEccHhhHHhh-----cCCCCCeEEEEEEEEE
Confidence 444455566554432 2899999999998875
No 237
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.02 E-value=2.7e+02 Score=22.40 Aligned_cols=58 Identities=16% Similarity=0.134 Sum_probs=33.1
Q ss_pred hcCCCC--CCEEEEE-------eEeEEEEEecCCCceeEEEEEEccCcCCccccCc---cccccCC--CEEEEEEEEEeC
Q 030172 53 SSRVNV--EDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEG--DEVRVKVIKIDR 118 (182)
Q Consensus 53 ~~~~~~--G~iv~g~-------~~G~fV~l~~~~g~~~~~glv~~sels~~~~~~~---~~~~~~G--d~v~vkV~~id~ 118 (182)
...++. |++|.|+ -||++++ + +..-+|..+|..-+...+ .+.|-.= -.|+++|+..+.
T Consensus 67 ~~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G-------~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~ 138 (225)
T PF09883_consen 67 VYSLEPVKGETYVGTLISWDEDGYGVDVD-G-------IFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVED 138 (225)
T ss_pred CchhcccCCceEEEEEEeecccceEEEee-c-------ccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEccc
Confidence 344555 9999999 4555553 3 556666666633322223 3334333 345588888764
No 238
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=28.92 E-value=59 Score=26.88 Aligned_cols=71 Identities=23% Similarity=0.298 Sum_probs=0.0
Q ss_pred CCCCCCEEEEE-----eEeEEEEEecCCCceeEEEEEEccCcCCcccc----------CccccccCCCEEEEEEEEEeCC
Q 030172 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------DIRDILNEGDEVRVKVIKIDRE 119 (182)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~~~~glv~~sels~~~~~----------~~~~~~~~Gd~v~vkV~~id~~ 119 (182)
..++||+|.|+ ++-+=|+++.. ..+.+.++.+.-.--. .++++|+.||.|.+-|-.+-.
T Consensus 82 ~pEvGDvVVgRV~eVq~KRWkvd~nsk-----~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~- 155 (301)
T KOG3013|consen 82 APEVGDVVVGRVIEVQQKRWKVDLNSK-----QDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH- 155 (301)
T ss_pred CCccCCEEEEEeeeeecceeEEecccc-----cceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc-
Q ss_pred CCeEEEEEeecc
Q 030172 120 KSRITLSIKQLE 131 (182)
Q Consensus 120 ~~ki~lS~k~~~ 131 (182)
++.+.|-.+...
T Consensus 156 dGs~sLhTRS~K 167 (301)
T KOG3013|consen 156 DGSLSLHTRSLK 167 (301)
T ss_pred CCeEEEEecchh
No 239
>COG1912 Uncharacterized conserved protein [Function unknown]
Probab=28.00 E-value=87 Score=25.86 Aligned_cols=66 Identities=11% Similarity=0.057 Sum_probs=43.1
Q ss_pred EEEEEEEEEeCCCCeEEEEEeeccCCchhHHHh----------------hhcCCCCceeEeeEeeecCCeeEEecCCChh
Q 030172 108 EVRVKVIKIDREKSRITLSIKQLEEDPLLETLE----------------KVIPQDGSVISDSSSMSSSNSNTIEPLPGLG 171 (182)
Q Consensus 108 ~v~vkV~~id~~~~ki~lS~k~~~~~p~~~~~~----------------~~~~~~g~~v~G~V~~v~~~G~fV~l~~gv~ 171 (182)
.+++.|++++++-+-+.+|.--...|.|....- -..|++|....+.|..- ...+||-.++|+-
T Consensus 20 ~MkgVil~inp~~~IvDiTH~i~p~nI~~gay~L~~~~~YfP~gtV~V~VVDPGVGT~Rraivvkt-~~~yfVgPDNG~l 98 (268)
T COG1912 20 AMKGVILSINPDAKIVDITHEIPPFNIWEGAYVLYQTVPYFPEGTVFVAVVDPGVGTERRAIVVKT-NGQYFVGPDNGLL 98 (268)
T ss_pred hhhhhhhhcCCCCEEEEcccCCCccchHHhHhhHhhhcccCCCCcEEEEEECCCCCCceeEEEEEe-CCcEEEeCCCcee
Confidence 356778888886666777775444555644321 11256788887777776 6678999888874
Q ss_pred hhc
Q 030172 172 AIF 174 (182)
Q Consensus 172 gl~ 174 (182)
-++
T Consensus 99 ~~~ 101 (268)
T COG1912 99 TPV 101 (268)
T ss_pred ehh
Confidence 433
No 240
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=26.79 E-value=1.8e+02 Score=19.15 Aligned_cols=41 Identities=24% Similarity=0.275 Sum_probs=26.0
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~ 127 (182)
..-++|++--- .. +-.++.||.|.|.....|..+++|..-.
T Consensus 23 ~~~la~i~gK~----rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 23 KKRLCRIRGKM----RK-RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred CEEEEEEchhh----cc-cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 67777665421 11 2337899999999888776555554433
No 241
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=26.56 E-value=3.3e+02 Score=24.69 Aligned_cols=61 Identities=20% Similarity=0.329 Sum_probs=42.2
Q ss_pred eEe--EEEEEecCCCceeEEEEEEccCcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEe
Q 030172 66 DYG--AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (182)
Q Consensus 66 ~~G--~fV~l~~~~g~~~~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k 128 (182)
.+| +|..+...+| ++..++...++......+..+.+..||.|.|+-.=.-..++.+++...
T Consensus 75 ~~GK~~F~~i~d~~g--kiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~ 137 (502)
T COG1190 75 NMGKASFADLQDGSG--KIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVE 137 (502)
T ss_pred ccCceeEEEEecCCc--eEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEE
Confidence 444 7888875556 688888877766655555666678999999876544444666665554
No 242
>COG4110 Uncharacterized protein involved in stress response [General function prediction only]
Probab=26.33 E-value=40 Score=25.86 Aligned_cols=20 Identities=15% Similarity=0.092 Sum_probs=18.1
Q ss_pred CCeeEEecCCChhhhchhhh
Q 030172 159 SNSNTIEPLPGLGAIFEELL 178 (182)
Q Consensus 159 ~~G~fV~l~~gv~gl~~~~~ 178 (182)
+-|+|++|.+|-.|++++|=
T Consensus 53 DLG~~~~LnDGskGviQALG 72 (200)
T COG4110 53 DLGAFVELNDGSKGVIQALG 72 (200)
T ss_pred ccceEEEecCCchHHHHHHh
Confidence 57999999999999999873
No 243
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=25.67 E-value=1.1e+02 Score=17.99 Aligned_cols=23 Identities=9% Similarity=0.086 Sum_probs=18.1
Q ss_pred CceeEeeEeeecCCee-EEecCCC
Q 030172 147 GSVISDSSSMSSSNSN-TIEPLPG 169 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~-fV~l~~g 169 (182)
++.++|++..+.+.|. .|+.++|
T Consensus 12 ~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 12 DGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp SCEEEEEEEEEETTSEEEEEETTE
T ss_pred CeEEEEEEEEECCCCEEEEEECCC
Confidence 6778999999999886 4556665
No 244
>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=25.34 E-value=1.9e+02 Score=18.35 Aligned_cols=30 Identities=23% Similarity=0.323 Sum_probs=22.6
Q ss_pred EEEEEEccCcCCccccCccccccCCCEEEEEEEE
Q 030172 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (182)
Q Consensus 82 ~~glv~~sels~~~~~~~~~~~~~Gd~v~vkV~~ 115 (182)
-+.|+|++.+...-. ..++.||.|...+..
T Consensus 25 ~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 25 GDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred ccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 799999999874322 347789999987644
No 245
>TIGR00307 S8e ribosomal protein S8.e. Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not.
Probab=25.30 E-value=2.8e+02 Score=20.33 Aligned_cols=35 Identities=11% Similarity=0.235 Sum_probs=28.8
Q ss_pred CceeEeeEeeecCCeeEEecCCChhhhchhhhhcc
Q 030172 147 GSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED 181 (182)
Q Consensus 147 g~~v~G~V~~v~~~G~fV~l~~gv~gl~~~~~~~~ 181 (182)
+.++.|.|..+...=|-|.--||-+|.+...|-|+
T Consensus 93 niitKGaIIetd~g~A~VTsrPgQdG~vNavll~~ 127 (127)
T TIGR00307 93 NVITKGAIVETDIGYARVTSRPGQDGVVNGVLIEE 127 (127)
T ss_pred CcEecceEEEEeeeEEEEecCCCcCceEeEEEecC
Confidence 88899999988875577777899999998877664
No 246
>PTZ00319 NADH-cytochrome B5 reductase; Provisional
Probab=24.69 E-value=3.1e+02 Score=22.65 Aligned_cols=12 Identities=33% Similarity=0.393 Sum_probs=8.8
Q ss_pred CCCeEEEEEeec
Q 030172 119 EKSRITLSIKQL 130 (182)
Q Consensus 119 ~~~ki~lS~k~~ 130 (182)
+.+.+.+++|..
T Consensus 97 ~~~~i~~~Ik~~ 108 (300)
T PTZ00319 97 EKGYVDFLIKVY 108 (300)
T ss_pred cCCEEEEEEEEe
Confidence 457788888864
No 247
>PRK13605 endoribonuclease SymE; Provisional
Probab=24.44 E-value=92 Score=22.33 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=26.6
Q ss_pred CcCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 030172 90 EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (182)
Q Consensus 90 els~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~ 131 (182)
.|...|...+. |..|+.|.|+| ..+.|.++.....
T Consensus 41 ~LkG~WLeeAG--F~tG~~V~V~V-----~~G~LVIt~~~~~ 75 (113)
T PRK13605 41 TLKGQWLEAAG--FATGTAVDVRV-----MEGCIVLTAQPPA 75 (113)
T ss_pred eECchhHHhhC--CCCCCeEEEEE-----eCCEEEEEeCCCC
Confidence 34555666555 99999999988 5899999988653
No 248
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=24.29 E-value=72 Score=21.06 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=19.9
Q ss_pred CCCCCccHHHhhhhc-CCCeEEEEE
Q 030172 7 CKEPQKSIHEIAKGL-TGSIISVKV 30 (182)
Q Consensus 7 ~p~~e~~~~~~~~~~-vG~~v~~~v 30 (182)
||+|.+..++.+..+ .|+.+++..
T Consensus 15 CP~Pv~~~kk~l~~m~~Ge~LeV~~ 39 (78)
T COG0425 15 CPGPVVETKKALAKLKPGEILEVIA 39 (78)
T ss_pred CCccHHHHHHHHHcCCCCCEEEEEe
Confidence 999999999877776 788887665
No 249
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=23.73 E-value=1.4e+02 Score=19.12 Aligned_cols=13 Identities=15% Similarity=-0.013 Sum_probs=10.0
Q ss_pred CeeEEecCCChhh
Q 030172 160 NSNTIEPLPGLGA 172 (182)
Q Consensus 160 ~G~fV~l~~gv~g 172 (182)
.|+.|++.+|-.-
T Consensus 43 iG~vv~~~ng~~~ 55 (64)
T PF11061_consen 43 IGVVVEFSNGSRT 55 (64)
T ss_pred EEEEEEecCCcee
Confidence 6899999887543
No 250
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=23.34 E-value=1.9e+02 Score=21.60 Aligned_cols=22 Identities=14% Similarity=0.169 Sum_probs=16.5
Q ss_pred hcCCCCCCEEEEE-----eEeEEEEEe
Q 030172 53 SSRVNVEDIFVGR-----DYGAFIHLR 74 (182)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~ 74 (182)
+.-++.||+|.|+ +.-++|..+
T Consensus 76 ykyYk~GDvV~GtLnIedESni~V~Cg 102 (160)
T PF03293_consen 76 YKYYKVGDVVRGTLNIEDESNITVQCG 102 (160)
T ss_pred EEEEeeCCEEEEEEEecccCceEEEcC
Confidence 3458899999999 566777653
No 251
>PF11580 DUF3239: Protein of unknown function (DUF3239); InterPro: IPR021632 This entry contains possible membrane proteins, however this cannot be confirmed. Currently they have no known function. ; PDB: 3C8I_B.
Probab=23.21 E-value=2e+02 Score=21.11 Aligned_cols=38 Identities=16% Similarity=0.362 Sum_probs=19.0
Q ss_pred ccCccccccCCCEEEEEEEEEeCCCCeEEEEEeeccCCc
Q 030172 96 IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134 (182)
Q Consensus 96 ~~~~~~~~~~Gd~v~vkV~~id~~~~ki~lS~k~~~~~p 134 (182)
+.++.+.|.-|+.+-+.|.++++ +.-..|++.....++
T Consensus 4 vg~~~~~Y~~~~LvPavV~ev~p-r~v~llalvd~~~d~ 41 (128)
T PF11580_consen 4 VGSAQSLYDNGPLVPAVVAEVNP-RDVVLLALVDTAVDP 41 (128)
T ss_dssp ------------EEEEEEEEE-S-S-EEEEEEEE-BSST
T ss_pred ccchhhhhhcCCCCcEEEEEecC-cceehhhhhhhcCCC
Confidence 45677889999999999999997 788888887665554
No 252
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=22.72 E-value=1.9e+02 Score=22.25 Aligned_cols=29 Identities=31% Similarity=0.526 Sum_probs=23.4
Q ss_pred ccccCCCEEEE----------EEEEEeCCCCeEEEEEee
Q 030172 101 DILNEGDEVRV----------KVIKIDREKSRITLSIKQ 129 (182)
Q Consensus 101 ~~~~~Gd~v~v----------kV~~id~~~~ki~lS~k~ 129 (182)
..|.+||.|++ +|..+|.+++++.+.+-.
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~i 160 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSI 160 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEE
Confidence 45889999875 799999988888877754
No 253
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=22.65 E-value=70 Score=31.89 Aligned_cols=36 Identities=6% Similarity=0.049 Sum_probs=28.4
Q ss_pred hhcCCCCceeEeeEeeecCCe---eEEecCCChhhhchhhh
Q 030172 141 KVIPQDGSVISDSSSMSSSNS---NTIEPLPGLGAIFEELL 178 (182)
Q Consensus 141 ~~~~~~g~~v~G~V~~v~~~G---~fV~l~~gv~gl~~~~~ 178 (182)
++.. |..+.++|++++..- +-|.+++|+.|+|++.-
T Consensus 982 t~~~--g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~ 1020 (1299)
T KOG1856|consen 982 TFYE--GAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKN 1020 (1299)
T ss_pred Hhcc--CceEEEeeeEEEecccceeEEEecCCCceeeeccc
Confidence 4444 899999999998744 45689999999998653
No 254
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=21.96 E-value=2.6e+02 Score=18.72 Aligned_cols=39 Identities=8% Similarity=0.189 Sum_probs=31.7
Q ss_pred EEEeCCCCEEEEEechhHHhhhhcCCCCCCEEEEEeEeE
Q 030172 31 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGA 69 (182)
Q Consensus 31 ~~~d~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~~~G~ 69 (182)
+-+|++..++.++.+......+...+++|.++.=.+|.+
T Consensus 3 vL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V 41 (95)
T PF02721_consen 3 VLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTV 41 (95)
T ss_pred EEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEE
Confidence 457888899999998887778888999999988666643
No 255
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=21.43 E-value=3.5e+02 Score=20.80 Aligned_cols=56 Identities=11% Similarity=0.194 Sum_probs=31.5
Q ss_pred ccCCCEEEEEEEE----------EeCCCCeEEEEEeeccCCchhHHH-hhhcCCCCceeEeeEeeecCCeeEE
Q 030172 103 LNEGDEVRVKVIK----------IDREKSRITLSIKQLEEDPLLETL-EKVIPQDGSVISDSSSMSSSNSNTI 164 (182)
Q Consensus 103 ~~~Gd~v~vkV~~----------id~~~~ki~lS~k~~~~~p~~~~~-~~~~~~~g~~v~G~V~~v~~~G~fV 164 (182)
+++||.+.+++-. .+.+.+.+.+.+|......+.... +..++ |+.+ .|. .++|.|.
T Consensus 26 ~~pGQ~v~l~~~~~~~r~ySi~s~~~~~~~l~~~vk~~~~G~~s~~l~~~l~~--G~~v--~i~--gP~G~~~ 92 (224)
T cd06189 26 FLAGQYLDLLLDDGDKRPFSIASAPHEDGEIELHIRAVPGGSFSDYVFEELKE--NGLV--RIE--GPLGDFF 92 (224)
T ss_pred cCCCCEEEEEcCCCCceeeecccCCCCCCeEEEEEEecCCCccHHHHHHhccC--CCEE--EEe--cCCccEE
Confidence 6677777666421 122357899999876544554433 33555 7755 233 2566554
No 256
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=21.31 E-value=90 Score=25.96 Aligned_cols=38 Identities=18% Similarity=0.184 Sum_probs=28.9
Q ss_pred CCCccHHH--hhhhc--CCCeEEEEEEEEeCCCCEEEEEech
Q 030172 9 EPQKSIHE--IAKGL--TGSIISVKVIQANEEMKKLVFSEKD 46 (182)
Q Consensus 9 ~~e~~~~~--~~~~~--vG~~v~~~v~~~d~~~~~i~lS~k~ 46 (182)
.+|+|-++ ..+.+ +|..=.|.|+.+|+++|.+.||.++
T Consensus 48 lsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 48 LSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred hhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence 34555553 23333 8999999999999999999999764
No 257
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=21.07 E-value=2.2e+02 Score=17.67 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=10.4
Q ss_pred EEEEEEEeCCCCeEEE
Q 030172 110 RVKVIKIDREKSRITL 125 (182)
Q Consensus 110 ~vkV~~id~~~~ki~l 125 (182)
+++|+++|..+++-.+
T Consensus 24 e~kV~~~d~~~~~y~V 39 (55)
T PF09465_consen 24 EGKVLSYDSKSDRYTV 39 (55)
T ss_dssp EEEEEEEETTTTEEEE
T ss_pred EEEEEEecccCceEEE
Confidence 5678888875555443
No 258
>cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.
Probab=20.32 E-value=3.3e+02 Score=20.88 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=16.1
Q ss_pred CCeEEEEEeeccCCchhHHHhhhcCCCCcee
Q 030172 120 KSRITLSIKQLEEDPLLETLEKVIPQDGSVI 150 (182)
Q Consensus 120 ~~ki~lS~k~~~~~p~~~~~~~~~~~~g~~v 150 (182)
.+.+.+.+|.....+....+.+.++ |+.+
T Consensus 59 ~~~~~~~v~~~~~G~~s~~l~~~~~--G~~v 87 (234)
T cd06183 59 KGYFDLLIKIYPGGKMSQYLHSLKP--GDTV 87 (234)
T ss_pred CCEEEEEEEECCCCcchhHHhcCCC--CCEE
Confidence 4567888876533334444444445 6655
Done!