Query 002487
Match_columns 916
No_of_seqs 561 out of 4329
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 00:55:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002487.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002487hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00207 polyribonucleotide nu 100.0 7E-181 2E-185 1604.5 88.7 820 23-845 10-835 (891)
2 TIGR02696 pppGpp_PNP guanosine 100.0 5E-168 1E-172 1468.6 79.0 686 89-831 7-718 (719)
3 COG1185 Pnp Polyribonucleotide 100.0 3E-169 6E-174 1443.3 61.6 690 87-836 2-691 (692)
4 KOG1067 Predicted RNA-binding 100.0 8E-159 2E-163 1308.9 54.2 735 46-845 4-749 (760)
5 PRK11824 polynucleotide phosph 100.0 6E-152 1E-156 1362.7 82.2 692 87-836 2-693 (693)
6 TIGR03591 polynuc_phos polyrib 100.0 7E-152 2E-156 1359.0 78.6 681 97-830 3-684 (684)
7 TIGR02065 ECX1 archaeal exosom 100.0 1.9E-40 4.1E-45 352.1 24.8 224 442-684 2-228 (230)
8 PRK03983 exosome complex exonu 100.0 3.4E-39 7.3E-44 345.5 25.8 224 442-684 8-234 (244)
9 PRK00173 rph ribonuclease PH; 100.0 2.8E-36 6.1E-41 321.7 25.2 220 448-683 1-237 (238)
10 PLN00207 polyribonucleotide nu 100.0 2.7E-36 5.9E-41 362.5 26.7 219 97-319 447-683 (891)
11 COG0689 Rph RNase PH [Translat 100.0 2.5E-36 5.5E-41 314.8 22.7 220 444-682 4-229 (230)
12 KOG1068 Exosomal 3'-5' exoribo 100.0 4.5E-37 9.7E-42 318.6 16.8 224 443-684 8-234 (245)
13 TIGR02065 ECX1 archaeal exosom 100.0 6.2E-36 1.3E-40 317.6 22.4 204 98-311 18-229 (230)
14 TIGR01966 RNasePH ribonuclease 100.0 2.6E-35 5.7E-40 313.9 25.2 218 449-682 1-235 (236)
15 PRK04282 exosome complex RNA-b 100.0 1.2E-33 2.5E-38 307.3 28.3 234 431-683 8-270 (271)
16 PRK00173 rph ribonuclease PH; 100.0 3E-33 6.4E-38 298.6 22.1 205 98-309 11-237 (238)
17 PRK03983 exosome complex exonu 100.0 4E-33 8.7E-38 298.6 22.7 210 98-313 24-237 (244)
18 TIGR03591 polynuc_phos polyrib 100.0 2.9E-32 6.3E-37 328.0 24.5 219 97-320 319-550 (684)
19 TIGR01966 RNasePH ribonuclease 100.0 6.3E-32 1.4E-36 288.0 22.1 204 98-308 10-235 (236)
20 PRK11824 polynucleotide phosph 100.0 1.3E-31 2.8E-36 323.1 23.5 212 97-313 323-546 (693)
21 COG0689 Rph RNase PH [Translat 100.0 1E-30 2.3E-35 272.8 19.3 201 97-308 17-229 (230)
22 COG2123 RNase PH-related exori 100.0 6.1E-29 1.3E-33 261.7 26.2 232 433-683 9-271 (272)
23 KOG1069 Exosomal 3'-5' exoribo 100.0 6.3E-29 1.4E-33 249.2 15.5 201 457-684 4-210 (217)
24 TIGR02696 pppGpp_PNP guanosine 100.0 1.8E-28 3.9E-33 290.1 20.0 213 98-319 345-576 (719)
25 PRK04282 exosome complex RNA-b 99.9 3.1E-26 6.7E-31 249.1 23.2 203 98-309 34-270 (271)
26 COG0539 RpsA Ribosomal protein 99.9 2.9E-27 6.3E-32 272.1 11.6 171 726-901 155-352 (541)
27 COG0539 RpsA Ribosomal protein 99.9 4.3E-27 9.4E-32 270.7 9.9 247 643-904 155-445 (541)
28 KOG1068 Exosomal 3'-5' exoribo 99.9 4.3E-26 9.3E-31 237.1 15.3 207 98-313 23-237 (245)
29 KOG1069 Exosomal 3'-5' exoribo 99.9 1.1E-25 2.4E-30 225.9 14.9 192 98-310 5-210 (217)
30 KOG1614 Exosomal 3'-5' exoribo 99.9 1.3E-22 2.9E-27 208.5 21.0 228 437-686 12-273 (291)
31 KOG1613 Exosomal 3'-5' exoribo 99.9 6.3E-23 1.4E-27 210.3 17.1 241 429-679 17-297 (298)
32 PF01138 RNase_PH: 3' exoribon 99.9 8.8E-23 1.9E-27 198.1 15.7 130 457-591 1-132 (132)
33 COG1185 Pnp Polyribonucleotide 99.9 5.5E-23 1.2E-27 238.2 12.1 354 459-836 14-381 (692)
34 COG2123 RNase PH-related exori 99.9 1.3E-21 2.8E-26 206.5 20.8 193 99-309 34-271 (272)
35 PRK12269 bifunctional cytidyla 99.9 2.5E-22 5.3E-27 245.5 11.6 191 695-897 519-737 (863)
36 PRK07899 rpsA 30S ribosomal pr 99.8 3.5E-21 7.6E-26 223.3 12.9 170 725-898 170-365 (486)
37 PRK13806 rpsA 30S ribosomal pr 99.8 2E-21 4.3E-26 227.5 10.5 168 724-898 253-451 (491)
38 KOG1067 Predicted RNA-binding 99.8 5.6E-21 1.2E-25 214.2 12.4 203 98-313 368-589 (760)
39 PRK12269 bifunctional cytidyla 99.8 4.2E-20 9E-25 226.1 15.3 160 734-897 465-650 (863)
40 PRK13806 rpsA 30S ribosomal pr 99.8 8.4E-20 1.8E-24 213.9 13.8 169 726-897 165-364 (491)
41 KOG1612 Exosomal 3'-5' exoribo 99.8 1.2E-17 2.6E-22 173.2 23.8 225 444-684 17-276 (288)
42 PRK06299 rpsA 30S ribosomal pr 99.8 1.5E-18 3.2E-23 207.3 12.7 167 726-896 164-357 (565)
43 PRK06676 rpsA 30S ribosomal pr 99.8 3.6E-18 7.9E-23 195.1 14.3 169 728-900 157-351 (390)
44 COG1098 VacB Predicted RNA bin 99.8 7.1E-19 1.5E-23 164.6 5.5 82 760-842 2-83 (129)
45 PRK06299 rpsA 30S ribosomal pr 99.7 5.7E-18 1.2E-22 202.3 11.5 170 726-902 340-536 (565)
46 PF01138 RNase_PH: 3' exoribon 99.7 9.9E-18 2.1E-22 162.8 9.7 125 98-229 2-132 (132)
47 PRK00087 4-hydroxy-3-methylbut 99.7 2.3E-17 4.9E-22 199.5 13.2 173 726-902 439-638 (647)
48 TIGR00717 rpsA ribosomal prote 99.7 2.1E-17 4.5E-22 195.5 12.6 165 725-896 325-516 (516)
49 TIGR00717 rpsA ribosomal prote 99.7 3.3E-17 7.1E-22 193.7 12.1 166 725-897 238-431 (516)
50 PTZ00248 eukaryotic translatio 99.7 6.9E-17 1.5E-21 176.9 8.5 98 761-860 15-115 (319)
51 PRK07400 30S ribosomal protein 99.6 1.2E-15 2.7E-20 169.4 12.8 157 728-898 86-267 (318)
52 PRK07899 rpsA 30S ribosomal pr 99.6 1.3E-15 2.7E-20 177.2 7.7 161 726-896 88-277 (486)
53 KOG1614 Exosomal 3'-5' exoribo 99.6 1.1E-13 2.3E-18 143.3 19.1 205 99-317 33-278 (291)
54 PRK08582 hypothetical protein; 99.6 1.1E-14 2.3E-19 143.4 10.7 83 760-843 2-84 (139)
55 PRK07400 30S ribosomal protein 99.6 9.4E-15 2E-19 162.4 10.7 141 755-899 23-186 (318)
56 PRK06676 rpsA 30S ribosomal pr 99.5 2.1E-14 4.6E-19 164.3 9.9 161 728-897 73-262 (390)
57 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 3.1E-14 6.6E-19 124.7 8.1 71 761-833 1-72 (72)
58 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 5.4E-14 1.2E-18 123.9 8.0 70 761-831 1-74 (74)
59 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 1.1E-13 2.3E-18 121.4 9.3 71 761-832 1-72 (73)
60 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 3.8E-13 8.2E-18 117.5 8.2 68 764-832 1-71 (71)
61 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 4.5E-13 9.7E-18 116.0 8.3 69 764-833 1-70 (70)
62 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 4.9E-13 1.1E-17 120.0 8.1 74 758-832 9-83 (83)
63 cd04452 S1_IF2_alpha S1_IF2_al 99.4 8.2E-13 1.8E-17 116.0 9.2 73 761-834 1-76 (76)
64 PF00575 S1: S1 RNA binding do 99.4 9.8E-13 2.1E-17 115.0 9.6 73 760-833 1-74 (74)
65 PRK05807 hypothetical protein; 99.4 1.1E-12 2.3E-17 128.9 10.7 75 760-836 2-76 (136)
66 cd05684 S1_DHX8_helicase S1_DH 99.4 1.1E-12 2.3E-17 116.7 9.7 74 764-839 1-78 (79)
67 PRK07252 hypothetical protein; 99.4 1.4E-12 3E-17 125.4 10.9 77 762-839 2-79 (120)
68 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 1.4E-12 3E-17 113.9 9.6 71 762-833 2-73 (73)
69 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 9.3E-13 2E-17 115.7 8.4 69 764-833 1-72 (73)
70 PRK00087 4-hydroxy-3-methylbut 99.4 5.5E-13 1.2E-17 161.6 9.1 161 728-897 357-547 (647)
71 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 1.2E-12 2.5E-17 113.3 8.1 68 764-832 1-69 (69)
72 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 1.6E-12 3.5E-17 112.1 7.5 67 764-831 1-68 (68)
73 PHA02945 interferon resistance 99.4 3.1E-12 6.6E-17 113.9 9.3 75 759-837 7-86 (88)
74 cd05691 S1_RPS1_repeat_ec6 S1_ 99.3 4.4E-12 9.5E-17 110.3 9.2 71 764-835 1-72 (73)
75 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 2.4E-12 5.2E-17 110.9 7.4 67 764-831 1-69 (69)
76 PRK08059 general stress protei 99.3 5.8E-12 1.3E-16 121.7 9.9 80 759-839 3-83 (123)
77 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 7.2E-12 1.6E-16 107.0 8.8 69 764-833 1-69 (69)
78 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 1E-11 2.2E-16 109.4 9.8 70 761-837 2-73 (74)
79 cd05708 S1_Rrp5_repeat_sc12 S1 99.3 8.7E-12 1.9E-16 109.4 9.3 73 762-835 1-75 (77)
80 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 7.3E-12 1.6E-16 109.1 8.2 70 761-831 1-72 (72)
81 COG1093 SUI2 Translation initi 99.3 2.2E-12 4.8E-17 135.7 5.4 78 760-838 8-88 (269)
82 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 1.7E-11 3.6E-16 106.3 8.5 69 764-833 1-70 (70)
83 PF03726 PNPase: Polyribonucle 99.2 5.5E-11 1.2E-15 107.0 10.1 83 326-454 1-83 (83)
84 cd05685 S1_Tex S1_Tex: The C-t 99.2 2.4E-11 5.3E-16 103.5 7.2 67 764-831 1-68 (68)
85 cd04472 S1_PNPase S1_PNPase: P 99.2 4E-11 8.6E-16 102.6 8.4 68 764-832 1-68 (68)
86 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 3.6E-11 7.8E-16 108.5 8.3 75 760-835 3-81 (86)
87 cd04453 S1_RNase_E S1_RNase_E: 99.2 5.7E-11 1.2E-15 108.2 8.8 72 760-832 4-81 (88)
88 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.1 1.1E-10 2.4E-15 100.5 7.8 65 764-831 1-66 (66)
89 PRK03987 translation initiatio 99.1 1.2E-10 2.6E-15 126.1 9.5 79 760-839 5-86 (262)
90 COG2183 Tex Transcriptional ac 99.1 8.1E-11 1.8E-15 140.0 8.9 114 712-837 618-732 (780)
91 cd04465 S1_RPS1_repeat_ec2_hs2 99.1 1.7E-10 3.7E-15 99.3 8.3 66 764-833 1-67 (67)
92 cd04471 S1_RNase_R S1_RNase_R: 99.1 2.3E-10 4.9E-15 102.0 9.1 69 763-832 1-82 (83)
93 cd05688 S1_RPS1_repeat_ec3 S1_ 99.1 1.9E-10 4.1E-15 98.3 7.8 67 763-831 1-68 (68)
94 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 1.5E-10 3.3E-15 107.9 7.1 74 761-835 1-97 (100)
95 KOG1612 Exosomal 3'-5' exoribo 99.1 1.6E-08 3.6E-13 106.0 20.9 200 98-308 31-274 (288)
96 smart00316 S1 Ribosomal protei 99.1 5.9E-10 1.3E-14 95.1 8.6 71 762-833 1-72 (72)
97 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 1.3E-09 2.9E-14 97.5 8.7 74 760-834 3-76 (82)
98 cd04473 S1_RecJ_like S1_RecJ_l 99.0 2.5E-09 5.5E-14 94.9 9.5 65 759-832 12-76 (77)
99 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 1.7E-09 3.7E-14 94.0 7.5 62 764-826 1-64 (70)
100 cd02393 PNPase_KH Polynucleoti 98.9 3.4E-09 7.3E-14 90.0 6.3 60 694-754 1-60 (61)
101 cd00164 S1_like S1_like: Ribos 98.9 4.5E-09 9.7E-14 87.9 6.6 64 767-831 1-65 (65)
102 KOG1070 rRNA processing protei 98.8 5.8E-09 1.3E-13 128.4 9.4 143 758-901 1157-1328(1710)
103 KOG1613 Exosomal 3'-5' exoribo 98.8 2.2E-08 4.7E-13 104.2 11.8 195 99-304 47-296 (298)
104 PF03725 RNase_PH_C: 3' exorib 98.8 8.5E-09 1.8E-13 89.1 7.3 65 232-296 1-68 (68)
105 cd04460 S1_RpoE S1_RpoE: RpoE, 98.8 2.1E-08 4.5E-13 93.2 8.4 77 765-843 1-94 (99)
106 TIGR02063 RNase_R ribonuclease 98.7 3.1E-08 6.6E-13 121.9 11.0 81 751-832 615-708 (709)
107 PRK09521 exosome complex RNA-b 98.7 1.8E-08 3.9E-13 104.6 7.6 78 754-834 55-142 (189)
108 PRK13763 putative RNA-processi 98.7 1E-08 2.2E-13 105.6 5.1 84 694-779 2-96 (180)
109 PRK04163 exosome complex RNA-b 98.7 4.2E-08 9.1E-13 105.2 8.7 74 760-834 60-137 (235)
110 TIGR03665 arCOG04150 arCOG0415 98.7 1.6E-08 3.4E-13 103.5 3.9 79 699-779 2-90 (172)
111 PRK08563 DNA-directed RNA poly 98.6 8.4E-08 1.8E-12 99.4 6.9 103 729-835 49-168 (187)
112 PRK11642 exoribonuclease R; Pr 98.6 3.4E-07 7.3E-12 113.5 13.0 79 757-836 637-728 (813)
113 TIGR00358 3_prime_RNase VacB a 98.6 2.2E-07 4.9E-12 113.2 10.7 81 751-832 560-653 (654)
114 TIGR00448 rpoE DNA-directed RN 98.5 2.5E-07 5.4E-12 95.3 8.8 80 756-837 74-170 (179)
115 cd04455 S1_NusA S1_NusA: N-uti 98.5 4.2E-07 9.2E-12 78.5 7.9 63 762-832 2-67 (67)
116 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.4 7E-07 1.5E-11 82.2 7.7 74 760-834 3-86 (92)
117 COG1095 RPB7 DNA-directed RNA 98.3 7.3E-07 1.6E-11 90.6 6.4 86 755-842 73-177 (183)
118 KOG1070 rRNA processing protei 98.3 1.5E-06 3.3E-11 107.9 9.9 140 759-899 505-672 (1710)
119 PHA02858 EIF2a-like PKR inhibi 98.2 4E-06 8.6E-11 74.5 6.4 71 759-832 12-85 (86)
120 PRK09202 nusA transcription el 98.2 1.9E-06 4.1E-11 100.7 5.5 71 756-834 125-200 (470)
121 cd02395 SF1_like-KH Splicing f 98.1 7.1E-06 1.5E-10 79.1 6.3 61 703-764 14-99 (120)
122 PF03725 RNase_PH_C: 3' exorib 98.0 1.2E-05 2.5E-10 69.5 6.5 66 594-670 1-68 (68)
123 PRK05054 exoribonuclease II; P 97.8 6.1E-05 1.3E-09 91.9 10.5 79 753-832 549-643 (644)
124 KOG2916 Translation initiation 97.8 1.4E-05 3.1E-10 84.6 3.0 83 760-843 13-98 (304)
125 COG1097 RRP4 RNA-binding prote 97.7 0.00019 4.1E-09 76.1 9.4 89 760-857 61-153 (239)
126 TIGR00757 RNaseEG ribonuclease 97.6 7.4E-05 1.6E-09 86.4 6.8 61 761-822 23-97 (414)
127 TIGR01953 NusA transcription t 97.6 9.9E-05 2.1E-09 83.3 7.3 73 755-835 121-199 (341)
128 cd02394 vigilin_like_KH K homo 97.6 8.6E-05 1.9E-09 62.9 4.7 56 697-754 2-61 (62)
129 PRK12327 nusA transcription el 97.5 0.00016 3.5E-09 82.0 7.2 69 757-833 126-199 (362)
130 COG0557 VacB Exoribonuclease R 97.5 0.00027 5.8E-09 87.4 9.4 80 753-833 612-704 (706)
131 TIGR02062 RNase_B exoribonucle 97.5 0.00031 6.8E-09 85.7 9.4 79 752-831 544-638 (639)
132 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.5 0.00057 1.2E-08 62.2 8.5 74 760-835 3-76 (86)
133 COG1107 Archaea-specific RecJ- 97.4 0.00028 6.1E-09 82.1 7.0 71 759-836 118-189 (715)
134 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.3 0.00086 1.9E-08 61.3 7.6 60 763-824 1-71 (88)
135 PRK04163 exosome complex RNA-b 97.3 0.00024 5.2E-09 76.4 4.3 62 698-760 148-209 (235)
136 PF10447 EXOSC1: Exosome compo 97.2 0.0009 1.9E-08 60.4 6.2 61 761-822 2-82 (82)
137 PF00013 KH_1: KH domain syndr 97.1 0.00034 7.3E-09 58.8 3.2 56 697-754 2-60 (60)
138 PTZ00162 DNA-directed RNA poly 97.1 0.0013 2.9E-08 67.7 7.5 78 755-834 73-165 (176)
139 COG1096 Predicted RNA-binding 97.0 0.0016 3.4E-08 66.7 7.4 73 758-833 59-141 (188)
140 COG2996 Predicted RNA-bindinin 97.0 0.0022 4.8E-08 69.0 8.0 75 753-836 142-219 (287)
141 cd00105 KH-I K homology RNA-bi 97.0 0.0014 3E-08 55.3 5.3 55 697-753 2-62 (64)
142 cd05705 S1_Rrp5_repeat_hs14 S1 96.8 0.0043 9.3E-08 54.8 7.6 67 809-894 1-74 (74)
143 COG1098 VacB Predicted RNA bin 96.7 0.0009 1.9E-08 64.0 2.3 79 808-904 2-82 (129)
144 PF13509 S1_2: S1 domain; PDB: 96.6 0.0097 2.1E-07 50.7 7.7 61 763-833 1-61 (61)
145 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.5 0.0064 1.4E-07 53.4 6.3 66 764-833 1-72 (72)
146 cd05703 S1_Rrp5_repeat_hs12_sc 96.4 0.0036 7.8E-08 55.1 4.3 66 812-896 1-72 (73)
147 smart00322 KH K homology RNA-b 96.4 0.01 2.2E-07 49.7 6.6 60 695-756 3-66 (69)
148 cd05695 S1_Rrp5_repeat_hs3 S1_ 96.4 0.013 2.9E-07 50.4 7.2 64 812-894 1-66 (66)
149 COG2996 Predicted RNA-bindinin 96.3 0.023 5E-07 61.4 10.1 153 729-896 44-216 (287)
150 PRK10811 rne ribonuclease E; R 96.1 0.01 2.2E-07 73.6 7.2 61 762-823 37-108 (1068)
151 PTZ00248 eukaryotic translatio 96.0 0.00015 3.3E-09 80.5 -8.4 93 724-822 70-173 (319)
152 PRK11712 ribonuclease G; Provi 95.9 0.011 2.5E-07 69.8 6.1 62 761-823 36-111 (489)
153 cd02396 PCBP_like_KH K homolog 95.8 0.017 3.6E-07 49.6 5.2 54 698-753 3-63 (65)
154 PF00575 S1: S1 RNA binding do 95.5 0.0091 2E-07 52.0 2.3 69 809-896 2-74 (74)
155 cd04461 S1_Rrp5_repeat_hs8_sc7 95.2 0.017 3.6E-07 51.8 3.3 70 807-895 10-83 (83)
156 PRK12328 nusA transcription el 95.1 0.055 1.2E-06 61.6 7.9 64 762-833 137-205 (374)
157 TIGR03665 arCOG04150 arCOG0415 95.1 0.032 6.9E-07 57.4 5.5 60 704-766 98-157 (172)
158 cd05708 S1_Rrp5_repeat_sc12 S1 95.1 0.015 3.2E-07 50.7 2.6 72 810-899 1-76 (77)
159 cd05706 S1_Rrp5_repeat_sc10 S1 94.7 0.042 9.1E-07 47.8 4.3 68 809-895 1-72 (73)
160 cd05696 S1_Rrp5_repeat_hs4 S1_ 94.5 0.11 2.4E-06 45.4 6.5 32 864-895 40-71 (71)
161 KOG1856 Transcription elongati 94.4 0.047 1E-06 68.4 5.3 74 761-835 983-1060(1299)
162 cd05689 S1_RPS1_repeat_ec4 S1_ 94.4 0.061 1.3E-06 46.6 4.7 71 809-894 1-72 (72)
163 cd05690 S1_RPS1_repeat_ec5 S1_ 94.4 0.046 1E-06 46.7 3.8 32 863-894 38-69 (69)
164 cd05698 S1_Rrp5_repeat_hs6_sc5 94.4 0.034 7.3E-07 47.9 3.0 66 812-896 1-70 (70)
165 cd05687 S1_RPS1_repeat_ec1_hs1 94.3 0.036 7.9E-07 47.7 3.0 66 812-896 1-70 (70)
166 cd05694 S1_Rrp5_repeat_hs2_sc2 94.3 0.043 9.4E-07 48.5 3.5 67 809-896 2-69 (74)
167 cd05704 S1_Rrp5_repeat_hs13 S1 94.3 0.099 2.2E-06 45.7 5.7 67 809-896 1-72 (72)
168 PRK13763 putative RNA-processi 94.1 0.04 8.6E-07 57.1 3.4 60 705-767 105-164 (180)
169 cd05707 S1_Rrp5_repeat_sc11 S1 93.9 0.059 1.3E-06 46.3 3.5 64 812-894 1-68 (68)
170 cd05697 S1_Rrp5_repeat_hs5 S1_ 93.9 0.047 1E-06 47.0 2.9 65 812-895 1-69 (69)
171 PRK08582 hypothetical protein; 93.9 0.058 1.3E-06 53.6 3.8 71 808-898 2-76 (139)
172 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 93.7 0.094 2E-06 47.2 4.5 71 809-899 4-82 (86)
173 cd04454 S1_Rrp4_like S1_Rrp4_l 93.7 0.075 1.6E-06 47.5 3.8 69 810-898 5-77 (82)
174 PRK12329 nusA transcription el 93.5 0.21 4.6E-06 58.0 8.0 66 761-833 150-224 (449)
175 cd05686 S1_pNO40 S1_pNO40: pNO 93.4 0.075 1.6E-06 46.5 3.3 67 810-895 2-72 (73)
176 PRK07252 hypothetical protein; 93.4 0.08 1.7E-06 51.3 3.8 70 810-898 2-75 (120)
177 cd05691 S1_RPS1_repeat_ec6 S1_ 93.3 0.052 1.1E-06 46.8 2.2 67 812-897 1-71 (73)
178 KOG1676 K-homology type RNA bi 93.3 0.29 6.2E-06 58.2 8.7 67 696-764 231-304 (600)
179 PF13014 KH_3: KH domain 93.2 0.071 1.5E-06 41.9 2.6 27 706-733 2-28 (43)
180 cd05693 S1_Rrp5_repeat_hs1_sc1 93.0 0.16 3.4E-06 47.7 5.0 31 866-896 62-95 (100)
181 PRK05807 hypothetical protein; 93.0 0.1 2.2E-06 51.6 4.0 70 808-898 2-75 (136)
182 KOG2191 RNA-binding protein NO 92.8 0.46 1E-05 52.7 8.8 114 638-767 83-212 (402)
183 cd04452 S1_IF2_alpha S1_IF2_al 92.7 0.16 3.5E-06 44.2 4.4 71 810-897 2-76 (76)
184 cd05688 S1_RPS1_repeat_ec3 S1_ 92.4 0.13 2.8E-06 43.5 3.4 64 811-894 1-68 (68)
185 COG1530 CafA Ribonucleases G a 92.1 0.16 3.4E-06 60.5 4.7 62 761-824 35-103 (487)
186 PRK08059 general stress protei 92.0 0.11 2.4E-06 50.4 2.8 72 808-898 4-79 (123)
187 cd05685 S1_Tex S1_Tex: The C-t 91.7 0.16 3.4E-06 42.8 3.0 29 866-894 40-68 (68)
188 COG2183 Tex Transcriptional ac 91.5 0.12 2.6E-06 63.3 2.9 55 846-900 654-732 (780)
189 PRK09202 nusA transcription el 91.4 0.023 4.9E-07 67.0 -3.3 104 790-900 73-203 (470)
190 PRK09521 exosome complex RNA-b 91.4 0.43 9.2E-06 49.8 6.5 110 777-898 23-143 (189)
191 PRK12442 translation initiatio 90.8 0.93 2E-05 41.3 7.1 63 766-833 8-72 (87)
192 KOG0119 Splicing factor 1/bran 90.8 0.93 2E-05 52.8 8.8 89 670-760 111-230 (554)
193 TIGR00008 infA translation ini 89.4 1.4 3E-05 38.6 6.8 59 766-829 6-66 (68)
194 COG1094 Predicted RNA-binding 89.3 0.57 1.2E-05 48.8 5.1 72 693-765 6-82 (194)
195 smart00316 S1 Ribosomal protei 89.0 0.27 5.8E-06 41.3 2.1 67 810-895 1-71 (72)
196 KOG3409 Exosomal 3'-5' exoribo 88.1 1.6 3.4E-05 44.6 7.1 72 761-833 66-147 (193)
197 cd04472 S1_PNPase S1_PNPase: P 87.8 0.58 1.3E-05 39.5 3.5 30 865-895 39-68 (68)
198 KOG3298 DNA-directed RNA polym 87.8 1.4 3.1E-05 44.5 6.5 66 756-823 74-150 (170)
199 cd05692 S1_RPS1_repeat_hs4 S1_ 87.1 0.49 1.1E-05 39.8 2.6 31 865-896 39-69 (69)
200 cd04473 S1_RecJ_like S1_RecJ_l 87.0 0.77 1.7E-05 40.7 3.9 64 807-894 12-75 (77)
201 cd04465 S1_RPS1_repeat_ec2_hs2 85.6 1.5 3.1E-05 37.5 4.8 25 872-896 43-67 (67)
202 PHA02945 interferon resistance 84.9 0.77 1.7E-05 41.9 2.8 29 868-897 55-83 (88)
203 PRK03987 translation initiatio 84.7 0.79 1.7E-05 50.4 3.4 74 807-897 4-81 (262)
204 KOG1676 K-homology type RNA bi 84.7 2.4 5.1E-05 50.8 7.4 60 696-757 319-386 (600)
205 PF00313 CSD: 'Cold-shock' DNA 83.4 9.2 0.0002 32.6 8.8 56 767-828 1-59 (66)
206 cd05702 S1_Rrp5_repeat_hs11_sc 83.4 1.7 3.7E-05 37.5 4.3 63 812-893 1-69 (70)
207 cd05684 S1_DHX8_helicase S1_DH 83.3 1.5 3.2E-05 38.7 4.0 31 865-897 43-73 (79)
208 cd04455 S1_NusA S1_NusA: N-uti 81.8 3.4 7.5E-05 35.5 5.5 58 810-889 2-59 (67)
209 PRK04012 translation initiatio 81.5 5 0.00011 37.8 6.8 66 760-832 17-84 (100)
210 TIGR01953 NusA transcription t 79.1 0.21 4.7E-06 56.7 -3.7 92 806-899 81-200 (341)
211 PF08292 RNA_pol_Rbc25: RNA po 79.0 8.5 0.00018 37.6 7.8 62 762-824 2-76 (122)
212 cd02134 NusA_KH NusA_K homolog 78.8 2.9 6.2E-05 35.6 4.0 36 695-731 25-60 (61)
213 PF10447 EXOSC1: Exosome compo 78.3 6.2 0.00013 35.9 6.1 74 810-884 3-82 (82)
214 COG1093 SUI2 Translation initi 77.4 0.83 1.8E-05 49.5 0.3 78 808-899 8-86 (269)
215 COG0361 InfA Translation initi 76.5 12 0.00027 33.4 7.3 66 762-833 5-72 (75)
216 smart00652 eIF1a eukaryotic tr 76.4 9.9 0.00021 34.6 6.9 65 761-832 2-68 (83)
217 cd00164 S1_like S1_like: Ribos 75.8 2 4.4E-05 35.1 2.2 29 866-894 37-65 (65)
218 TIGR00448 rpoE DNA-directed RN 74.0 4.2 9.2E-05 42.0 4.5 34 867-900 132-170 (179)
219 TIGR03319 YmdA_YtgF conserved 70.5 16 0.00034 44.2 8.8 64 695-759 204-269 (514)
220 PTZ00329 eukaryotic translatio 69.6 12 0.00026 38.0 6.3 65 761-832 29-95 (155)
221 KOG2193 IGF-II mRNA-binding pr 69.1 3.2 7E-05 47.5 2.5 62 666-732 255-316 (584)
222 COG1094 Predicted RNA-binding 68.6 5.5 0.00012 41.7 3.8 59 706-767 113-171 (194)
223 PRK00106 hypothetical protein; 68.5 20 0.00043 43.5 9.0 64 695-759 225-290 (535)
224 PF09883 DUF2110: Uncharacteri 68.4 8.5 0.00018 40.9 5.2 117 717-835 22-149 (225)
225 KOG2190 PolyC-binding proteins 68.2 7.9 0.00017 46.3 5.6 62 694-757 137-205 (485)
226 cd05793 S1_IF1A S1_IF1A: Trans 68.2 14 0.0003 33.2 5.8 59 768-832 3-63 (77)
227 PRK12327 nusA transcription el 68.0 0.53 1.2E-05 54.0 -4.0 50 849-898 133-201 (362)
228 PLN00208 translation initiatio 67.6 14 0.0003 37.2 6.2 65 761-832 29-95 (145)
229 PRK12704 phosphodiesterase; Pr 66.0 25 0.00055 42.5 9.3 64 695-759 210-275 (520)
230 PRK13764 ATPase; Provisional 65.9 3.7 8E-05 50.3 2.3 144 669-819 456-601 (602)
231 COG5176 MSL5 Splicing factor ( 64.2 20 0.00044 37.8 6.9 54 704-758 163-219 (269)
232 cd04471 S1_RNase_R S1_RNase_R: 63.9 3.9 8.4E-05 36.0 1.5 29 867-895 54-82 (83)
233 cd04460 S1_RpoE S1_RpoE: RpoE, 63.3 3.4 7.4E-05 38.3 1.1 34 867-900 50-88 (99)
234 COG1855 ATPase (PilT family) [ 61.8 6.8 0.00015 45.9 3.3 60 671-732 463-522 (604)
235 KOG3013 Exosomal 3'-5' exoribo 61.5 6.1 0.00013 42.8 2.7 75 760-835 82-166 (301)
236 PRK09937 stationary phase/star 61.3 45 0.00097 29.7 7.7 62 768-835 3-67 (74)
237 cd05791 S1_CSL4 S1_CSL4: CSL4, 59.1 17 0.00037 33.5 4.9 75 810-896 5-85 (92)
238 PRK09890 cold shock protein Cs 58.7 54 0.0012 28.7 7.7 55 767-827 5-62 (70)
239 COG1097 RRP4 RNA-binding prote 57.8 18 0.00038 39.2 5.3 53 697-750 148-200 (239)
240 TIGR00523 eIF-1A eukaryotic/ar 57.0 38 0.00083 31.9 6.8 62 762-830 17-81 (99)
241 PRK09507 cspE cold shock prote 56.8 31 0.00067 30.2 5.8 51 766-821 3-56 (69)
242 PRK15464 cold shock-like prote 56.7 26 0.00057 30.8 5.4 55 767-827 5-62 (70)
243 cd04453 S1_RNase_E S1_RNase_E: 56.1 32 0.00069 31.4 6.1 70 807-894 3-80 (88)
244 COG4044 Uncharacterized protei 56.0 29 0.00062 36.8 6.3 99 736-835 45-161 (247)
245 PRK00468 hypothetical protein; 55.2 11 0.00024 33.7 2.8 30 695-724 30-59 (75)
246 PRK15463 cold shock-like prote 55.2 29 0.00063 30.5 5.4 54 767-826 5-61 (70)
247 PRK02821 hypothetical protein; 52.8 12 0.00025 33.7 2.6 31 695-725 31-61 (77)
248 COG1837 Predicted RNA-binding 52.8 13 0.00029 33.3 2.9 30 695-724 30-59 (76)
249 PF08121 Toxin_33: Waglerin fa 51.7 6.5 0.00014 26.0 0.6 11 8-18 3-13 (22)
250 PRK10943 cold shock-like prote 51.4 41 0.00089 29.4 5.7 51 766-821 3-56 (69)
251 cd04456 S1_IF1A_like S1_IF1A_l 51.4 48 0.001 29.9 6.2 58 769-832 4-64 (78)
252 PRK12705 hypothetical protein; 50.9 32 0.00069 41.5 6.6 65 695-760 198-264 (508)
253 PRK14998 cold shock-like prote 50.8 81 0.0018 28.0 7.5 60 768-833 3-65 (73)
254 PRK08563 DNA-directed RNA poly 50.6 25 0.00054 36.5 5.0 33 868-900 133-170 (187)
255 PF01176 eIF-1a: Translation i 50.3 18 0.00039 31.2 3.3 59 763-828 2-62 (65)
256 PF10246 MRP-S35: Mitochondria 49.9 63 0.0014 30.7 6.9 55 761-823 21-75 (104)
257 cd04458 CSP_CDS Cold-Shock Pro 48.4 73 0.0016 26.9 6.8 49 768-822 2-54 (65)
258 KOG2192 PolyC-binding hnRNP-K 48.0 25 0.00054 38.4 4.5 59 697-757 317-381 (390)
259 KOG1588 RNA-binding protein Sa 47.5 56 0.0012 35.9 7.2 31 704-735 107-137 (259)
260 PRK10354 RNA chaperone/anti-te 45.5 59 0.0013 28.4 5.8 53 767-826 5-61 (70)
261 COG1278 CspC Cold shock protei 43.8 76 0.0017 27.9 6.1 47 771-821 5-54 (67)
262 PRK01064 hypothetical protein; 43.2 26 0.00057 31.6 3.3 31 695-725 30-60 (78)
263 PRK11642 exoribonuclease R; Pr 42.0 62 0.0013 41.4 7.5 29 867-895 696-724 (813)
264 TIGR02381 cspD cold shock doma 41.5 1.1E+02 0.0023 26.7 6.8 54 768-827 3-59 (68)
265 PRK08406 transcription elongat 40.4 27 0.00059 34.8 3.3 37 695-732 99-135 (140)
266 COG1096 Predicted RNA-binding 40.1 4.7E+02 0.01 27.6 12.3 73 806-885 59-133 (188)
267 cd05700 S1_Rrp5_repeat_hs9 S1_ 39.0 85 0.0018 27.0 5.4 63 764-831 1-64 (65)
268 PRK12328 nusA transcription el 36.6 60 0.0013 37.7 5.6 68 810-898 137-207 (374)
269 CHL00010 infA translation init 35.6 1.9E+02 0.0042 25.9 7.6 62 767-833 9-72 (78)
270 cd02414 jag_KH jag_K homology 35.2 41 0.00088 29.8 3.3 31 696-726 25-55 (77)
271 KOG2814 Transcription coactiva 35.1 31 0.00067 39.0 2.9 64 697-760 59-125 (345)
272 PF13083 KH_4: KH domain; PDB: 34.1 23 0.0005 30.9 1.5 34 693-726 27-60 (73)
273 cd04322 LysRS_N LysRS_N: N-ter 32.1 2E+02 0.0042 27.0 7.5 68 766-834 3-76 (108)
274 PRK00276 infA translation init 30.5 2.5E+02 0.0054 24.7 7.4 61 766-831 8-70 (72)
275 COG0195 NusA Transcription elo 30.3 40 0.00086 35.5 2.7 36 696-732 77-112 (190)
276 KOG2191 RNA-binding protein NO 29.3 98 0.0021 35.1 5.5 37 695-732 39-75 (402)
277 PRK08406 transcription elongat 29.2 46 0.001 33.2 2.9 34 698-732 35-68 (140)
278 KOG0336 ATP-dependent RNA heli 28.9 33 0.00073 39.9 2.0 61 696-758 48-111 (629)
279 TIGR01952 nusA_arch NusA famil 27.9 51 0.0011 33.1 2.9 36 696-732 34-69 (141)
280 KOG1004 Exosomal 3'-5' exoribo 27.9 2.2E+02 0.0048 30.5 7.5 71 760-832 62-132 (230)
281 PF07650 KH_2: KH domain syndr 26.5 32 0.00069 30.3 1.1 44 696-740 26-69 (78)
282 TIGR00358 3_prime_RNase VacB a 24.7 93 0.002 38.9 5.0 27 868-894 626-652 (654)
283 COG1095 RPB7 DNA-directed RNA 23.9 1.4E+02 0.003 31.3 5.2 84 811-900 81-170 (183)
284 PF13184 KH_5: NusA-like KH do 23.0 29 0.00062 30.5 0.1 27 704-731 17-44 (69)
285 PF02599 CsrA: Global regulato 22.0 86 0.0019 26.4 2.7 31 804-835 7-37 (54)
286 COG4604 CeuD ABC-type enteroch 20.7 1.2E+02 0.0025 32.7 3.9 106 698-816 21-143 (252)
287 TIGR03498 FliI_clade3 flagella 20.3 7.7E+02 0.017 29.2 11.0 166 147-359 245-415 (418)
No 1
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=7.5e-181 Score=1604.49 Aligned_cols=820 Identities=83% Similarity=1.242 Sum_probs=776.8
Q ss_pred ccceeeccccCCCCCcccCCC----CCccccccccccccccccccccccccCCCCCCc--cccCCCCCCCCCceeEEeee
Q 002487 23 LSARCKLSLSSNCPRFSTSQK----SSKFRSLSLLLSRRKYSERFSVRASATGPEVSE--PVLSDALPSFPQPVSVKIPF 96 (916)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 96 (916)
.--||.|++|+||||+.++.+ +.+.|..++|..+.+ +.|..|+.. +|..++ +.+.+..+.|++.+++.+++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (891)
T PLN00207 10 HLLRSPLPPSRNLPRFHDSESSPSISSSLPEAGLLKSSIK--KARSVRALL-RPVDSEDTSSVGEGPGPFPQQFSVKIPV 86 (891)
T ss_pred hhccCCCCCCcCCceeecCCCCCCCCCCCccccccccccc--cccccceec-cccccccccccccCCCCCCcceEEEEEE
Confidence 346899999999998876655 456667777999888 999999887 777666 66788888889999988899
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCCCCCchhhhH
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLV 176 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil~ 176 (916)
|.|+|.+|||++|+||||||++++|+|+|||||+..++++++.|||||+|+|+||+||+|||||||+||||+|+++|+|+
T Consensus 87 g~~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL~ 166 (891)
T PLN00207 87 GDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVLI 166 (891)
T ss_pred CCEEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHHH
Confidence 88899999999999999999999999999999999888999999999999999999999999999999999999999999
Q ss_pred HHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCChHHHh
Q 002487 177 CRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEME 256 (916)
Q Consensus 177 sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt~~E~~ 256 (916)
+|||||+|||+||++|++++||+++|||+||+++++++||||||+||++|||||++||+|||||++||++|||||++|++
T Consensus 167 sRlIdR~lRPlfp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~~E~~ 246 (891)
T PLN00207 167 CRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTKEME 246 (891)
T ss_pred HHHHCccchhhccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCCCCChhHHHHHHHHHH
Q 002487 257 DSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAG 336 (916)
Q Consensus 257 ~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~~~~~~~~~~~~~~~~~ 336 (916)
.|++||+|+||.++|+|||++++++++++|.+||++||++|+.||++|+++++++|++|+++.....+++|.+.|++++.
T Consensus 247 ~s~ldLvvagt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~~~~~~~~~l~~~v~~~~~ 326 (891)
T PLN00207 247 ESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPELYKHVKEIAG 326 (891)
T ss_pred cCCeeEEEEEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999998877789999999999999
Q ss_pred HHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCCccccCCCCCC
Q 002487 337 EELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRK 416 (916)
Q Consensus 337 ~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 416 (916)
++|++|+++.+|++|+++++++++++++.|.++++..++..++..++++++++.++.+++.+++||+|+||+||+|.+|+
T Consensus 327 ~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 406 (891)
T PLN00207 327 DELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDEGDVHIKPIPRK 406 (891)
T ss_pred HHHHHHHhccchHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhcccccccccccccccccccc
Confidence 99999999999999999999999999999977555677888999999999987765444467899999999999999999
Q ss_pred CCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCcccc
Q 002487 417 STPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMA 496 (916)
Q Consensus 417 ~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~ 496 (916)
++|.++...+++.+|++++++++|++|+++|+|+|||+++|+|||+|++|++++|||||+|++|+|||||+||+||.++.
T Consensus 407 ~~~~~~~~~~i~~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~ 486 (891)
T PLN00207 407 SSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMA 486 (891)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCcccc
Confidence 99999998899999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred ccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEEEecCCCcchh
Q 002487 497 QRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMA 576 (916)
Q Consensus 497 ~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~VLesdGs~~~A 576 (916)
|..+.+......++|++||+|||||++++++.|+|+|||++|+++++|+|+|+||.++.|||+|+|+++||++|||++||
T Consensus 487 q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~tIrV~~~VLesDGSssmA 566 (891)
T PLN00207 487 QRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMA 566 (891)
T ss_pred ccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCEEEEEEEEEEeCCCChHHH
Confidence 88777654456789999999999999999999999999999999999999999998668999999999999999999999
Q ss_pred HHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEEEeeccccCCC
Q 002487 577 SVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGIT 656 (916)
Q Consensus 577 sv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~d~K~ggis 656 (916)
+|||+|||||||||||+++|+||+||++.+.++++++++|.+|+||++.|++.|+|||+||||.+|||++|||+|+++++
T Consensus 567 aV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd~k~~gis 646 (891)
T PLN00207 567 SVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGIT 646 (891)
T ss_pred HHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEecccCCCC
Confidence 99999999999999999999999999996544444456788999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcc
Q 002487 657 LPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGT 736 (916)
Q Consensus 657 ~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~ 736 (916)
.++|.+||++|+++|.+|++.|+++++.||.++++|+|++++++|+|+||+++||+||+|||+|+++||++.|||+|+|.
T Consensus 647 ~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~ 726 (891)
T PLN00207 647 LPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGT 726 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999997699999999
Q ss_pred eeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEE
Q 002487 737 VKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVD 816 (916)
Q Consensus 737 v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~ 816 (916)
|.|++.+.+++++|+++|+.++.++++|++|+|++|++|++||+||+|.+|++||||+|+|+|+++.++.++|++||.|+
T Consensus 727 V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~ 806 (891)
T PLN00207 727 VKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRID 806 (891)
T ss_pred EEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEE
Confidence 99999999999999999999999999999996339999999999999999999999999999999999999999999999
Q ss_pred EEEEEEcCCCceEEEEeecCCCCCCCCCC
Q 002487 817 VKLIEVNDKGQLRLSRRALLPEADAENPP 845 (916)
Q Consensus 817 VKVi~iD~~gkI~LS~K~~~~~p~~~~~~ 845 (916)
|||+++|.+|||.||+|+++++||..+..
T Consensus 807 VkVi~ID~~grI~LSlK~l~~~Pw~~~~~ 835 (891)
T PLN00207 807 VKLIEVNDKGQLRLSRRALLPEANSEKSS 835 (891)
T ss_pred EEEEEECCCCcEEEEEeccccCchhhhhh
Confidence 99999999899999999999999998764
No 2
>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=100.00 E-value=5.3e-168 Score=1468.57 Aligned_cols=686 Identities=41% Similarity=0.675 Sum_probs=651.5
Q ss_pred ceeEEeeeCCeeEEEEeCccccCCCceEEEEe-CCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCC
Q 002487 89 PVSVKIPFGDRQILVETGHMGRQASGAVTVTD-GETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREG 167 (916)
Q Consensus 89 ~~~~~~~~~~R~i~~etG~la~qAdGSa~v~~-G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg 167 (916)
.+.+.+++|++++.+|||++|+||||||++++ |+|+|||||+..++++++.|||||+|+|+||+||+|||||||+||||
T Consensus 7 ~~~~~~~~~~~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREg 86 (719)
T TIGR02696 7 AVIDNGRFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGRIPGSFFRREG 86 (719)
T ss_pred eEEEEEEECCEEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCCCCCcceeEeeeehhhhcCccCCceeccCC
Confidence 34456677666999999999999999999999 99999999999888898999999999999999999999999999999
Q ss_pred CCCchhhhHHHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEE
Q 002487 168 RTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFI 247 (916)
Q Consensus 168 ~p~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~i 247 (916)
+|+++|+|++||||||||||||++|+|+|||+|+|||+|+.++||++|+||||+||++|+|||+|||+|||||++||+||
T Consensus 87 rps~~eiL~sRliDR~iRPLFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~v 166 (719)
T TIGR02696 87 RPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWV 166 (719)
T ss_pred CCChhhhHHHHhhCCCCccCCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ECCChHHHhhCCeeEEEEeec----C-eEEEEEe------------cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 248 VNPTTQEMEDSQLDLLLAGSD----D-AILMIEG------------YCDFLSEEMLIQAVQVGQDAVREISNEVKALVEM 310 (916)
Q Consensus 248 ldPt~~E~~~s~~dl~vagt~----~-~i~mie~------------~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~ 310 (916)
+|||++|++.|+|||+||||+ + +|+|||+ ++++++|++|++||++||++++.+|++|+++.++
T Consensus 167 iNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~~ 246 (719)
T TIGR02696 167 AFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEK 246 (719)
T ss_pred ECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999997 5 8999998 8899999999999999999999999999999999
Q ss_pred hCCCCcccC-CCCCChhHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCcccccccccccccccccc
Q 002487 311 CGKPKMLDT-IKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLE 389 (916)
Q Consensus 311 ~gk~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 389 (916)
+||+|+++. ....+++|.+.+++++.++|++++.+.+|.+|+++++++++++.+.|.+.
T Consensus 247 ~gk~k~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~~-------------------- 306 (719)
T TIGR02696 247 AAKPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTIAGKQEREEALDEVKALVAAKLAEQ-------------------- 306 (719)
T ss_pred hCCCccccCCCCCCCHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhhcc--------------------
Confidence 999999887 66678999999999999999999999999999999999999999987431
Q ss_pred CccccchhhccCcccCCccccCCCCCCCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCC
Q 002487 390 DEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLP 469 (916)
Q Consensus 390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~ 469 (916)
. +. ...+++.+|++++++.+|++++++|+|+|||+++++|||+|++|++|
T Consensus 307 -~-~~----------------------------~~~~i~~~~~~~~k~~~r~~il~~g~R~DGR~~~eiR~i~~~~g~l~ 356 (719)
T TIGR02696 307 -F-EG----------------------------REKEISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIP 356 (719)
T ss_pred -c-cc----------------------------cHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCccccccceeecCCCC
Confidence 0 00 12468899999999999999999999999999999999999999999
Q ss_pred CCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccc
Q 002487 470 RAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPV 549 (916)
Q Consensus 470 ~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~v 549 (916)
++||||+|++|+|||+|++|+||..+.|..+.+.. ...++|+|||+|||||++++++.++++|||++|++|++|+|+++
T Consensus 357 ~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~-~~~~~~~~~YnfpPFSt~er~~~~~~~RReighg~La~rALe~v 435 (719)
T TIGR02696 357 RVHGSALFERGETQILGVTTLNMLKMEQQIDSLSP-ETSKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALVPV 435 (719)
T ss_pred CCCceEEEEecCcEEEEEEeCCCchhhhhcccccc-cccceEEEEEeCCCCcccCCCCCCCCCccHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999988887664 45789999999999999999999999999999999999999999
Q ss_pred cCCCCCCCeEEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCC-CceeecCCChhhhh
Q 002487 550 LPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDG-TPLILSDITGSEDA 628 (916)
Q Consensus 550 ip~~~~fp~tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~-~~~iL~Dpt~~Ed~ 628 (916)
||..+.|||+|+++++|||||||++||||||+|||||||||||+++||||+||++.+.+ +++ +|.+|+||++.||+
T Consensus 436 I~~~e~fP~TIrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~---~~~~~~~iL~Di~g~ED~ 512 (719)
T TIGR02696 436 LPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEV---DGETRYVALTDILGAEDA 512 (719)
T ss_pred hCcHhhCCCEEEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEEEEEecccc---CCCcceeEEeCCCchhhh
Confidence 99548999999999999999999999999999999999999999999999999996521 012 68999999999999
Q ss_pred cCCccEEEEecCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeee
Q 002487 629 SGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINL 708 (916)
Q Consensus 629 ~gdmdf~Vagt~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~ 708 (916)
+|+|||+|+||.+|||++|||+|+.|++.++|.+||++|++||.+|++.|++++..| .++++|+|++++++|+|+||++
T Consensus 513 ~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~ 591 (719)
T TIGR02696 513 FGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGE 591 (719)
T ss_pred cCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhh
Confidence 999999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred eecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhc--CCCCCcEEEccEEEEEecceEEEEECC
Q 002487 709 IIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTM--VPTVGDIYRNCEIKSIAPYGVFVEIAP 786 (916)
Q Consensus 709 vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~--~~~vG~i~~G~~V~~I~~fGaFVel~~ 786 (916)
+||||||+||+|+++||++ |||+|+|+|.|++.+.+.+++|+++|+.+.. .+++|++|+| +|++|++||+||+|.+
T Consensus 592 vIG~gGk~I~~i~~~tg~~-Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~G-kV~~I~dfGaFVel~~ 669 (719)
T TIGR02696 592 VIGPKGKMINQIQDETGAE-ISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLG-TVVKTTAFGAFVSLLP 669 (719)
T ss_pred eeCCCcHhHHHHHHHHCCE-EEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEE-EEEEEECceEEEEecC
Confidence 9999999999999999997 9999999999999999999999999999998 6999999999 9999999999999999
Q ss_pred CeeeEEeccccC----cccccCccccccCCCEEEEEEEEEcCCCceEEE
Q 002487 787 GREGLCHISELS----SNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLS 831 (916)
Q Consensus 787 g~eGlvhiSels----~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS 831 (916)
|++||||+|||+ |.++.++.++|++||+|+|||+++|.+|||+|+
T Consensus 670 G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 670 GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred CceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 999999999996 478999999999999999999999998999986
No 3
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-169 Score=1443.32 Aligned_cols=690 Identities=51% Similarity=0.793 Sum_probs=668.5
Q ss_pred CCceeEEeeeCCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccC
Q 002487 87 PQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKRE 166 (916)
Q Consensus 87 ~~~~~~~~~~~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kRe 166 (916)
++...+++++|||++++|||++|+||+|||+++||+|.|||||++.+ ++++.|||||||+|+||+||+|||||||+|||
T Consensus 2 ~~~~~~~~~~~~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kRE 80 (692)
T COG1185 2 FNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKEGQDFFPLTVNYEEKTYAAGKIPGGFFKRE 80 (692)
T ss_pred CcceEEEEEECCeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CCCCCCccceeEeeeeehhccCcCCCcccccC
Confidence 45567788999999999999999999999999999999999999998 78899999999999999999999999999999
Q ss_pred CCCCchhhhHHHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEE
Q 002487 167 GRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKF 246 (916)
Q Consensus 167 g~p~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ 246 (916)
|||+++|+|+|||||||||||||++|++++||+++|+|+|+.++||++||+|||+||++|+|||.+||+|||||++||+|
T Consensus 81 Grpse~e~L~sRLIDRpiRPlFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~ 160 (692)
T COG1185 81 GRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIF 160 (692)
T ss_pred CCCCccchhhhhhcccccccccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EECCChHHHhhCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCCCCChh
Q 002487 247 IVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPE 326 (916)
Q Consensus 247 ildPt~~E~~~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~~~~~~~ 326 (916)
++|||.+|.+.|++||+||||.++|+|+|+++++++|++|++||.+||++++.+|++|+++...+|++++++.....+++
T Consensus 161 vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~~ 240 (692)
T COG1185 161 VLNPTLEELEESKLDLVVAGTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEE 240 (692)
T ss_pred EECCChHHhhhcceeeEecCChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988888887778999
Q ss_pred HHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCC
Q 002487 327 LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEG 406 (916)
Q Consensus 327 ~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 406 (916)
+...+++.+.+++.+++.+.+|++|..+++++++++.++|..+ + ..
T Consensus 241 l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~~~---------------------e--~~----------- 286 (692)
T COG1185 241 LEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGE---------------------E--ES----------- 286 (692)
T ss_pred HHHHHHHHhHHHHHHHhcccchhhhhhhHHHHHHHHHHHHhhh---------------------c--cc-----------
Confidence 9999999999999999999999999999999999999988531 0 00
Q ss_pred ccccCCCCCCCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEE
Q 002487 407 DVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLA 486 (916)
Q Consensus 407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~ 486 (916)
+..+++.+|+.|+++.+|++|++.++|+|||..+++|||.+++|++|++|||++|+||+||.++
T Consensus 287 ----------------~~~~~~~~~~~l~~~~vR~~Il~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~ 350 (692)
T COG1185 287 ----------------SLKEIKAILEKLEKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALV 350 (692)
T ss_pred ----------------cHHHHHHHHHHHhHHHHHHHHhcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceE
Confidence 1357889999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEE
Q 002487 487 VITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTI 566 (916)
Q Consensus 487 ~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~V 566 (916)
++|||+..+.|..|.+.. +..++||+||||||||+||++|.|.|+|||+|||+|++|+|.+++|..+.|||+||++++|
T Consensus 351 v~TLG~~~d~Qvid~l~~-e~~krfm~hYNFPp~SvGE~g~~g~p~RREiGHG~LA~Ral~~vlp~~e~fpytiRvVsEi 429 (692)
T COG1185 351 VVTLGTPRDAQVIDILEG-EYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEEFPYTIRVVSEI 429 (692)
T ss_pred EEEcCCcchhhhhhhccc-hhhhheeeeccCCCCCccccCCCCCCCcccccCchhhHHHHhhhCCchhcCCceeeeeehh
Confidence 999999999999998876 6789999999999999999999999999999999999999999999889999999999999
Q ss_pred EecCCCcchhHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEE
Q 002487 567 TESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAF 646 (916)
Q Consensus 567 LesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItal 646 (916)
|+||||++||++||+||||||||||++.+|||++|||+++++ +|+||+||.|+|||+||||||||||.+|||++
T Consensus 430 ~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~------~~~vLsDI~G~EDhlGDMDFKVAGT~~GiTAl 503 (692)
T COG1185 430 LESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------KYAVLSDILGDEDHLGDMDFKVAGTDDGITAL 503 (692)
T ss_pred hcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCC------ceEeeccccccccccCCceeEEecCCCcceee
Confidence 999999999999999999999999999999999999999874 57999999999999999999999999999999
Q ss_pred EeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCC
Q 002487 647 QMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGV 726 (916)
Q Consensus 647 q~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v 726 (916)
|||+|+.|++.++|.+||.||+.||.+|+..|.+++..||+++++|+|++++++|+++||+++|||||++|++|+++||+
T Consensus 504 QMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~ 583 (692)
T COG1185 504 QMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGV 583 (692)
T ss_pred eeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 727 EAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 727 ~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
+ |||+|||+|+|++.+.+..++|+++|+.++.++++|++|.| +|+++.+||+||+|.||.+||||+|++++.++.+++
T Consensus 584 ~-IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G-~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~ 661 (692)
T COG1185 584 K-IDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEG-TVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVE 661 (692)
T ss_pred E-EEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEE-EEEEEeecceEEEecCCcceeEEehhhhhhhhhccc
Confidence 6 99999999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred ccccCCCEEEEEEEEEcCCCceEEEEeecC
Q 002487 807 DVVKVGDLVDVKLIEVNDKGQLRLSRRALL 836 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~ 836 (916)
+++++||.|.||++++|++||++||+|.++
T Consensus 662 dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 662 DVLKEGDEVKVKVIEIDKQGRIRLSIKAVL 691 (692)
T ss_pred ceeecCceEEEEEeeecccCCccceehhcc
Confidence 999999999999999999999999999764
No 4
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=100.00 E-value=8.2e-159 Score=1308.89 Aligned_cols=735 Identities=45% Similarity=0.703 Sum_probs=682.3
Q ss_pred ccccccccccccccccccccccccCCCCCCccccCCCCC--CCCCceeEEeeeCCeeEEEEeCccccCCCceEEEEeCCe
Q 002487 46 KFRSLSLLLSRRKYSERFSVRASATGPEVSEPVLSDALP--SFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGET 123 (916)
Q Consensus 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~R~i~~etG~la~qAdGSa~v~~G~T 123 (916)
+.||+++|+.++. .+|..++.. ++-.+...-.+... .+.+.+++++.+|+|.|.||||++|++|||||++++|+|
T Consensus 4 ~~csls~l~~~~a--~kf~~~~l~-r~~~~~~~~~~~~~s~t~~~~vsveipfGnR~i~~etGklaRfAngsvvv~~GeT 80 (760)
T KOG1067|consen 4 SSCSLSNLLARRA--LKFRTILLG-RLRALPQLQVRALGSSTGPNAVSVEIPFGNREILFETGKLARFANGSVVVQMGET 80 (760)
T ss_pred ceeeehhhhcccc--cCcceeecc-CccCCCCCCccccccccCccceeeeeccCCeEEEEecchhhhhcCCcEEEccCCe
Confidence 4577888888887 778777664 43322222222211 445677788888999999999999999999999999999
Q ss_pred EEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCCCCCchhhhHHHHhcCcccccccCCCcCeEEEEEEEE
Q 002487 124 IIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVL 203 (916)
Q Consensus 124 ~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VL 203 (916)
.|++||+....|.+++ |+||.|+|+||+||+|+||++|+||||+|+|+|+|++|||||+|||+||++|++++||.|++|
T Consensus 81 ~Vm~Tv~~a~~PSp~q-FlPL~VdYqeK~aAvGRip~~fmRREg~tkdkEiL~~rLidrsirplfp~g~~~etqi~~n~L 159 (760)
T KOG1067|consen 81 AVMTTVVLADKPSPPQ-FLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVL 159 (760)
T ss_pred EEEEEEEecCCCCccc-cceEEEehhhhhhhhccCCCcccccccCCcchhheeeeccccccccCCcccchhHHHHHhhhe
Confidence 9999999998888777 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCChHHHhhCCeeEEEEeecCeEEEEEecCCCCCH
Q 002487 204 SYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSE 283 (916)
Q Consensus 204 s~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt~~E~~~s~~dl~vagt~~~i~mie~~~~~~~e 283 (916)
++||.++||++|+|||++||+.|+|||++|+++||+|+++|+||||||..|++.|++||+||||++.++|+|+.++++++
T Consensus 160 s~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNPT~kEmssS~Lnlvvagt~~~~vmle~~s~~i~q 239 (760)
T KOG1067|consen 160 SSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQ 239 (760)
T ss_pred ecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCcchhhhhhccceeEEEeccceEEEEEcccccccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccC-CCCCChhHHHHHHHHHHHHHHHHHhc--cCchHHHHHHHHHHH
Q 002487 284 EMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDT-IKLPPPELYKHVEEIAGEELVKVLQI--KNKIPRRKALSSLEE 360 (916)
Q Consensus 284 ~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~ 360 (916)
++|++||+.|+.+.+++|..|+.+++++||+|+++. ...+++||.+++++++.++|+++++. ++|.+|++|++.++.
T Consensus 240 qdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~ 319 (760)
T KOG1067|consen 240 QDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPDPELVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRL 319 (760)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHhCccccchhhhcCCCHHHHHHHHHHHHHHHHHHhcccccccchhhhHHhhhcc
Confidence 999999999999999999999999999999998765 66789999999999999999999996 679999999999987
Q ss_pred HHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCCccccCCCCCCCCCcccchHHHHHHHHHHHHHHHH
Q 002487 361 KVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLR 440 (916)
Q Consensus 361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r 440 (916)
+..+++.+. +++. ...+|.+.|+.+.++.||
T Consensus 320 ~~e~~~~e~------------------~pe~-------------------------------e~~~i~~~fn~vskkv~R 350 (760)
T KOG1067|consen 320 DDEDKVKEE------------------FPEQ-------------------------------EPSEIIESFNTVSKKVFR 350 (760)
T ss_pred chHHHHHhh------------------cCCc-------------------------------cHHHHHHHHHHHHHHHHH
Confidence 766655331 1110 124688999999999999
Q ss_pred HHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCC
Q 002487 441 RRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPS 520 (916)
Q Consensus 441 ~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~ 520 (916)
++|+++|+|+|||.++|+|||+|+++.+++.|||++|+||+|||+|+||+|..+.+|+.|++.......+||+||+||||
T Consensus 351 s~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPy 430 (760)
T KOG1067|consen 351 SRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPY 430 (760)
T ss_pred HHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999988765555699999999999
Q ss_pred CcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEE
Q 002487 521 SVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVA 600 (916)
Q Consensus 521 s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvs 600 (916)
|++|.++.|+++|||+||+.|+|+||.+++| ++|||+|||.++|||||||++||++||+||||||||||++.+||||+
T Consensus 431 at~Evgkig~~nRRE~GhgaLAEkaL~~vlP--~dfPftIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGva 508 (760)
T KOG1067|consen 431 ATNEVGKIGGLNRRELGHGALAEKALLPVLP--EDFPFTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVA 508 (760)
T ss_pred cccccccccCCcccccCchhHhhhhhhccCc--ccCceEEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeE
Confidence 9999999999999999999999999999999 59999999999999999999999999999999999999999999999
Q ss_pred EEEEccCC-CCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHH
Q 002487 601 MGMVLDTD-EFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEML 679 (916)
Q Consensus 601 vgli~~~~-~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~ 679 (916)
|||+.+-+ ++++.++|.||+||+|.||+.||||||||||++|||++ ||+.+++.++|.+|++++.+|++.|.
T Consensus 509 iGlvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-------gi~l~Iv~eal~~a~~ar~~Il~~m~ 581 (760)
T KOG1067|consen 509 IGLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-------GIPLKIVMEALQKAREARLQILDIME 581 (760)
T ss_pred EEeEeccCcccCCcccceeehhhcchhhhcCCcceeeccccCcceec-------CCcHHHHHHHHHhhhHHHHHHHHHHH
Confidence 99998876 56677789999999999999999999999999999998 68899999999999999999999999
Q ss_pred hcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhc
Q 002487 680 KCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTM 759 (916)
Q Consensus 680 ~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~ 759 (916)
+++..||...+.|+|++++++++|+|...+|||||+..|.|+.|||. |+..|+|+++|++++..++++|+++|..+..
T Consensus 582 k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGa--i~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 582 KNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGA--ISQVDEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred hhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccc--eeeecCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999994 8888999999999999999999999999886
Q ss_pred C-----CCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEee
Q 002487 760 V-----PTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRA 834 (916)
Q Consensus 760 ~-----~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~ 834 (916)
. ++.|.+|++ +|+++.++|+||+|+|+..||+|+|||+.+++.+|++.+++||+|.||+++.|++|.+.||.|+
T Consensus 660 ~~~~~~l~~g~vy~~-tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ra 738 (760)
T KOG1067|consen 660 DDQVQDLEFGGVYTA-TITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRA 738 (760)
T ss_pred CccccceEeeeEEEE-EEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhhh
Confidence 5 577888897 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCC
Q 002487 835 LLPEADAENPP 845 (916)
Q Consensus 835 ~~~~p~~~~~~ 845 (916)
++++|..+...
T Consensus 739 lLp~p~~~~~s 749 (760)
T KOG1067|consen 739 LLPDPATKESS 749 (760)
T ss_pred hcCCcccCCcc
Confidence 99988766654
No 5
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=6.4e-152 Score=1362.71 Aligned_cols=692 Identities=51% Similarity=0.807 Sum_probs=660.7
Q ss_pred CCceeEEeeeCCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccC
Q 002487 87 PQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKRE 166 (916)
Q Consensus 87 ~~~~~~~~~~~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kRe 166 (916)
++.+++.+++++|+++++||++|+||||||++++|+|+|||||+++.+|+++.+|+||+|+|+|++||+|||||+|+|||
T Consensus 2 ~~~~~~~~~~~~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~v~y~e~~~A~gkiP~~f~kre 81 (693)
T PRK11824 2 FNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKRE 81 (693)
T ss_pred CceEEEEEEECCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCCeeeeEEEEEehhhhccCCCcccccCC
Confidence 34556677889999999999999999999999999999999999999988899999999999999999999999999999
Q ss_pred CCCCchhhhHHHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEE
Q 002487 167 GRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKF 246 (916)
Q Consensus 167 g~p~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ 246 (916)
|+|+++|+|++|+|||+|||+||++|++++||+++||++||++++|++||||||+||++|||||++||+|||||++||++
T Consensus 82 g~pse~eil~srlIdR~lrplfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~~ 161 (693)
T PRK11824 82 GRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEF 161 (693)
T ss_pred CCCChHHHHHHHHHhhhHHHhCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EECCChHHHhhCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCCCCChh
Q 002487 247 IVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPE 326 (916)
Q Consensus 247 ildPt~~E~~~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~~~~~~~ 326 (916)
|+|||.+|++.|++||+|+|+.+.|+|+|++++++++++|.+||++|+++|++++++|+++++++| +|+++.....+++
T Consensus 162 ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~ 240 (693)
T PRK11824 162 VLNPTVEELEESDLDLVVAGTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDEE 240 (693)
T ss_pred EEcCCHHHHhhCcceEEEEEccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccCCCCCCHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999 8988887778999
Q ss_pred HHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCC
Q 002487 327 LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEG 406 (916)
Q Consensus 327 ~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 406 (916)
|.+.+++++.++|++|+.+.+|.+|+++++++++++.+.|.+.. .. +
T Consensus 241 ~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~--------------------~~--~----------- 287 (693)
T PRK11824 241 LKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEE--------------------EE--E----------- 287 (693)
T ss_pred HHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHhhhcc--------------------cc--c-----------
Confidence 99999999999999999999999999999999999999885310 00 0
Q ss_pred ccccCCCCCCCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEE
Q 002487 407 DVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLA 486 (916)
Q Consensus 407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~ 486 (916)
....++..+|++++++.+|++|+++|+|+|||+++|+|||+|++|++|+|||||+|++|+|||+|
T Consensus 288 ---------------~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~ 352 (693)
T PRK11824 288 ---------------EDEKEIKEAFKKLEKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALV 352 (693)
T ss_pred ---------------ccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEE
Confidence 12357889999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEE
Q 002487 487 VITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTI 566 (916)
Q Consensus 487 ~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~V 566 (916)
+||+||..+.+..+.+.. ...++|++||+|||||++++++.|+|+|||++|+++++|+|+++||++++|||+|+|+++|
T Consensus 353 ~vt~g~~~~~~~~~~~~~-~~~~~~~~~y~~~pfs~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p~~I~v~~~V 431 (693)
T PRK11824 353 VATLGTLRDEQIIDGLEG-EYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEEEFPYTIRVVSEI 431 (693)
T ss_pred EEecCCCcccccccccCC-CCcEEEEEEEEcCCCCCCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCCEEEEEEEEE
Confidence 999999877776665543 4679999999999999999999999999999999999999999999878999999999999
Q ss_pred EecCCCcchhHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEE
Q 002487 567 TESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAF 646 (916)
Q Consensus 567 LesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItal 646 (916)
|++|||++|||+||++||||||||||+++|+||+||++.++ ++|.+|+||++.||++|||||+|++|.+|||++
T Consensus 432 Le~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~------~~~~il~D~~~~Ed~~~d~d~~va~t~~gi~~l 505 (693)
T PRK11824 432 LESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEG------DKYAVLTDILGDEDHLGDMDFKVAGTRDGITAL 505 (693)
T ss_pred EecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCC------CceEEEcCCChhhHhhCCceEEEEecCCceEEE
Confidence 99999999999999999999999999999999999999653 257899999999999999999999999999999
Q ss_pred EeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCC
Q 002487 647 QMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGV 726 (916)
Q Consensus 647 q~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v 726 (916)
|||+|.++++.++|.+||++|++||.+|++.|++++..||.++++|+|++++++|+|+||+++||+||+|||+|+++||+
T Consensus 506 q~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~ 585 (693)
T PRK11824 506 QMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGA 585 (693)
T ss_pred EEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 727 EAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 727 ~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
+ ||++|+|.|.|++.+.+++++|+++|+.+..++++|++|.| +|++|.+||+||+|.++.+||+|+|+++|++++++.
T Consensus 586 ~-idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G-~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~ 663 (693)
T PRK11824 586 K-IDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEG-KVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVE 663 (693)
T ss_pred c-cccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEE-EEEEEECCeEEEEECCCCEEEEEeeeccCccccCcc
Confidence 5 99999999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred ccccCCCEEEEEEEEEcCCCceEEEEeecC
Q 002487 807 DVVKVGDLVDVKLIEVNDKGQLRLSRRALL 836 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~ 836 (916)
++|++||.|+|||+++|..|+|.||+|+++
T Consensus 664 ~v~kvGD~V~VkV~~iD~~grI~LS~k~~~ 693 (693)
T PRK11824 664 DVLKEGDEVKVKVLEIDKRGRIRLSRKAVL 693 (693)
T ss_pred ceeCCCCEEEEEEEEECCCCcEEEEEEecC
Confidence 999999999999999998899999999863
No 6
>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=100.00 E-value=7.3e-152 Score=1359.02 Aligned_cols=681 Identities=51% Similarity=0.817 Sum_probs=649.5
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCCCCCchhhhH
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLV 176 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil~ 176 (916)
|+|+++++||++|+||||||++++|||+|||||+++.+++++.+|+||+|+|+|++||+|+|||+|+||||+|+++|+|+
T Consensus 3 ~~R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil~ 82 (684)
T TIGR03591 3 GGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETLT 82 (684)
T ss_pred CCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHHH
Confidence 67899999999999999999999999999999999999888899999999999999999999999999999999999999
Q ss_pred HHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCChHHHh
Q 002487 177 CRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEME 256 (916)
Q Consensus 177 sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt~~E~~ 256 (916)
+|+|||+|||+||++|+++|||+++||++||++++|++||||||+||++|||||++||+|||||++||++|+|||.+|++
T Consensus 83 srlIdR~lrplfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~~E~~ 162 (684)
T TIGR03591 83 SRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELE 162 (684)
T ss_pred HHHHhhHHHHhcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCCCCChhHHHHHHHHHH
Q 002487 257 DSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAG 336 (916)
Q Consensus 257 ~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~~~~~~~~~~~~~~~~~ 336 (916)
.|++||+|+|+.++|+|+|++++++++++|.+||++|+++|++++++|+++++++|++|+++.....+++|.+.+++++.
T Consensus 163 ~s~~~l~va~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~ 242 (684)
T TIGR03591 163 KSDLDLVVAGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKELAY 242 (684)
T ss_pred hCCceEEEEccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999998877789999999999999
Q ss_pred H-HHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCCccccCCCCC
Q 002487 337 E-ELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSR 415 (916)
Q Consensus 337 ~-~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (916)
+ +|++|+.+.+|.+|+++++++++++.+.|.+.. ..++++
T Consensus 243 ~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~-------------------~~~~~~-------------------- 283 (684)
T TIGR03591 243 EAGLKEAYQITEKQERYAALDAIKEEVLEALAEEE-------------------EEEEEA-------------------- 283 (684)
T ss_pred hHHHHHHhhccchHHHHHHHHHHHHHHHHHhhhhc-------------------cccccc--------------------
Confidence 9 999999999999999999999999999885420 000000
Q ss_pred CCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccc
Q 002487 416 KSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQM 495 (916)
Q Consensus 416 ~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~ 495 (916)
....++..+|++++++.+|++++++|+|+|||+++|+|||+|++|++|+|||||+|++|+|||+|+||+||.++
T Consensus 284 ------~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~ 357 (684)
T TIGR03591 284 ------DREKEIKEAFKDLEKKIVRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERD 357 (684)
T ss_pred ------ccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCccc
Confidence 01246889999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEEEecCCCcch
Q 002487 496 AQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSM 575 (916)
Q Consensus 496 ~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~VLesdGs~~~ 575 (916)
.+..+.+.. ...++|++||+|||||++++++.|+|+|||++|+++++|+|+++||++++|||+|+|+++||++|||++|
T Consensus 358 ~~~~~~~~~-~~~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~~ 436 (684)
T TIGR03591 358 EQIIDDLEG-EYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPYTIRVVSEILESNGSSSM 436 (684)
T ss_pred ccCCcccCC-CccEEEEEEEEcCCCCCCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCCeEEEEEEEEEeCCCChHH
Confidence 877776654 5679999999999999999999999999999999999999999999778999999999999999999999
Q ss_pred hHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEEEeeccccCC
Q 002487 576 ASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGI 655 (916)
Q Consensus 576 Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~d~K~ggi 655 (916)
||+||+|||||||||||+++|+||+||++.++ +++|.+|+||++.||+++||||+|++|.+|||++|||+|.+++
T Consensus 437 Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~-----~~~~~il~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i 511 (684)
T TIGR03591 437 ASVCGGSLALMDAGVPIKAPVAGIAMGLIKEG-----DERFAVLSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGI 511 (684)
T ss_pred HHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCC-----CcceEEEeCCChHHHhcCCceEEEEEcCCceEEEEEEcCcCCc
Confidence 99999999999999999999999999999643 1257899999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCc
Q 002487 656 TLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDG 735 (916)
Q Consensus 656 s~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g 735 (916)
+.++|.+||++|++++.+|++.|++++..++.++++|+|++++++|+|+||+++|||||++||+|+++||++ |||+|+|
T Consensus 512 ~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~-I~i~ddG 590 (684)
T TIGR03591 512 TREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAK-IDIEDDG 590 (684)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCE-EEEecCe
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997 9999999
Q ss_pred ceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEE
Q 002487 736 TVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLV 815 (916)
Q Consensus 736 ~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V 815 (916)
+|+|++.+.+.+++|+++|+.+...+++|++|.| +|++|.+||+||+|.++.+||||+|+++|+++.++.++|++||.|
T Consensus 591 ~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G-~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V 669 (684)
T TIGR03591 591 TVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEG-KVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEV 669 (684)
T ss_pred EEEEEECcHHHHHHHHHHHHhhhcccccCcEEEE-EEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEE
Confidence 9999999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEcCCCceEE
Q 002487 816 DVKLIEVNDKGQLRL 830 (916)
Q Consensus 816 ~VKVi~iD~~gkI~L 830 (916)
+|||+++|.+|+|+|
T Consensus 670 ~VkVi~id~~gki~L 684 (684)
T TIGR03591 670 KVKVLEIDKQGRIKL 684 (684)
T ss_pred EEEEEEECCCCCccC
Confidence 999999998888765
No 7
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=100.00 E-value=1.9e-40 Score=352.12 Aligned_cols=224 Identities=33% Similarity=0.484 Sum_probs=202.6
Q ss_pred HHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCC
Q 002487 442 RIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSS 521 (916)
Q Consensus 442 ~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s 521 (916)
.++++|+|+|||+++|+|++.+++|++++|||||+|++|+|+|+|+| +||++..+..... ...+.+.++|+|+||+
T Consensus 2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V-~gp~e~~~~~~~~---~~~~~l~v~~~~~~~a 77 (230)
T TIGR02065 2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAV-YGPREMHPRHLQL---PDRAVLRVRYHMAPFS 77 (230)
T ss_pred cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEE-eCCCccccccccC---CCceEEEEEEEeCCcc
Confidence 46889999999999999999999999999999999999999999999 8998765443222 2357899999999999
Q ss_pred cccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCe-EEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEE
Q 002487 522 VGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVA 600 (916)
Q Consensus 522 ~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~-tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvs 600 (916)
+.++++. ++++++++++++++++|++++++ +.||+ +|+|+++||++||+.++|++||+++||+||||||+++|+|++
T Consensus 78 ~~~~~~~-~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avt 155 (230)
T TIGR02065 78 TDERKRP-GPSRREIEISKVIREALEPAILL-EQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVA 155 (230)
T ss_pred cCCccCC-CCCccHHHHHHHHHHHHHHHhCh-hhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEE
Confidence 9877664 58999999999999999999998 78997 599999999999999999999999999999999999999999
Q ss_pred EEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEe--cCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHH
Q 002487 601 MGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEM 678 (916)
Q Consensus 601 vgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vag--t~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m 678 (916)
++++.+ .+++||+..|+..++++++|+. +.+.|+++|++ |.++.+.+.+|++.|++++..+.+.|
T Consensus 156 v~~~~~----------~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~---g~~~~e~~~~~l~~a~~~~~~l~~~~ 222 (230)
T TIGR02065 156 VGKVDG----------VVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLD---GDMTPDEFRQALDLAVKGIKIIYQIQ 222 (230)
T ss_pred EEEECC----------eEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEe---cCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 999843 3678999999999999999995 67889999998 57899999999999999999999999
Q ss_pred HhcCCC
Q 002487 679 LKCSPP 684 (916)
Q Consensus 679 ~~~i~~ 684 (916)
++++.+
T Consensus 223 ~~~l~~ 228 (230)
T TIGR02065 223 REALKN 228 (230)
T ss_pred HHHHHh
Confidence 998864
No 8
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=3.4e-39 Score=345.45 Aligned_cols=224 Identities=33% Similarity=0.486 Sum_probs=202.1
Q ss_pred HHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCC
Q 002487 442 RIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSS 521 (916)
Q Consensus 442 ~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s 521 (916)
.++++|+|+|||+++|+|++.+++|++++|+|||+|++|+|+|+|+| +||.+........ ...+.+.++|+|+||+
T Consensus 8 ~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V-~gp~e~~~~~~~~---~~~~~l~v~~~~~p~~ 83 (244)
T PRK03983 8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV-YGPREMHPRHLQL---PDRAVLRVRYNMAPFS 83 (244)
T ss_pred hhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEE-ecCCccccccccC---CCcEEEEEEEEcCCCc
Confidence 35789999999999999999999999999999999999999999999 7998765432222 3467899999999999
Q ss_pred cccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCe-EEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEE
Q 002487 522 VGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVA 600 (916)
Q Consensus 522 ~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~-tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvs 600 (916)
+.++++. ++++++++++++++++|+++++. +.||+ +|+|+++||++|||.++|++||+++||+||||||++++++++
T Consensus 84 ~~~~~~~-~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avt 161 (244)
T PRK03983 84 VDERKRP-GPDRRSIEISKVIREALEPAIML-ELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCA 161 (244)
T ss_pred cccccCC-CCChhHHHHHHHHHHHHHHhccH-HhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEE
Confidence 9876654 58999999999999999999998 88998 599999999999999999999999999999999999999999
Q ss_pred EEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEec--CCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHH
Q 002487 601 MGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGN--EDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEM 678 (916)
Q Consensus 601 vgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt--~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m 678 (916)
++++.+ .+|+||+..|+..++++++|+.+ .+.|+++|++ |.++.+.+.+|++.|++++.+|.+.|
T Consensus 162 v~~~~~----------~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~---G~~~~~~~~~~i~~A~~~~~~i~~~i 228 (244)
T PRK03983 162 VGKVDG----------VIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLD---GNLTREEFLEALELAKKGIKRIYQLQ 228 (244)
T ss_pred EEEECC----------EEEECCCHHHhccCCceEEEEEECCCCCEEEEEEe---cCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 999843 37789999999999999999975 4569999998 67899999999999999999999999
Q ss_pred HhcCCC
Q 002487 679 LKCSPP 684 (916)
Q Consensus 679 ~~~i~~ 684 (916)
++++..
T Consensus 229 ~~~l~~ 234 (244)
T PRK03983 229 REALKS 234 (244)
T ss_pred HHHHHH
Confidence 998764
No 9
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=2.8e-36 Score=321.75 Aligned_cols=220 Identities=23% Similarity=0.319 Sum_probs=193.1
Q ss_pred CCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccC
Q 002487 448 RRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGR 527 (916)
Q Consensus 448 ~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r 527 (916)
.|+|||+++|+|++.+++|++++|+|||+|++|+|+|+|+| .++...... . .....+.++++|+++|||+.++++
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V-~~~~~~p~~---~-~~~~~g~l~v~~~~~p~a~~~~~~ 75 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTA-SVEEGVPRF---L-KGQGQGWVTAEYGMLPRATHTRND 75 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEE-EcCCCCCCc---c-CCCCcEEEEEEEecCCCCCccccc
Confidence 49999999999999999999999999999999999999999 455442211 1 113467899999999999988742
Q ss_pred ----CCCCChhhHHHHHHHHHHhccccCCCCCCC-eEEEEEEEEEecCCCcchhHHhHHHHHHHhc-----------CCC
Q 002487 528 ----IGAPSRREIGHGTLAERALEPVLPSDNDFP-YTIRVESTITESNGSSSMASVCGGCLALQDA-----------GVP 591 (916)
Q Consensus 528 ----~g~~~rrei~~~~l~eraL~~vip~~~~fp-~tI~V~~~VLesdGs~~~Asv~aaslAL~dA-----------GIP 591 (916)
.|++++++++++++++|+|+++|++ +.|| ++|+|+++||++|||.++|+++|+++||+|| |+|
T Consensus 76 ~~~~~g~~~~~~~~~sr~i~r~lr~~i~l-~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip 154 (238)
T PRK00173 76 REAAKGKQGGRTQEIQRLIGRSLRAVVDL-KALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNP 154 (238)
T ss_pred ccccCCCCCccHHHHHHHHHHHHHHhcCH-HHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCc
Confidence 3568899999999999999999998 6676 4899999999999999999999999999999 999
Q ss_pred cccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCc-eeEEEeeccccCCCHHHHHHHHHHHHhh
Q 002487 592 IKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG-ITAFQMDIKVGGITLPVMKKALQQAKDG 670 (916)
Q Consensus 592 ~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~g-Italq~d~K~ggis~e~l~eaL~~A~~a 670 (916)
|+++++++++|++.+ .+|+||+.+|+..++++++|+.+..+ |+++|+++.-+.++.+.|.+|++.|+++
T Consensus 155 ~~~~~~~vt~~~~~~----------~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~ 224 (238)
T PRK00173 155 LKDQVAAVSVGIVDG----------EPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKG 224 (238)
T ss_pred ccCceeEEEEEEECC----------EEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHH
Confidence 999999999999953 37889999999999999999987654 9999986433469999999999999999
Q ss_pred hHHHHHHHHhcCC
Q 002487 671 RRHILAEMLKCSP 683 (916)
Q Consensus 671 ~~~Il~~m~~~i~ 683 (916)
+.+|.+.|++++.
T Consensus 225 ~~~l~~~~~~~l~ 237 (238)
T PRK00173 225 IAELVALQKAALA 237 (238)
T ss_pred HHHHHHHHHHHhc
Confidence 9999999998874
No 10
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=2.7e-36 Score=362.53 Aligned_cols=219 Identities=21% Similarity=0.198 Sum_probs=196.6
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEE-ecCCCCCCCCCCccccceeecccccccCCCCCc---ccCCCCCch
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVC-LADVPSEPSDFFPLNVNYQERFSAAGRTSGGFF---KREGRTKDH 172 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~-~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~---kReg~p~~~ 172 (916)
.-|+|++++|.++ .|||||++++|+|+|||+|+ |+++.....+++ ++++|++++|+.++||+.+. ||+|+|+++
T Consensus 447 eiRpI~~e~G~Lp-~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l-~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrR 524 (891)
T PLN00207 447 EIRPINSSCGLLP-RAHGSALFTRGETQALAVVTLGDKQMAQRIDNL-VDADEVKRFYLQYSFPPSCVGEVGRIGAPSRR 524 (891)
T ss_pred ccceEEEEeCCcC-CCCceEEEEECCeEEEEEEEecCcccccccccc-ccccceeeEEEEEEcCCCCCccccCCCCCCHH
Confidence 5699999999995 59999999999999999997 665544456776 68899999999999999665 899999999
Q ss_pred hhhHHHHhcCcccccccCC--CcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEE-C------
Q 002487 173 EVLVCRLIDRPLRPTLIKG--FYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLV-G------ 243 (916)
Q Consensus 173 eil~sRlIdR~LRplfp~~--~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i-~------ 243 (916)
|++++|+++|+|||+||.. |.+.|+|+++||++||+.+ +||+|||||||++|||||+++|+||+||++ |
T Consensus 525 Ei~hg~L~eRALrpvip~~~~fP~tIrV~~~VLesDGSss--mAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~ 602 (891)
T PLN00207 525 EIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSS--MASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGG 602 (891)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCEEEEEEEEEEeCCCChH--HHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCC
Confidence 9999999999999999976 9999999999999999855 999999999999999999999999999999 3
Q ss_pred -CEE--EECCChHHHhhCCeeEEEEeecCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccc
Q 002487 244 -DKF--IVNPTTQEMEDSQLDLLLAGSDDAILMIEGYC--DFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLD 318 (916)
Q Consensus 244 -g~~--ildPt~~E~~~s~~dl~vagt~~~i~mie~~~--~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~ 318 (916)
|++ ++||+..|+..+++||.||||.++|+|+|+++ ++++++.|.+||++|+++|..|++.|++.+.+.......+
T Consensus 603 ~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~ 682 (891)
T PLN00207 603 DGSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKY 682 (891)
T ss_pred CCcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccc
Confidence 354 46999999999999999999999999999954 6789999999999999999999999999998776544443
Q ss_pred C
Q 002487 319 T 319 (916)
Q Consensus 319 ~ 319 (916)
.
T Consensus 683 a 683 (891)
T PLN00207 683 A 683 (891)
T ss_pred C
Confidence 3
No 11
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-36 Score=314.76 Aligned_cols=220 Identities=28% Similarity=0.424 Sum_probs=196.9
Q ss_pred hcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCcc
Q 002487 444 VEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVG 523 (916)
Q Consensus 444 l~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~ 523 (916)
.+++.|.|||.++|+|||.++.|++++++||++|++|+|+|+|+| .||++..++.. .....++..++|++.|||+.
T Consensus 4 ~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~v-sGp~e~~p~~l---~~~~~g~~t~ey~m~p~sT~ 79 (230)
T COG0689 4 SEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTV-SGPREPVPRFL---RGTGKGWLTAEYGMLPRSTD 79 (230)
T ss_pred cccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEE-ecCCCCCChhh---cCCCceEEEEEEeccccccc
Confidence 468999999999999999999999999999999999999999999 79998766532 22457899999999999997
Q ss_pred cccCCCCCCh-hhHHHHHHHHHHhccccCCCCCCCe-EEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEEE
Q 002487 524 EVGRIGAPSR-REIGHGTLAERALEPVLPSDNDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAM 601 (916)
Q Consensus 524 e~~r~g~~~r-rei~~~~l~eraL~~vip~~~~fp~-tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsv 601 (916)
++.+.+ +.+ |++++++++.++|++++.+ +.||. +|+|+++||+.||++..|+|+||++||+|||+||+++|++|++
T Consensus 80 ~R~~~~-~~~gR~~eisrli~~al~~~i~L-~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSv 157 (230)
T COG0689 80 ERKKRE-ADRGRTKEISRLIGRALRAVIDL-ELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISV 157 (230)
T ss_pred cccccc-ccccchhHHHHHHHHHHHHHhhh-hhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEE
Confidence 766554 455 9999999999999999999 89998 7999999999999999999999999999999999999999999
Q ss_pred EEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEe--cCC--ceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHH
Q 002487 602 GMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAG--NED--GITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAE 677 (916)
Q Consensus 602 gli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vag--t~~--gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~ 677 (916)
|++.+ .+++|+.+.||..+..|..|+. +.+ .|+.+|.+ +.++++.|.++|+.|++++..+.+.
T Consensus 158 gi~~~----------~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~---~~~~~del~~lL~la~~g~~~~~~~ 224 (230)
T COG0689 158 GIVDG----------VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAED---GPFTEDELLELLDLAIKGCNELREL 224 (230)
T ss_pred EEECC----------ceEecCcchhhcccccCceEEEEecCCeEEEEEEecc---CCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 99965 2778999999998888877774 444 47777777 8899999999999999999999999
Q ss_pred HHhcC
Q 002487 678 MLKCS 682 (916)
Q Consensus 678 m~~~i 682 (916)
|+++|
T Consensus 225 ~~~al 229 (230)
T COG0689 225 QREAL 229 (230)
T ss_pred HHHHh
Confidence 99876
No 12
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.5e-37 Score=318.62 Aligned_cols=224 Identities=25% Similarity=0.378 Sum_probs=203.3
Q ss_pred HhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCc
Q 002487 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSV 522 (916)
Q Consensus 443 il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~ 522 (916)
+.++|.|.|||+++|+|+|.+++|++.+++||||+++|||||+|+| +||++........ .....+.|.|++.+|++
T Consensus 8 ~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV-~GPre~~~~~~~~---~~~a~lnc~~~~a~Fst 83 (245)
T KOG1068|consen 8 LSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAV-YGPREIRGKSARR---PDKAVLNCEVSSAQFST 83 (245)
T ss_pred cCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEE-eCCcccccccccc---cccceEEEEEeeecccc
Confidence 5679999999999999999999999999999999999999999999 9999876533221 23456889999999999
Q ss_pred ccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCe-EEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEEE
Q 002487 523 GEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAM 601 (916)
Q Consensus 523 ~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~-tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsv 601 (916)
+++++....+||+.+++.+++++|+++|.+ +.||+ +|+|+++||++||+.++|++||++|||.||||||+|+|+|+++
T Consensus 84 ~~r~~~~~~~rr~~e~s~~L~~afe~~I~~-~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~ 162 (245)
T KOG1068|consen 84 GDRKKRPKGDRREKELSLMLQQAFEPVILL-ELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTA 162 (245)
T ss_pred chhccCCCccHHHHHHHHHHHHHHHHHHHh-hhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhcee
Confidence 999976678899999999999999999999 99999 6999999999999999999999999999999999999999999
Q ss_pred EEEccCCCCCCCCCceeecCCChhhhhcCCccEEEE--ecCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHH
Q 002487 602 GMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVA--GNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEML 679 (916)
Q Consensus 602 gli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Va--gt~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~ 679 (916)
|+..+ ..++|++..|+..+...++|+ ++.+.|..+|++ ++++.+.+...|+.|.++|+++.+.|+
T Consensus 163 ~l~~~----------~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~---~~~~~d~l~~vl~~a~~~c~~v~~~l~ 229 (245)
T KOG1068|consen 163 GLADG----------TPLLDLTSLEESARAPGLTVAALPNREEIALLQLD---ERLHCDHLETVLELAIAGCKRVYERLR 229 (245)
T ss_pred eecCC----------ccccccccchhhccCCceEEEEecCcceEEEEEec---CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99964 367899999999888888887 678889999999 788999999999999999999999998
Q ss_pred hcCCC
Q 002487 680 KCSPP 684 (916)
Q Consensus 680 ~~i~~ 684 (916)
..+..
T Consensus 230 ~~l~~ 234 (245)
T KOG1068|consen 230 LVLRE 234 (245)
T ss_pred HHHHH
Confidence 87644
No 13
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=100.00 E-value=6.2e-36 Score=317.63 Aligned_cols=204 Identities=20% Similarity=0.226 Sum_probs=181.1
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCC----CCCCccccceeecccccccCCCCCcccCCCCCchh
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEP----SDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHE 173 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~----~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~e 173 (916)
-|++.+++|.+ .+|||||++++|+|+|+|+|++|++...+ .++.+|+|+|....||. +.+|+++|+++|
T Consensus 18 ~R~~~~~~g~~-~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~------~~~~~~~~~~~~ 90 (230)
T TIGR02065 18 LRPIKIEAGVL-KNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFST------DERKRPGPSRRE 90 (230)
T ss_pred ccCeEEEECCC-CCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCccc------CCccCCCCCccH
Confidence 48999999999 89999999999999999999998765433 35667888888766544 345567899999
Q ss_pred hhHHHHhcCcccccccCCCcC--eEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCC
Q 002487 174 VLVCRLIDRPLRPTLIKGFYH--ETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPT 251 (916)
Q Consensus 174 il~sRlIdR~LRplfp~~~~~--~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt 251 (916)
++++|+|+|+|||+++..+++ .++|.++||+.||+ ++.+|+|||++||++|||||+++|+||+||+++|++|+|||
T Consensus 91 ~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~--~~~aai~aa~lAL~dagIp~~~~v~avtv~~~~~~~v~Dpt 168 (230)
T TIGR02065 91 IEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAG--TRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLN 168 (230)
T ss_pred HHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCC--HHHHHHHHHHHHHHHcCCccccceeeEEEEEECCeEEECCC
Confidence 999999999999999988754 56666779999986 55999999999999999999999999999999999999999
Q ss_pred hHHHhhCCeeEEEEe--ecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002487 252 TQEMEDSQLDLLLAG--SDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMC 311 (916)
Q Consensus 252 ~~E~~~s~~dl~vag--t~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~ 311 (916)
.+|+..++.+++|+. +.+.|+|+|..| .+++++|.+||++|+++|+.++++|++.++++
T Consensus 169 ~~Ee~~~~~~l~va~~~~~~~i~~i~~~g-~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 169 EEEDMYGEADMPVAMMPKLGEITLLQLDG-DMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred HHHhhcCCCceEEEEeCCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999997 456799999998 89999999999999999999999999988753
No 14
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=2.6e-35 Score=313.94 Aligned_cols=218 Identities=27% Similarity=0.375 Sum_probs=188.2
Q ss_pred CCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCccccc-C
Q 002487 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVG-R 527 (916)
Q Consensus 449 R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~-r 527 (916)
|+|||+++|+|++.+++|++++|+|||+|++|+|+|+|+|+ ++........ ....+.+.++|+|+||++.+++ +
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~-~~~~~p~~~~----~~~~g~l~v~~~~~p~a~~~~~~r 75 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTAS-VEEKVPPFLR----GSGEGWITAEYGMLPRATQTRNRR 75 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEE-ccCccCCccc----CCCcEEEEEEEecCCCCCCCCccc
Confidence 89999999999999999999999999999999999999994 4433211111 1235789999999999998763 3
Q ss_pred ---CCCCChhhHHHHHHHHHHhccccCCCCCCC-eEEEEEEEEEecCCCcchhHHhHHHHHHHhc-----------CCCc
Q 002487 528 ---IGAPSRREIGHGTLAERALEPVLPSDNDFP-YTIRVESTITESNGSSSMASVCGGCLALQDA-----------GVPI 592 (916)
Q Consensus 528 ---~g~~~rrei~~~~l~eraL~~vip~~~~fp-~tI~V~~~VLesdGs~~~Asv~aaslAL~dA-----------GIP~ 592 (916)
.|.+++++++++++++|+|+++|++ +.|| ++|+|+++||++|||.++||+||+++||+|| ||||
T Consensus 76 ~~~~g~~~~~~~e~~~~i~r~lr~~i~l-~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~ 154 (236)
T TIGR01966 76 ESAKGKQSGRTQEIQRLIGRALRAVVDL-EALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPI 154 (236)
T ss_pred cccCCCCCccHHHHHHHHHHHHHHhcCH-hhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCc
Confidence 2567778999999999999999998 6776 4799999999999999999999999999999 9999
Q ss_pred ccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecC-CceeEEEeeccccCCCHHHHHHHHHHHHhhh
Q 002487 593 KCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNE-DGITAFQMDIKVGGITLPVMKKALQQAKDGR 671 (916)
Q Consensus 593 ~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~-~gItalq~d~K~ggis~e~l~eaL~~A~~a~ 671 (916)
+++++++++|++.+ .+++||+..|+..+++.++++.+. +.|+++|+++..+.++.+.+.+|++.|++++
T Consensus 155 ~~~~~~vt~~~~~~----------~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~ 224 (236)
T TIGR01966 155 RDFVAAVSVGIVDG----------EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGI 224 (236)
T ss_pred cCceeEEEEEEECC----------EEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHH
Confidence 99999999999953 377899999999998888888543 4589999864335699999999999999999
Q ss_pred HHHHHHHHhcC
Q 002487 672 RHILAEMLKCS 682 (916)
Q Consensus 672 ~~Il~~m~~~i 682 (916)
.++.+.|++++
T Consensus 225 ~~l~~~~~~~l 235 (236)
T TIGR01966 225 RELIELQKQAL 235 (236)
T ss_pred HHHHHHHHHHh
Confidence 99999999876
No 15
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=1.2e-33 Score=307.26 Aligned_cols=234 Identities=21% Similarity=0.306 Sum_probs=202.0
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeE
Q 002487 431 FKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKR 510 (916)
Q Consensus 431 ~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~ 510 (916)
++..+++++++.+ ++|+|+|||+++|+|++.+++|++++++|||+++.|+|+|+|+|+.++.+. ..+...+++
T Consensus 8 ~~~~e~~~i~~~l-~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p------~~~~~~~g~ 80 (271)
T PRK04282 8 IPEIKKDYILSLL-KKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEP------FPDTPNEGV 80 (271)
T ss_pred hhHHHHHHHHHHH-hcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecC------CCCCCCCCE
Confidence 5667778877775 789999999999999999999999999999999999999999997554332 111234688
Q ss_pred EEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCC--------CCCCCeEEEEEEEEEecCCCcchhHHhHHH
Q 002487 511 FYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPS--------DNDFPYTIRVESTITESNGSSSMASVCGGC 582 (916)
Q Consensus 511 ~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~--------~~~fp~tI~V~~~VLesdGs~~~Asv~aas 582 (916)
+.++|+|+|||+..+ +.+++++++++++++++|+|++..+. +.++.|+|+|+++||++|||..+|+++|++
T Consensus 81 i~~~v~~~~~a~~~~-~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~ 159 (271)
T PRK04282 81 LIVNAELLPLASPTF-EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAV 159 (271)
T ss_pred EEEEEEECCCcCccc-cCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHH
Confidence 999999999998765 45678999999999999999874222 246689999999999999999999999999
Q ss_pred HHHHhcCCC--------------------cccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCC-
Q 002487 583 LALQDAGVP--------------------IKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNED- 641 (916)
Q Consensus 583 lAL~dAGIP--------------------~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~- 641 (916)
+||+|+++| |++++.++++|++.+ .+++||+.+|+..++..++|+.+.+
T Consensus 160 aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~~~~p~~vt~~~~~~----------~~v~Dpt~~Ee~~~~~~l~va~~~~g 229 (271)
T PRK04282 160 AALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGN----------YLIVDPTLEEESVMDARITITTDEDG 229 (271)
T ss_pred HHHHhCCCCcEEEcCCceeccCCCcccCCCCCeeEEEEEEEECC----------EEEECCCHHHHhhcCceEEEEECCCC
Confidence 999999995 999999999999943 4778999999999999999998877
Q ss_pred ceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCC
Q 002487 642 GITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSP 683 (916)
Q Consensus 642 gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~ 683 (916)
.|++++..+ .++++.+.+.+|++.|+++++.+.+.|+++++
T Consensus 230 ~i~~l~~~g-~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 230 NIVAIQKSG-IGSFTEEEVDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred cEEEEEcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 688888652 24599999999999999999999999998874
No 16
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=3e-33 Score=298.55 Aligned_cols=205 Identities=20% Similarity=0.216 Sum_probs=177.1
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCC---CCCCCCccccceeecccccccCCCCCccc---CCCCCc
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPS---EPSDFFPLNVNYQERFSAAGRTSGGFFKR---EGRTKD 171 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~---~~~~f~pL~v~y~ek~~A~g~iPg~f~kR---eg~p~~ 171 (916)
-|++++++|.+ .+|+|||++++|+|+|+|+|+++...+ .+.+..+|+|+|.-..+|..+ |.+| .|+|++
T Consensus 11 ~R~i~~~~g~~-~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~----~~~~~~~~g~~~~ 85 (238)
T PRK00173 11 LRPVTITRNFT-KHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHT----RNDREAAKGKQGG 85 (238)
T ss_pred ccCeEEEeCCC-CCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcc----cccccccCCCCCc
Confidence 48999999998 899999999999999999999864422 233566789998644433332 1122 378899
Q ss_pred hhhhHHHHhcCcccccccCCCcCe--EEEEEEEEeecCCCChhHHHHHHHHHHhcCC-----------CCCCCCceEEEE
Q 002487 172 HEVLVCRLIDRPLRPTLIKGFYHE--TQILSWVLSYDGLHFPDALAVTAAGIAVALS-----------EVPNSKVIAGVR 238 (916)
Q Consensus 172 ~eil~sRlIdR~LRplfp~~~~~~--iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S-----------~IP~~~~VaaV~ 238 (916)
++++++|+|+|+|||+||..+++. ++|+++||++||+. +.+|+|||++||+++ ++||++++++|+
T Consensus 86 ~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~--~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~~vt 163 (238)
T PRK00173 86 RTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGT--RTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVS 163 (238)
T ss_pred cHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCH--HHHHHHHHHHHHHHhhhhhhccCcccCCcccCceeEEE
Confidence 999999999999999999777655 99999999999986 489999999999977 999999999999
Q ss_pred EEEECCEEEECCChHHHhhCCeeEEEEeecC-eEEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 239 VGLVGDKFIVNPTTQEMEDSQLDLLLAGSDD-AILMIEGY--CDFLSEEMLIQAVQVGQDAVREISNEVKALVE 309 (916)
Q Consensus 239 vg~i~g~~ildPt~~E~~~s~~dl~vagt~~-~i~mie~~--~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~ 309 (916)
+|+++|++|+|||.+|+..++.+|+|+++.+ .|+|++.. ++.+++++|.+|+++|++++++++++|++.++
T Consensus 164 ~~~~~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 164 VGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237 (238)
T ss_pred EEEECCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999875 59999983 46899999999999999999999999998764
No 17
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=4e-33 Score=298.62 Aligned_cols=210 Identities=18% Similarity=0.238 Sum_probs=176.9
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCCCCCchhhhHH
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVC 177 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil~s 177 (916)
-|++++++|.+ ++|||||++++|+|+|+|+|+||++...+....|....+...+. ...+.+.+ +++++|++++++++
T Consensus 24 ~R~i~i~~G~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~-~~p~~~~~-~~~~~~~~~~~~~s 100 (244)
T PRK03983 24 LRPIKIEVGVL-KNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYN-MAPFSVDE-RKRPGPDRRSIEIS 100 (244)
T ss_pred ccceEEEeCCC-CCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEE-cCCCcccc-ccCCCCChhHHHHH
Confidence 48899999999 89999999999999999999999876555545553333222211 11222333 44567999999999
Q ss_pred HHhcCcccccccCCCcCe--EEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCChHHH
Q 002487 178 RLIDRPLRPTLIKGFYHE--TQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEM 255 (916)
Q Consensus 178 RlIdR~LRplfp~~~~~~--iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt~~E~ 255 (916)
|+|+|+|||+++..+++. ++|.++||+.||+ ...+|+|||++||++|||||+++++||+|++++|++++|||.+|+
T Consensus 101 ~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~--~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~~~~~i~DPt~~Ee 178 (244)
T PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLQADAG--TRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEED 178 (244)
T ss_pred HHHHHHHHHhccHHhCCCeEEEEEEEEEECCCC--HHHHHHHHHHHHHHhcCCccccceeEEEEEEECCEEEECCCHHHh
Confidence 999999999998777776 6666679999987 458999999999999999999999999999999999999999999
Q ss_pred hhCCeeEEEEee--cCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002487 256 EDSQLDLLLAGS--DDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK 313 (916)
Q Consensus 256 ~~s~~dl~vagt--~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk 313 (916)
..++.+|+||++ .+.|+|+|..| .++++++.+|+++|+++|++|+++|++.+++...
T Consensus 179 ~~~~~~l~va~~~~~~~I~~l~~~G-~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~ 237 (244)
T PRK03983 179 NYGEADMPVAIMPRLGEITLLQLDG-NLTREEFLEALELAKKGIKRIYQLQREALKSKYG 237 (244)
T ss_pred ccCCceEEEEEECCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999997 35699999998 8999999999999999999999999997765443
No 18
>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=100.00 E-value=2.9e-32 Score=327.98 Aligned_cols=219 Identities=21% Similarity=0.242 Sum_probs=198.3
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEE-ecCCCCCCCCCCccccceeecccccccCCC---CCcccCCCCCch
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVC-LADVPSEPSDFFPLNVNYQERFSAAGRTSG---GFFKREGRTKDH 172 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~-~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg---~f~kReg~p~~~ 172 (916)
.-|+|++++|.+ .+|||||++++|+|+|||+|+ |+.+ ..+.+.++..+++.+++....||+ ++++|.|+|+++
T Consensus 319 e~Rpi~~~~g~l-~~a~GSa~~~~G~Tqvl~~vt~g~~~--~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rr 395 (684)
T TIGR03591 319 TIRPISIEVGVL-PRTHGSALFTRGETQALVVTTLGTER--DEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRR 395 (684)
T ss_pred CcCceEEEeCCC-CCCCceEEEEeCCeEEEEEEecCCcc--cccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChH
Confidence 358999999999 679999999999999999996 6644 234555677788888888888886 888999999999
Q ss_pred hhhHHHHhcCccccccc--CCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEEC-C----E
Q 002487 173 EVLVCRLIDRPLRPTLI--KGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVG-D----K 245 (916)
Q Consensus 173 eil~sRlIdR~LRplfp--~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~-g----~ 245 (916)
|++++++++|+|||++| ..|.|.++|+++||++||+.. +||+||||+||++|||||.++|+||++|+++ | .
T Consensus 396 ei~~~~l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~--~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~ 473 (684)
T TIGR03591 396 EIGHGALAERALKAVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFA 473 (684)
T ss_pred HHHHHHHHHHHHHHhcCccccCCeEEEEEEEEEeCCCChH--HHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceE
Confidence 99999999999999999 788999999999999999888 9999999999999999999999999999994 3 5
Q ss_pred EEECCChHHHhhCCeeEEEEeecCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCC
Q 002487 246 FIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYC--DFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTI 320 (916)
Q Consensus 246 ~ildPt~~E~~~s~~dl~vagt~~~i~mie~~~--~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~ 320 (916)
+++||+..|+..+++||.|+||.++|+++|+++ ..++.+.|.+||+.|++++++|++.|++.+.+.+++...+.+
T Consensus 474 il~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p 550 (684)
T TIGR03591 474 VLSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAP 550 (684)
T ss_pred EEeCCChHHHhcCCceEEEEEcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCC
Confidence 899999999999999999999999999999954 458999999999999999999999999999999987766665
No 19
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=6.3e-32 Score=288.01 Aligned_cols=204 Identities=20% Similarity=0.235 Sum_probs=169.5
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCC---CCCCCccccceeecccccccCCCCCcccC---CCCCc
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSE---PSDFFPLNVNYQERFSAAGRTSGGFFKRE---GRTKD 171 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~---~~~f~pL~v~y~ek~~A~g~iPg~f~kRe---g~p~~ 171 (916)
-|++++++|.+ +||+|||++++|+|+|||+|+++...+. ..+..+|+|+|.-..+|.. .+.+|+ |++++
T Consensus 10 ~R~i~i~~G~~-~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~----~~~~r~~~~g~~~~ 84 (236)
T TIGR01966 10 LRPVSITRDFL-KHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQ----TRNRRESAKGKQSG 84 (236)
T ss_pred ccCeEEEeCCc-CCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCC----CCccccccCCCCCc
Confidence 48999999966 9999999999999999999997543221 1234567777653322221 111344 78888
Q ss_pred hhhhHHHHhcCcccccccCCCcC--eEEEEEEEEeecCCCChhHHHHHHHHHHhcCC-----------CCCCCCceEEEE
Q 002487 172 HEVLVCRLIDRPLRPTLIKGFYH--ETQILSWVLSYDGLHFPDALAVTAAGIAVALS-----------EVPNSKVIAGVR 238 (916)
Q Consensus 172 ~eil~sRlIdR~LRplfp~~~~~--~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S-----------~IP~~~~VaaV~ 238 (916)
++++++|+|+|+|||+|+..+++ .++|+++||++||+. +.||+|||++||+++ +|||++++++|+
T Consensus 85 ~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~--~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt 162 (236)
T TIGR01966 85 RTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGT--RTASITGAFVALADAISKLHKRGILKESPIRDFVAAVS 162 (236)
T ss_pred cHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCH--HHHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEE
Confidence 89999999999999999987665 458999999999976 599999999999977 999999999999
Q ss_pred EEEECCEEEECCChHHHhhCCeeEEEEeecC-eEEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 239 VGLVGDKFIVNPTTQEMEDSQLDLLLAGSDD-AILMIEGY--CDFLSEEMLIQAVQVGQDAVREISNEVKALV 308 (916)
Q Consensus 239 vg~i~g~~ildPt~~E~~~s~~dl~vagt~~-~i~mie~~--~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~ 308 (916)
+|++++++|+|||.+|+..++.+|.++.+.+ .|+|+|.. ++.++++++.+||++|++++++++++|++.+
T Consensus 163 ~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 163 VGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred EEEECCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999877777776544 59999984 4789999999999999999999999998764
No 20
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.98 E-value=1.3e-31 Score=323.07 Aligned_cols=212 Identities=21% Similarity=0.256 Sum_probs=188.2
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEE-ecCCCCCCCCCCccccceeecccccccCCC---CCcccCCCCCch
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVC-LADVPSEPSDFFPLNVNYQERFSAAGRTSG---GFFKREGRTKDH 172 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~-~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg---~f~kReg~p~~~ 172 (916)
.-|+|.+++|.+ .+|||||++++|+|+|||+|+ |+.. +.+.+.++..+++.+++....||+ ++++|.|+|+++
T Consensus 323 e~Rpi~~~~g~l-~~a~GSal~~~G~T~Vl~~vt~g~~~--~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rr 399 (693)
T PRK11824 323 EIRPISIEVGVL-PRTHGSALFTRGETQALVVATLGTLR--DEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRR 399 (693)
T ss_pred cccceEEEeCCC-CCCCceEEEEECCeEEEEEEecCCCc--ccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChh
Confidence 358999999999 679999999999999999996 5532 334455666677777777778886 788899999999
Q ss_pred hhhHHHHhcCccccccc--CCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEEC-C---EE
Q 002487 173 EVLVCRLIDRPLRPTLI--KGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVG-D---KF 246 (916)
Q Consensus 173 eil~sRlIdR~LRplfp--~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~-g---~~ 246 (916)
|++++++++|+|||++| ..|.|.++|+++||++||+.. +||+||||+||++|||||.++|+||++|+++ | .+
T Consensus 400 e~~~~~li~ral~~vi~~~~~~p~~I~v~~~VLe~dGs~~--~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~i 477 (693)
T PRK11824 400 EIGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAV 477 (693)
T ss_pred HHHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEecCCCHH--HHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEE
Confidence 99999999999999999 478899999999999999888 9999999999999999999999999999994 4 37
Q ss_pred EECCChHHHhhCCeeEEEEeecCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002487 247 IVNPTTQEMEDSQLDLLLAGSDDAILMIEGYC--DFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK 313 (916)
Q Consensus 247 ildPt~~E~~~s~~dl~vagt~~~i~mie~~~--~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk 313 (916)
++||+..|+..+++||.|+||.++|+++|+++ +.++.+.|.+||+.|+++++.|++.|++.+.+...
T Consensus 478 l~D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~ 546 (693)
T PRK11824 478 LTDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRA 546 (693)
T ss_pred EcCCChhhHhhCCceEEEEecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChh
Confidence 88999999999999999999999999999875 35899999999999999999999999998865544
No 21
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1e-30 Score=272.77 Aligned_cols=201 Identities=19% Similarity=0.253 Sum_probs=170.1
Q ss_pred CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCC----CCCCCccccceeecccccccCCCCCcccCCC-CC-
Q 002487 97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSE----PSDFFPLNVNYQERFSAAGRTSGGFFKREGR-TK- 170 (916)
Q Consensus 97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~----~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~-p~- 170 (916)
.-|+|.++.|.+ ++|+||+++++|||+|+|+|+||+++.+ +.+..+++++|.- .|.+-..|.-+ ++
T Consensus 17 elR~i~~~~~~~-~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m-------~p~sT~~R~~~~~~~ 88 (230)
T COG0689 17 ELRPIKITRGVL-KHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGM-------LPRSTDERKKREADR 88 (230)
T ss_pred cccceEEEeccc-cCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEec-------ccccccccccccccc
Confidence 469999999999 8999999999999999999999988754 3467789999964 44443333211 22
Q ss_pred chhhhHHHHhcCcccccccCCCc--CeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEE
Q 002487 171 DHEVLVCRLIDRPLRPTLIKGFY--HETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIV 248 (916)
Q Consensus 171 ~~eil~sRlIdR~LRplfp~~~~--~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~il 248 (916)
.|+.+++|+|.|+||+.+....+ ..|+|+|+|+++||++. +++||||++||++++|||.+.|+||+||.++|.+++
T Consensus 89 gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTr--ta~It~A~lAL~DAgipl~~~vaaiSvgi~~~~~~l 166 (230)
T COG0689 89 GRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTR--TASITGASLALADAGIPLRDLVAAISVGIVDGVIVL 166 (230)
T ss_pred cchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCee--eehhhHHHHHHHHcCCchhhheeEeEEEEECCceEe
Confidence 48999999999999994433322 27899999999999988 999999999999999999999999999999999999
Q ss_pred CCChHHHhhCCeeEEEEeecC-eEEEE---EecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 249 NPTTQEMEDSQLDLLLAGSDD-AILMI---EGYCDFLSEEMLIQAVQVGQDAVREISNEVKALV 308 (916)
Q Consensus 249 dPt~~E~~~s~~dl~vagt~~-~i~mi---e~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~ 308 (916)
||++.|++.+..|+.|+.+.+ +++-| +.++ .|++++|.++|++|.++|+++++.|++++
T Consensus 167 Dl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~-~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 167 DLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDG-PFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred cCcchhhcccccCceEEEEecCCeEEEEEEeccC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999888998888765 34444 4454 89999999999999999999999999875
No 22
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=6.1e-29 Score=261.68 Aligned_cols=232 Identities=22% Similarity=0.307 Sum_probs=200.2
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEE
Q 002487 433 EVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFY 512 (916)
Q Consensus 433 ~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~ 512 (916)
.+.++++.+. ++.|+|+|||.++|+|||.+++|+++.|+|||+++.|+|||+|+|+.+. ..++++...++.|.
T Consensus 9 ~~~~~~i~~l-l~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~ei------g~Pf~DtP~eG~~~ 81 (272)
T COG2123 9 EIKREYILNL-LKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEI------GEPFPDTPNEGVLV 81 (272)
T ss_pred hhHHHHHHHH-hccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEccc------CCCCCCCCCCceEE
Confidence 3444555554 5789999999999999999999999999999999999999999996433 33555556788999
Q ss_pred EEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhcc--------ccCCCCCCCeEEEEEEEEEecCCCcchhHHhHHHHH
Q 002487 513 LQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEP--------VLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLA 584 (916)
Q Consensus 513 ~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~--------vip~~~~fp~tI~V~~~VLesdGs~~~Asv~aaslA 584 (916)
++.++.|.+...+.+ |+|++.+++++++++|.|+. +++.++++.|.|+++++||++|||..+||..|+.+|
T Consensus 82 ~n~El~Plas~~fE~-Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aA 160 (272)
T COG2123 82 VNVELSPLASPSFEP-GPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAA 160 (272)
T ss_pred eeeeeeccccccccC-CCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHH
Confidence 999999999887765 67889999999999999865 555557889999999999999999999999999999
Q ss_pred HHhcCCC----------------------cccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCc
Q 002487 585 LQDAGVP----------------------IKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642 (916)
Q Consensus 585 L~dAGIP----------------------~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~g 642 (916)
|+++.+| +..++..++++.+.+ ++++||+.+|+..+|..++|.-+.+|
T Consensus 161 L~~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~----------~lvvDPsleEe~v~d~~ltit~~~~~ 230 (272)
T COG2123 161 LLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKIGN----------VLVVDPSLEEELVADGRLTITVNEDG 230 (272)
T ss_pred HHhcCCCceeecCCcceeecccCCCcccccCCCceEEEEEEECC----------EEEeCCCcchhhhcCceEEEEECCCC
Confidence 9999998 567788899999964 58899999999999999999988775
Q ss_pred -eeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCC
Q 002487 643 -ITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSP 683 (916)
Q Consensus 643 -Italq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~ 683 (916)
|+++|.-+ .+.++++.+.+|++.|.....++++.+.+++.
T Consensus 231 ~Iv~iqK~g-~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 231 EIVAIQKVG-GGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred cEEEEEEcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 88888542 24489999999999999999999999888764
No 23
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=6.3e-29 Score=249.15 Aligned_cols=201 Identities=20% Similarity=0.360 Sum_probs=177.9
Q ss_pred CccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhH
Q 002487 457 GIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREI 536 (916)
Q Consensus 457 eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei 536 (916)
.+|++.|+.|+|+++|||+.|.+|+|+|+|+| +||.+...+.+.+ .+..+++.+.|-+ |-++++|.
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V-~GP~dvk~r~E~~------~katleVi~rp~~-------G~~~~~eK 69 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSV-YGPIDVKARQEDP------EKATLEVIWRPKS-------GVNGTVEK 69 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEe-eCCcchhhcccCc------hhceEEEEEeccc-------CcchHHHH
Confidence 78999999999999999999999999999999 8999887765543 3467899999875 66888999
Q ss_pred HHHHHHHHHhccccCCCCCCCe-EEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCC
Q 002487 537 GHGTLAERALEPVLPSDNDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGT 615 (916)
Q Consensus 537 ~~~~l~eraL~~vip~~~~fp~-tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~ 615 (916)
.+++++++.|+++|.+ +.||+ +|+|.++|+++|||.+.++||||+|||.||||||+.+.+|+.+.+.+++
T Consensus 70 ~~e~iI~~tl~~~I~l-~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~-------- 140 (217)
T KOG1069|consen 70 VLERIIRKTLSKAIIL-ELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDG-------- 140 (217)
T ss_pred HHHHHHHHHHHHhhee-eecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCc--------
Confidence 9999999999999999 89999 5999999999999999999999999999999999999999999999875
Q ss_pred ceeecCCChhhhh--cCCccEEEEe---cCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCC
Q 002487 616 PLILSDITGSEDA--SGDMDFKVAG---NEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPP 684 (916)
Q Consensus 616 ~~iL~Dpt~~Ed~--~gdmdf~Vag---t~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~ 684 (916)
.+++||+..++. .+...+++.+ ...+++++... |.++.++|+.+++.|+.++.++..+|++.+..
T Consensus 141 -~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~---G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069|consen 141 -VLVLDPTAKQEKISTARATLSFEGGSLGEPKVIISETN---GEKSEDQLFYVLELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred -cEEECCcHHhhhhhhceEEEEEecCCCCCcceEEEecc---CCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence 477899999998 5555677754 34456666544 77999999999999999999999999998864
No 24
>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=99.96 E-value=1.8e-28 Score=290.09 Aligned_cols=213 Identities=19% Similarity=0.198 Sum_probs=183.8
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEec---CCCCC----CCCCCccccceeecccccccCCCCCcccCCCCC
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLA---DVPSE----PSDFFPLNVNYQERFSAAGRTSGGFFKREGRTK 170 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~---~e~~~----~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~ 170 (916)
-|++++++|.+ .+|+|||++++|+|+|||+++.. .+... +.+.-.+.++|....||.| ..+|.+.|+
T Consensus 345 iR~i~~~~g~l-~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~-----er~~~~~~~ 418 (719)
T TIGR02696 345 IRPLDAEVQVI-PRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTG-----ETGRVGSPK 418 (719)
T ss_pred cccceeecCCC-CCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCccc-----CCCCCCCCC
Confidence 48999999999 89999999999999999998852 11111 1223345688877776665 456778889
Q ss_pred chhhhHHHHhcCccccccc--CCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEEC----C
Q 002487 171 DHEVLVCRLIDRPLRPTLI--KGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVG----D 244 (916)
Q Consensus 171 ~~eil~sRlIdR~LRplfp--~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~----g 244 (916)
.||+++++|+.|+|+|.+| ..|.+.+.++++||++||+.. +|||||||+||++|||||+++|+||++|+++ |
T Consensus 419 RReighg~La~rALe~vI~~~e~fP~TIrvvseVLeSdGSss--~AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~~~ 496 (719)
T TIGR02696 419 RREIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTS--MGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDG 496 (719)
T ss_pred ccHHHHHHHHHHHHHHhhCcHhhCCCEEEEEEEeeccCCcHH--HHHHHHHHHHHHHcCcchhheeeEEEEEEeccccCC
Confidence 9999999999999999998 788888999999999999888 9999999999999999999999999999993 3
Q ss_pred E----EEECCChHHHhhCCeeEEEEeecCeEEEEEecCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccc
Q 002487 245 K----FIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDF--LSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLD 318 (916)
Q Consensus 245 ~----~ildPt~~E~~~s~~dl~vagt~~~i~mie~~~~~--~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~ 318 (916)
+ +++||+..|+..+++||.|+||.++|+.+|++++- ++.+.|.+||++|.++|..|++.|++.+... .+...+
T Consensus 497 ~~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~ 575 (719)
T TIGR02696 497 ETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMAEAIDTP-DEMSPY 575 (719)
T ss_pred CcceeEEeCCCchhhhcCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-cccccC
Confidence 3 89999999999999999999999999999998742 6999999999999999999999999999877 433333
Q ss_pred C
Q 002487 319 T 319 (916)
Q Consensus 319 ~ 319 (916)
.
T Consensus 576 a 576 (719)
T TIGR02696 576 A 576 (719)
T ss_pred C
Confidence 3
No 25
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.95 E-value=3.1e-26 Score=249.13 Aligned_cols=203 Identities=23% Similarity=0.267 Sum_probs=172.1
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecC-CCCC-CCCCCccccceeecccccccCCCCCcccCCCCCchhhh
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLAD-VPSE-PSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVL 175 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~-e~~~-~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil 175 (916)
-|++.+++|.+ ++|+|||++++|+|+|+|+|++.. +|.. ..+-.-++++|....+|.. . .+.|+|++++++
T Consensus 34 ~R~i~i~~g~l-~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~a~~---~---~~~~~~~~~~~~ 106 (271)
T PRK04282 34 YRPIEIETGVI-KKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP---T---FEPGPPDENAIE 106 (271)
T ss_pred ccCeEEEeCCc-cCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCCcCc---c---ccCCCCCHHHHH
Confidence 48999999999 999999999999999999999642 3321 1122236667664444432 1 256899999999
Q ss_pred HHHHhcCcccccc----------cCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCC----------------
Q 002487 176 VCRLIDRPLRPTL----------IKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVP---------------- 229 (916)
Q Consensus 176 ~sRlIdR~LRplf----------p~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP---------------- 229 (916)
++|+|+|+||+.+ |..+.|.++|+++||+.||+.. .+|++||++||++++||
T Consensus 107 l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~--daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~ 184 (271)
T PRK04282 107 LARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLL--DASMLAAVAALLNTKVPAVEEGEDGVVDKLGED 184 (271)
T ss_pred HHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhCCCCcEEEcCCceeccCCCc
Confidence 9999999999853 5555789999999999998733 59999999999999995
Q ss_pred ----CCCceEEEEEEEECCEEEECCChHHHhhCCeeEEEEeecC-eEEEEEec-CCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002487 230 ----NSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDD-AILMIEGY-CDFLSEEMLIQAVQVGQDAVREISNE 303 (916)
Q Consensus 230 ----~~~~VaaV~vg~i~g~~ildPt~~E~~~s~~dl~vagt~~-~i~mie~~-~~~~~e~~l~~al~~a~~~~~~i~~~ 303 (916)
|++++.+|++|++++.+|+|||.+|++.++.+++|+.+++ +|++++.. ++.++.++|.+|++.|++.+++++++
T Consensus 185 ~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~~g~~~~~~~~l~~~i~~A~~~~~~l~~~ 264 (271)
T PRK04282 185 FPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKAIDIALEKAKELREK 264 (271)
T ss_pred ccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999888 69999964 56799999999999999999999999
Q ss_pred HHHHHH
Q 002487 304 VKALVE 309 (916)
Q Consensus 304 ~~~~~~ 309 (916)
+++.++
T Consensus 265 ~~~~l~ 270 (271)
T PRK04282 265 LKEALG 270 (271)
T ss_pred HHHHhc
Confidence 998763
No 26
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.9e-27 Score=272.12 Aligned_cols=171 Identities=26% Similarity=0.377 Sum_probs=147.0
Q ss_pred CceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC
Q 002487 726 VEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK 804 (916)
Q Consensus 726 v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~ 804 (916)
.+++.++ +++++.++.+.....+.+. .-..++..+++|++++| +|++|++|||||+|+ |++||||+|+|||.++.+
T Consensus 155 ~kiie~d~~~n~vv~SrR~~~e~~~~~-~r~e~~~~l~~G~vV~G-~V~~It~~GafVdig-GvdGLlHiseiS~~rv~~ 231 (541)
T COG0539 155 FKILELDKKRNNVVLSRRAVLEEERSE-QREELLNKLEVGEVVEG-VVKNITDYGAFVDIG-GVDGLLHISEISWKRVDH 231 (541)
T ss_pred EEEEEEccccCcEEEEhHHHhhHHHHH-HHHHHHhcCCCCceEEE-EEEEeecCcEEEEec-CeeeEEehhhccccccCC
Confidence 3356777 5678888877654333332 23456778899999999 999999999999998 799999999999999999
Q ss_pred ccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee-------------------------
Q 002487 805 AEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA------------------------- 858 (916)
Q Consensus 805 ~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V------------------------- 858 (916)
|+++|++||+|+|+|+++|. ++||+||+|+++++||..... +|++|+++.|+|
T Consensus 232 P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~-~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEi 310 (541)
T COG0539 232 PSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEK-KYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred HHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhh-hcCCCCEEEEEEEEeecCcEEEEecCCccceeechhh
Confidence 99999999999999999998 999999999999999999986 999999999996
Q ss_pred ccccccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCCCCc
Q 002487 859 ASDKLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSN 901 (916)
Q Consensus 859 s~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~~~~ 901 (916)
+|.+.. .|++.+++||+|.|+|++||+++||||||+++.-.+
T Consensus 311 sw~~~~-~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~ 352 (541)
T COG0539 311 SWTKKN-VPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKEN 352 (541)
T ss_pred cccccC-CHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcC
Confidence 343333 389999999999999999999999999998754443
No 27
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.3e-27 Score=270.69 Aligned_cols=247 Identities=22% Similarity=0.337 Sum_probs=195.7
Q ss_pred eeEEEeeccccCCCHHHHHHHHHHH--HhhhHHHHHHHHh--cCCCCCCCCCCCCC---------eEEEEeeccceeeee
Q 002487 643 ITAFQMDIKVGGITLPVMKKALQQA--KDGRRHILAEMLK--CSPPPSNSLSKHAP---------LIHIMKVKPEKINLI 709 (916)
Q Consensus 643 Italq~d~K~ggis~e~l~eaL~~A--~~a~~~Il~~m~~--~i~~~r~~~~~~aP---------~i~~~~I~~~ki~~v 709 (916)
+..+.+|.+.+.+ -..++++..+ .+.+..+++.++. .+.+-.+.+.+|+. ++|..+|.|.++.++
T Consensus 155 ~kiie~d~~~n~v--v~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P 232 (541)
T COG0539 155 FKILELDKKRNNV--VLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHP 232 (541)
T ss_pred EEEEEEccccCcE--EEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCH
Confidence 4446666554432 1112222221 2344445555543 44556677888887 678889999998773
Q ss_pred ecCCchhHHHHHHHhCCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCe
Q 002487 710 IGSGGKKVKSIIEETGVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGR 788 (916)
Q Consensus 710 IG~gGk~Ik~I~~~~~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~ 788 (916)
..+-.+.++..+++|++| +.++|.++.+... .+.|+.+...+++|+.+.| +|+++++|||||++.+|+
T Consensus 233 -----~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~-----~dPw~~i~~~~~~g~~v~G-~Vt~i~~~GafVei~~Gv 301 (541)
T COG0539 233 -----SEVVKVGDEVKVKVISLDEERGRVSLSLKQLE-----EDPWEGIEKKYPVGDKVEG-KVTNLTDYGAFVEIEEGV 301 (541)
T ss_pred -----HHhcccCCEEEEEEEEEccCCCeEEEEehhcc-----cCcHHHHhhhcCCCCEEEE-EEEEeecCcEEEEecCCc
Confidence 344445556667789998 7899999988765 3789999999999999999 999999999999999999
Q ss_pred eeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee---------
Q 002487 789 EGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--------- 858 (916)
Q Consensus 789 eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--------- 858 (916)
+||+|+|||+|.+...|.+++++||+|.|+|+++|+ ++||+||+|++..+||..+.. .|++|++++|+|
T Consensus 302 EGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~-~~~~g~~v~g~v~~~t~~g~f 380 (541)
T COG0539 302 EGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFAD-KHPVGDVVEGKVKSITDFGAF 380 (541)
T ss_pred cceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhh-hcCCCCeEEEEEeeecccceE
Confidence 999999999999998899999999999999999999 999999999999999999997 799999999997
Q ss_pred ----------------ccccccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCC----CCCCcccc
Q 002487 859 ----------------ASDKLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKD----RPYSNKDR 904 (916)
Q Consensus 859 ----------------s~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~----~~~~~~~~ 904 (916)
+|....... ..|++|++++++|+.+|.+++||||+.+ +|+.+...
T Consensus 381 v~le~gidG~vh~~d~sw~~~~~~~-~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~ 445 (541)
T COG0539 381 VELEGGIDGLVHLSDLSWDRPGEEA-EKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSE 445 (541)
T ss_pred EccCCCccceEEHHhcCccccCcHH-HhhccCcEEEEEEEEEecccceeeeehhhhccCchhhhHh
Confidence 333333333 3899999999999999999999999965 46665554
No 28
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.3e-26 Score=237.05 Aligned_cols=207 Identities=19% Similarity=0.249 Sum_probs=172.8
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCC----CCCCccccceeecccccccCCCCCcccCCCCCchh
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEP----SDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHE 173 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~----~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~e 173 (916)
-|+|...+|++ .||+||||+++|||||||+|+||++++.. .+-.-+.|.|.-..|+.| -++++.+.+.++
T Consensus 23 lR~i~~~~g~~-~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~-----~r~~~~~~~rr~ 96 (245)
T KOG1068|consen 23 LRRIYARIGVL-TQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTG-----DRKKRPKGDRRE 96 (245)
T ss_pred hhhhhhhcCcc-ccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccc-----hhccCCCccHHH
Confidence 47899999987 89999999999999999999999987642 233447888876654444 455556778899
Q ss_pred hhHHHHhcCcccccccCCCcC--eEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCC
Q 002487 174 VLVCRLIDRPLRPTLIKGFYH--ETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPT 251 (916)
Q Consensus 174 il~sRlIdR~LRplfp~~~~~--~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt 251 (916)
.+++.++.+++.|.+-...++ .++|.++||+.||.+. ++|||||++||+++||||++.|.|+++|+.+|.+++|||
T Consensus 97 ~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~l--aa~inaatlAL~daGI~m~D~i~~~t~~l~~~~~l~Dl~ 174 (245)
T KOG1068|consen 97 KELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNL--AAAINAATLALADAGIPMYDLITACTAGLADGTPLLDLT 174 (245)
T ss_pred HHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccH--HHHHHHHHHHHHHcCCChhhhhhhceeeecCCccccccc
Confidence 999999999999843333333 6777788888888666 999999999999999999999999999999999999999
Q ss_pred hHHHhhCCeeEEEEe--ecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002487 252 TQEMEDSQLDLLLAG--SDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK 313 (916)
Q Consensus 252 ~~E~~~s~~dl~vag--t~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk 313 (916)
.-|+......++|+. +.+.|..+|.++ .++.|.+...|++|.++|+.+.+.++..+.++-+
T Consensus 175 ~~eesa~~~~ltVa~l~~~~~i~~l~~~~-~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~ 237 (245)
T KOG1068|consen 175 SLEESARAPGLTVAALPNREEIALLQLDE-RLHCDHLETVLELAIAGCKRVYERLRLVLREHLK 237 (245)
T ss_pred cchhhccCCceEEEEecCcceEEEEEecC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999998665666664 555699999997 7999999999999999999999999988876543
No 29
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.1e-25 Score=225.91 Aligned_cols=192 Identities=19% Similarity=0.254 Sum_probs=167.2
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCC---CCCccccceeecccccccCCCCCcccCCCCCchhh
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPS---DFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEV 174 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~---~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~ei 174 (916)
-|++..|.|.| .++|||+-+.+|+|+|+|+|+||.+++..+ +-+-|.|-||.+. |-+...|.
T Consensus 5 lr~~~cei~iL-sr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~--------------G~~~~~eK 69 (217)
T KOG1069|consen 5 LRGIACEISIL-SRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKS--------------GVNGTVEK 69 (217)
T ss_pred hhhhhhhhcee-cCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEeccc--------------CcchHHHH
Confidence 36788999999 899999999999999999999998775433 4556788888775 78888999
Q ss_pred hHHHHhcCcccc-----cccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEE-CCEEEE
Q 002487 175 LVCRLIDRPLRP-----TLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLV-GDKFIV 248 (916)
Q Consensus 175 l~sRlIdR~LRp-----lfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i-~g~~il 248 (916)
.++|+|.+.|.+ ++|.. .+||.++|++.||+.. ++|||||++||.|+||||+.+.+|+.+.+. ||.+++
T Consensus 70 ~~e~iI~~tl~~~I~l~l~Prt---~iqVsiqvv~ddgs~L--acaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~ 144 (217)
T KOG1069|consen 70 VLERIIRKTLSKAIILELYPRT---TIQVSIQVVEDDGSTL--ACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVL 144 (217)
T ss_pred HHHHHHHHHHHHhheeeecCCc---eEEEEEEEEecCCcch--HHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEE
Confidence 999999999887 55543 8999999999999865 999999999999999999999999999998 579999
Q ss_pred CCChHHHhhC--CeeEEEEe---ecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 249 NPTTQEMEDS--QLDLLLAG---SDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEM 310 (916)
Q Consensus 249 dPt~~E~~~s--~~dl~vag---t~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~ 310 (916)
|||..|+..+ ...|.+.+ ...++++.+..| .+++++|..++++|..+++.++.++++.+++
T Consensus 145 Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G-~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069|consen 145 DPTAKQEKISTARATLSFEGGSLGEPKVIISETNG-EKSEDQLFYVLELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred CCcHHhhhhhhceEEEEEecCCCCCcceEEEeccC-CCCHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence 9999999954 45556644 344799999998 8999999999999999999999999998764
No 30
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.3e-22 Score=208.48 Aligned_cols=228 Identities=23% Similarity=0.286 Sum_probs=193.9
Q ss_pred HHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEe
Q 002487 437 KFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYS 516 (916)
Q Consensus 437 ~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~ 516 (916)
+++.+. |+.|.|.|||++.|+|.+.++.|- -.||+.++.|+|+|+|.|| .|...++.+++.++.|.+..+
T Consensus 12 ~fvl~a-lk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt------~~ia~Py~dRP~eG~~~I~te 81 (291)
T KOG1614|consen 12 KFVLNA-LKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVT------AQIAQPYIDRPHEGSFSIFTE 81 (291)
T ss_pred HHHHHH-HHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEee------hhhcCcccCCCCCCeeeeeec
Confidence 334443 678999999999999999999995 5899999999999999995 455566777788899999999
Q ss_pred eCCCCcccccCCCCCChhhHHHHHHHHHHhcc--------ccCCCCCCCeEEEEEEEEEecCCCcchhHHhHHHHHHHhc
Q 002487 517 FPPSSVGEVGRIGAPSRREIGHGTLAERALEP--------VLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDA 588 (916)
Q Consensus 517 fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~--------vip~~~~fp~tI~V~~~VLesdGs~~~Asv~aaslAL~dA 588 (916)
+.|++...+.. |+++..+..++++++++++. ++....+-.|.||+++.+|+.|||..+||..|+..|||.-
T Consensus 82 lsPmA~~sfE~-Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hF 160 (291)
T KOG1614|consen 82 LSPMASPSFEP-GRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHF 160 (291)
T ss_pred cccccccccCC-CCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhc
Confidence 99998776654 45778899999999999854 4444467789999999999999999999999999999999
Q ss_pred C-----------------------CCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCc-ee
Q 002487 589 G-----------------------VPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG-IT 644 (916)
Q Consensus 589 G-----------------------IP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~g-It 644 (916)
+ +-|..++..++.|+++.| + ++++|||..|+..+|..++|+.+.++ |+
T Consensus 161 rrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG-------~-ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc 232 (291)
T KOG1614|consen 161 RRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKG-------E-IVVIDPTEKEEAVMDGSMVVTMNKNREVC 232 (291)
T ss_pred CCCCcccccceeEecChhccCCcceeeeeccceEEEEEecCc-------e-EEEeCCcHHHHhccCceEEEEEcCCccEE
Confidence 8 337788889999999754 2 67799999999999999999987664 88
Q ss_pred EEEeeccccC--CCHHHHHHHHHHHHhhhHHHHHHHHhcCCCCC
Q 002487 645 AFQMDIKVGG--ITLPVMKKALQQAKDGRRHILAEMLKCSPPPS 686 (916)
Q Consensus 645 alq~d~K~gg--is~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r 686 (916)
++|.. || ++..++..|...|......+.+.+.+++++..
T Consensus 233 ~i~k~---G~~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~ 273 (291)
T KOG1614|consen 233 AIQKS---GGEILDESVIERCYKLAKDRAVEVTGIILEALEEDQ 273 (291)
T ss_pred EEecC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99854 55 68999999999999999999999988887653
No 31
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=6.3e-23 Score=210.28 Aligned_cols=241 Identities=19% Similarity=0.247 Sum_probs=185.2
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCce
Q 002487 429 LVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508 (916)
Q Consensus 429 ~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~ 508 (916)
++|+++.|+.+.+++|.+++|+|||...|+|.+.++.|.+++++|||++..|+|.|+|+++-+= .++.++...+
T Consensus 17 ~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei------~epstdapde 90 (298)
T KOG1613|consen 17 EVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEI------AEPSTDAPDE 90 (298)
T ss_pred HHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeee------cccccCCCCC
Confidence 5899999999999999999999999999999999999999999999999999999999996322 2233333456
Q ss_pred eEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhcc--------ccCCCCCCCeEEEEEEEEEecCCCcchhHHhH
Q 002487 509 KRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEP--------VLPSDNDFPYTIRVESTITESNGSSSMASVCG 580 (916)
Q Consensus 509 ~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~--------vip~~~~fp~tI~V~~~VLesdGs~~~Asv~a 580 (916)
+.+..+|.+||.|+..++ .|+|.+.+.-+++.+...+.+ ++....+..|..+.++.||++||+.++||.+|
T Consensus 91 g~Iv~n~~lpplcs~r~R-pG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~a 169 (298)
T KOG1613|consen 91 GDIVPNYALPPLCSSRFR-PGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNA 169 (298)
T ss_pred cceeecccCCcccccCCC-CCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHH
Confidence 778899999999987654 578999999888888777643 33344677899999999999999999999999
Q ss_pred HHHHHHhcCCCcc---c-----------ceeEEEE----EEEccC-------CCCCC---CCCceeecCCChhhhhcCCc
Q 002487 581 GCLALQDAGVPIK---C-----------SIAGVAM----GMVLDT-------DEFGG---DGTPLILSDITGSEDASGDM 632 (916)
Q Consensus 581 aslAL~dAGIP~~---~-----------~Vagvsv----gli~~~-------~~~~~---~~~~~iL~Dpt~~Ed~~gdm 632 (916)
..+||.+-.+|.- + .++..+. .+-.+. ..|.. -++..++.|||.+||++.+.
T Consensus 170 l~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~ 249 (298)
T KOG1613|consen 170 LMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITS 249 (298)
T ss_pred HHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhc
Confidence 9999999999831 1 0111000 000000 00100 01235668999999999999
Q ss_pred cEEEEecCC-ceeEEEeeccccC---CCHHHHHHHHHHHHhhhHHHHHHHH
Q 002487 633 DFKVAGNED-GITAFQMDIKVGG---ITLPVMKKALQQAKDGRRHILAEML 679 (916)
Q Consensus 633 df~Vagt~~-gItalq~d~K~gg---is~e~l~eaL~~A~~a~~~Il~~m~ 679 (916)
.++|..++. +++.+. |+|| ++.+.++.|++.|+...+++-..|.
T Consensus 250 ~lTIvldss~n~v~l~---k~GG~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 250 TLTIVLDSSGNYVQLT---KVGGGALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred eEEEEEcCCCCEEEEE---ecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999886544 455444 4555 6779999999999999998877664
No 32
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.89 E-value=8.8e-23 Score=198.15 Aligned_cols=130 Identities=32% Similarity=0.533 Sum_probs=116.2
Q ss_pred CccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhH
Q 002487 457 GIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREI 536 (916)
Q Consensus 457 eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei 536 (916)
|+|+|.+++|+++++||||+|++|+|+|+|+| .||.......+. . ...+++.++|+|+|++.+++++.+.+++++.
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V-~~~~~~~~~~~~-~--~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~ 76 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSV-KGPIEPPPSNER-D--DAEGRLTVEVEFSPFASPSFRRGGRPDEEER 76 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEE-EEEEEGCSCSTT-S--SSSEEEEEEEEECCCGSTSSSSSSSTHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEE-Eecccccchhcc-c--CCCceEEEEEEeccccccccccccccchhHH
Confidence 79999999999999999999999999999999 688876322221 1 1247899999999999999888788999999
Q ss_pred HHHHHHHHHhccccCCCCCCC-eEEEEEEEEEecCC-CcchhHHhHHHHHHHhcCCC
Q 002487 537 GHGTLAERALEPVLPSDNDFP-YTIRVESTITESNG-SSSMASVCGGCLALQDAGVP 591 (916)
Q Consensus 537 ~~~~l~eraL~~vip~~~~fp-~tI~V~~~VLesdG-s~~~Asv~aaslAL~dAGIP 591 (916)
.++++++++|++++.. +.|| |+|+|+++||++|| |.++|+++|+++||+|+|||
T Consensus 77 ~l~~~l~~~l~~~~~~-~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 77 ELSSLLERALRSSILL-EGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHHTBST-TTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHHHHHhhhccccccc-cccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999998 5665 89999999999999 99999999999999999998
No 33
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=5.5e-23 Score=238.24 Aligned_cols=354 Identities=19% Similarity=0.258 Sum_probs=236.0
Q ss_pred cceEEEeCCCC-CCcceeEEEeCCeEEEEEEEecCccccccccCCCC-CCceeEEEEEEeeCCCCcccccCCCCCChhhH
Q 002487 459 RPISSRCGLLP-RAHGSALFTRGETQSLAVITLGDKQMAQRIDNLES-DDEVKRFYLQYSFPPSSVGEVGRIGAPSRREI 536 (916)
Q Consensus 459 R~I~ie~g~l~-~a~GSalf~~G~TqVl~~Vt~Gp~~~~~~~d~~~~-~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei 536 (916)
|++.+++|.+. ||+||+++++|+|.||++|+ +.+ .....|+++- ..+.+++|....+|. |-++|.|+|+++|+
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~-~~~-~~~~~dF~PLtV~y~Ek~yaaGkiPG---gf~kREGrpse~e~ 88 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVV-ASK-PKEGQDFFPLTVNYEEKTYAAGKIPG---GFFKREGRPSEKEI 88 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEe-ecC-CCCCCCccceeEeeeeehhccCcCCC---cccccCCCCCccch
Confidence 78999999996 89999999999999999995 443 2223343331 134445554445543 34789999999999
Q ss_pred HHHHHHHHHhccccCCCCCCCeEEEEEEEEEecCCCcc--hhHHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCC
Q 002487 537 GHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSS--MASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDG 614 (916)
Q Consensus 537 ~~~~l~eraL~~vip~~~~fp~tI~V~~~VLesdGs~~--~Asv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~ 614 (916)
..++|++|.++|++|. .|-+.++|.++|++.|+... .++++|+|+||.-++||+..+++|+.+|++++
T Consensus 89 L~sRLIDRpiRPlFp~--g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg-------- 158 (692)
T COG1185 89 LTSRLIDRPIRPLFPK--GFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDG-------- 158 (692)
T ss_pred hhhhhcccccccccch--hhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECC--------
Confidence 9999999999999995 99999999999999999865 78999999999999999999999999999943
Q ss_pred CceeecCCChhhhhcCCccEEEEecCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCC
Q 002487 615 TPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAP 694 (916)
Q Consensus 615 ~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP 694 (916)
+|+ +.|+..|-+.+++|++||||.+.|.+++.+. ..+++++|.+|+..+++..+.++++.++......+....+.|
T Consensus 159 ~~v--lNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a--~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~ 234 (692)
T COG1185 159 IFV--LNPTLEELEESKLDLVVAGTKDAVNMVESEA--DELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEP 234 (692)
T ss_pred EEE--ECCChHHhhhcceeeEecCChhhhheeeccc--ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccc
Confidence 344 4999999999999999999999999999887 458999999999999999999999988755443222222222
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceecc--C--CCcc-eeEEecccccHHHHHHHHHhhhcCCCCCcEEEc
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDT--E--DDGT-VKITAKDLSSLEKSKAIISNLTMVPTVGDIYRN 769 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi--~--d~g~-v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G 769 (916)
- ..+.+-...+.....+.+++...-++....+. + .+.. -.+...+..........++.+...+---.+|++
T Consensus 235 ~----~~~~~l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~~~e~~~~~~~~~~~~~l~~~~vR~~Il~~ 310 (692)
T COG1185 235 P----SLDEELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEESSLKEIKAILEKLEKKPVRRLILEG 310 (692)
T ss_pred c----CccHHHHHHHHHHhHHHHHHHhcccchhhhhhhHHHHHHHHHHHHhhhccccHHHHHHHHHHHhHHHHHHHHhcC
Confidence 1 01111111111111111111110000000000 0 0000 000000000011112222222222222234444
Q ss_pred cEEEEEecceEEEEECC---CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC--CCceEEEEeecC
Q 002487 770 CEIKSIAPYGVFVEIAP---GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND--KGQLRLSRRALL 836 (916)
Q Consensus 770 ~~V~~I~~fGaFVel~~---g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~--~gkI~LS~K~~~ 836 (916)
.|.-...++.||.... ++-...|.|.|..+.-.++..+...|+...+++++... .++..|+++-..
T Consensus 311 -~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFP 381 (692)
T COG1185 311 -KVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFP 381 (692)
T ss_pred -CcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCC
Confidence 4444444555544431 22234899999998888889999999999999999865 467777776653
No 34
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.3e-21 Score=206.53 Aligned_cols=193 Identities=23% Similarity=0.276 Sum_probs=166.1
Q ss_pred eeEEEEeCccccCCCceEEEEeCCeEEEEEEEec-CCCCCC----------CCCCccccceeecccccccCCCCCcccCC
Q 002487 99 RQILVETGHMGRQASGAVTVTDGETIIYTSVCLA-DVPSEP----------SDFFPLNVNYQERFSAAGRTSGGFFKREG 167 (916)
Q Consensus 99 R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~-~e~~~~----------~~f~pL~v~y~ek~~A~g~iPg~f~kReg 167 (916)
|+|.+++|.+ +.|+|||+|++|+|+|+|.|... .+|.++ .++.||...+.|. |
T Consensus 34 R~ieI~~~vi-~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~El~Plas~~fE~---------------G 97 (272)
T COG2123 34 RPLEIETGVI-PKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEP---------------G 97 (272)
T ss_pred cceEEEeCce-ecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeeeeeccccccccC---------------C
Confidence 8999999999 88999999999999999999974 233322 2555666555444 8
Q ss_pred CCCchhhhHHHHhcCcccc----------cccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCC--------
Q 002487 168 RTKDHEVLVCRLIDRPLRP----------TLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVP-------- 229 (916)
Q Consensus 168 ~p~~~eil~sRlIdR~LRp----------lfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP-------- 229 (916)
+|++.+++++|++||.||. ..+....|-++++++||++||+-- -||..|+.+||+...+|
T Consensus 98 ppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~--Da~~lA~~aAL~~t~vP~~~~~~~~ 175 (272)
T COG2123 98 PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLI--DAASLAAVAALLNTRVPKAVEVGDG 175 (272)
T ss_pred CCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHhcCCCceeecCCc
Confidence 9999999999999999997 567888999999999999999533 68889999999987666
Q ss_pred --------------CCCceEEEEEEEECCEEEECCChHHHhhCCeeEEEEeecCe-EEEEEe-cCCCCCHHHHHHHHHHH
Q 002487 230 --------------NSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDA-ILMIEG-YCDFLSEEMLIQAVQVG 293 (916)
Q Consensus 230 --------------~~~~VaaV~vg~i~g~~ildPt~~E~~~s~~dl~vagt~~~-i~mie~-~~~~~~e~~l~~al~~a 293 (916)
+.+++.+|+++.+|+.+++|||.+|+..++..|++.-++++ |+.+|. ++..++++.+.+|++.|
T Consensus 176 ~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~g~~~~~~~~~~~~~~~A 255 (272)
T COG2123 176 EIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTA 255 (272)
T ss_pred ceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcEEEEEEcCCCcCCHHHHHHHHHHH
Confidence 67888999999999999999999999999999999998884 776666 46789999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 002487 294 QDAVREISNEVKALVE 309 (916)
Q Consensus 294 ~~~~~~i~~~~~~~~~ 309 (916)
.+...+++..+.+.++
T Consensus 256 ~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 256 LSKAEKLREALKEALK 271 (272)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999998887664
No 35
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.87 E-value=2.5e-22 Score=245.52 Aligned_cols=191 Identities=18% Similarity=0.251 Sum_probs=156.5
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEE
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIK 773 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~ 773 (916)
++|..+++|.++.++ ...-.+.++..+++|+++ +++++.++.+... .+.|..+...+++|++++| +|+
T Consensus 519 fvp~SeiS~~~v~~~-----~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~-----~~p~~~~~~~~~vG~iV~G-~V~ 587 (863)
T PRK12269 519 LLHVNDMSWGHVARP-----REFVKKGQTIELKVIRLDQAEKRINLSLKHFQ-----PDPWLEFENKFGVNDVVKG-RVT 587 (863)
T ss_pred EEEchhccccccCCH-----HHhccCCCEEEEEEEEEecCCCeEEEEEeccc-----cchhhhhhccCCCCCEEEE-EEE
Confidence 555567777666542 111122344456678888 5789999988653 3556777778999999999 999
Q ss_pred EEecceEEEEECCCeeeEEeccccCc-ccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCC
Q 002487 774 SIAPYGVFVEIAPGREGLCHISELSS-NWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTG 851 (916)
Q Consensus 774 ~I~~fGaFVel~~g~eGlvhiSels~-~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G 851 (916)
+|++||+||+|.+|++||+|+||++| .++.+|.+.|++||+|+|+|+++|. ++||.||+|++.++||..+.. +|++|
T Consensus 588 ~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~-~~~vG 666 (863)
T PRK12269 588 KIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEA-RYPVG 666 (863)
T ss_pred EEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHH-hCCCC
Confidence 99999999999999999999999999 6789999999999999999999998 899999999999999999875 89999
Q ss_pred CcEEEeeccc-------------------------cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 852 DPTKDAAASD-------------------------KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 852 ~vv~g~Vs~i-------------------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
++++|+|.++ +....++..|++||.|+|+|+++|++++||+||.++
T Consensus 667 ~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~ 737 (863)
T PRK12269 667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQ 737 (863)
T ss_pred CEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence 9999997332 222334457999999999999999999999999763
No 36
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.85 E-value=3.5e-21 Score=223.27 Aligned_cols=170 Identities=19% Similarity=0.308 Sum_probs=142.7
Q ss_pred CCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCccccc
Q 002487 725 GVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLA 803 (916)
Q Consensus 725 ~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~ 803 (916)
.+++++++ +++++.+|.+..... .....++.+...+++|+++.| +|+++++||+||+|. |++||||+|+|+|.++.
T Consensus 170 ~vkVleid~~~~~ivLSrr~~l~~-~~~~~~~~~~~~lk~G~iv~G-~V~~i~~~G~FVdlg-gv~Glv~~Sels~~~v~ 246 (486)
T PRK07899 170 EAKIIELDKNRNNVVLSRRAWLEQ-TQSEVRSEFLNQLQKGQVRKG-VVSSIVNFGAFVDLG-GVDGLVHVSELSWKHID 246 (486)
T ss_pred EEEEEEEECCCCEEEEEhHHHHHh-hhHHHHHHHHHhccCCCEEEE-EEEEEECCeEEEEEC-CEEEEEEHHHCCCcccC
Confidence 45567777 457888887643211 122345566678899999999 999999999999996 89999999999999999
Q ss_pred CccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc---------------------
Q 002487 804 KAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--------------------- 861 (916)
Q Consensus 804 ~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--------------------- 861 (916)
++.+.|++||.|+|+|+++|. +++|.||+|++.++||..+.. ++++|+++.|+|..+
T Consensus 247 ~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~-~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~Se 325 (486)
T PRK07899 247 HPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFAR-THAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISE 325 (486)
T ss_pred CHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHH-hcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHH
Confidence 999999999999999999998 899999999999999988875 788999999997332
Q ss_pred ---cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCC
Q 002487 862 ---KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRP 898 (916)
Q Consensus 862 ---~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~ 898 (916)
.++..+...|++||+|+|+|+++|.+++||+|++++.
T Consensus 326 Ls~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~ 365 (486)
T PRK07899 326 LAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQA 365 (486)
T ss_pred cCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEc
Confidence 2344566789999999999999999999999997643
No 37
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.85 E-value=2e-21 Score=227.54 Aligned_cols=168 Identities=26% Similarity=0.345 Sum_probs=142.7
Q ss_pred hCCceeccCC-Cc----ceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccC
Q 002487 724 TGVEAIDTED-DG----TVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELS 798 (916)
Q Consensus 724 ~~v~~Idi~d-~g----~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels 798 (916)
..+.+++++. ++ ++.++.+.. ..+.|..+...+++|++|.| +|+++.+||+||++.+|++||+|+|+|+
T Consensus 253 i~vkVl~id~~~~~~~~ri~lS~K~~-----~~~p~~~~~~~~~~G~~v~G-~V~~v~~~G~fV~l~~gv~Glvh~sels 326 (491)
T PRK13806 253 VRVKVLGIERAKKGKGLRISLSIKQA-----GGDPWDTVGDRLKAGDKVTG-KVVRLAPFGAFVEILPGIEGLVHVSEMS 326 (491)
T ss_pred EEEEEEEEecccCCcceEEEEEehhh-----hcccchhhhccCCCCCEEEE-EEEEEeCceEEEEeCCCcEEEEEHHHcC
Confidence 3455567764 32 566776544 23457777788999999999 9999999999999999999999999999
Q ss_pred c-ccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc---------------
Q 002487 799 S-NWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--------------- 861 (916)
Q Consensus 799 ~-~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--------------- 861 (916)
| .++.++.+.|++||.|+|+|+++|. +++|.||+|++.++||..... +|++|++++|+|.++
T Consensus 327 ~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~-~~~vG~~v~G~V~~i~~~G~FV~l~~gv~G 405 (491)
T PRK13806 327 WTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAE-RFAPGTTVTGTVEKRAQFGLFVNLAPGVTG 405 (491)
T ss_pred cccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhh-hCCCCCEEEEEEEEEecCceEEEcCCCcEE
Confidence 9 5788999999999999999999998 899999999999999999886 999999999998332
Q ss_pred ---------cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCC
Q 002487 862 ---------KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRP 898 (916)
Q Consensus 862 ---------~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~ 898 (916)
.+..++...+++||+|+|+|+++|++++||+||+++.
T Consensus 406 li~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~ 451 (491)
T PRK13806 406 LLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGA 451 (491)
T ss_pred EEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence 2234556789999999999999999999999998743
No 38
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.84 E-value=5.6e-21 Score=214.17 Aligned_cols=203 Identities=21% Similarity=0.285 Sum_probs=171.3
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCC-CCCCCCC-------ccccceeecccccccCCCCCcccCCCC
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVP-SEPSDFF-------PLNVNYQERFSAAGRTSGGFFKREGRT 169 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~-~~~~~f~-------pL~v~y~ek~~A~g~iPg~f~kReg~p 169 (916)
-|+|.+|.+.+ +.++||++++.|+|+|||||+..... ....|-+ -....|....||. |..-|.|.+
T Consensus 368 lR~I~ce~~m~-~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat-----~Evgkig~~ 441 (760)
T KOG1067|consen 368 LRNISCEVDML-KTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYAT-----NEVGKIGGL 441 (760)
T ss_pred hcccceecCcc-ccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCccc-----cccccccCC
Confidence 58899999999 89999999999999999999985321 1112211 1234444444444 456677999
Q ss_pred CchhhhHHHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEE---C---
Q 002487 170 KDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLV---G--- 243 (916)
Q Consensus 170 ~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i---~--- 243 (916)
+.||+.+..|-.|+|-|.+|+.|.+.|.|..+||++||+.+ +|+++|.|+||+|||+|+..+||||.+|++ |
T Consensus 442 nRRE~GhgaLAEkaL~~vlP~dfPftIRv~SeVleSnGSsS--MASvCGGslALmDaGvPv~a~vAGvaiGlvt~td~e~ 519 (760)
T KOG1067|consen 442 NRRELGHGALAEKALLPVLPEDFPFTIRVTSEVLESNGSSS--MASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEK 519 (760)
T ss_pred cccccCchhHhhhhhhccCcccCceEEEEeeeeeecCCcch--HHhhhcchhhhhhcCCccccccceeEEEeEeccCccc
Confidence 99999999999999999999999999999999999999999 999999999999999999999999999997 2
Q ss_pred C-----EEEECCChHHHhhCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002487 244 D-----KFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK 313 (916)
Q Consensus 244 g-----~~ildPt~~E~~~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk 313 (916)
| .++-|-.--|+-.+|+|+-||||.++|+.+ .++.+.+.+||..|.++-.+|.+.|.+.+..-..
T Consensus 520 g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~ 589 (760)
T KOG1067|consen 520 GEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-----GIPLKIVMEALQKAREARLQILDIMEKNINSPRG 589 (760)
T ss_pred CCcccceeehhhcchhhhcCCcceeeccccCcceec-----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCccc
Confidence 1 255666667888899999999999999998 5899999999999999999999999887755443
No 39
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.82 E-value=4.2e-20 Score=226.11 Aligned_cols=160 Identities=18% Similarity=0.289 Sum_probs=140.8
Q ss_pred CcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCC
Q 002487 734 DGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGD 813 (916)
Q Consensus 734 ~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd 813 (916)
++++.+|.+.... +++.+.++.++..+++|++|+| +|+++.+||+||++. |++||||+|+++|.++.++.+.|++||
T Consensus 465 ~~~iVlSrr~~l~-e~~~~~~ee~~~~l~~G~~V~G-~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq 541 (863)
T PRK12269 465 NDNIVINRRRYLE-ERARQAREEFFNSVHIEDSVSG-VVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQ 541 (863)
T ss_pred CCeEEEEHHHHHH-HHHHHHHHHHHhcCCCCCEEEE-EEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCC
Confidence 4678888775433 3455566677778999999999 999999999999995 899999999999999999999999999
Q ss_pred EEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee-------------------------ccccccCCC
Q 002487 814 LVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA-------------------------ASDKLVGSP 867 (916)
Q Consensus 814 ~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V-------------------------s~i~~v~~p 867 (916)
+|+|+|+++|+ ++++.||+|++.++||....+ +|++|++++|+| +|.+++.+|
T Consensus 542 ~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~-~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p 620 (863)
T PRK12269 542 TIELKVIRLDQAEKRINLSLKHFQPDPWLEFEN-KFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKP 620 (863)
T ss_pred EEEEEEEEEecCCCeEEEEEeccccchhhhhhc-cCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCH
Confidence 99999999998 899999999999999998875 899999999997 333456677
Q ss_pred CCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 868 KPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 868 ~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
.+.|++||+|+|+|+++|++++||+||+++
T Consensus 621 ~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~ 650 (863)
T PRK12269 621 SDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650 (863)
T ss_pred HHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence 888999999999999999999999999863
No 40
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.81 E-value=8.4e-20 Score=213.88 Aligned_cols=169 Identities=26% Similarity=0.387 Sum_probs=141.9
Q ss_pred CceeccCC-CcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC
Q 002487 726 VEAIDTED-DGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK 804 (916)
Q Consensus 726 v~~Idi~d-~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~ 804 (916)
+.++.+++ ++++.++.+.....+ ..+.|+.+...+++|++|+| +|+++.+||+||+|.+|++||||+|+++|.++.+
T Consensus 165 ~~V~~id~~~~~v~lSrk~~~~~~-~~~~~~~~~~~l~~G~iv~G-~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~ 242 (491)
T PRK13806 165 FLITRVEENGRNIVVSRRALLERE-QKEALEAFMETVKEGDVVEG-TVTRLAPFGAFVELAPGVEGMVHISELSWSRVQK 242 (491)
T ss_pred EEEEEEECCCCeEEEEeehhhhhh-hHHHHHHHHhhCCCCCEEEE-EEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccC
Confidence 44567764 567777765443222 23445666667899999999 9999999999999988999999999999999999
Q ss_pred ccccccCCCEEEEEEEEEcC-C----CceEEEEeecCCCCCCCCCCCCCCCCCcEEEeecc-------------------
Q 002487 805 AEDVVKVGDLVDVKLIEVND-K----GQLRLSRRALLPEADAENPPVKLPTGDPTKDAAAS------------------- 860 (916)
Q Consensus 805 ~~~~~kvGd~V~VKVi~iD~-~----gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~------------------- 860 (916)
+.+.|++||.|+|+|+++|. + +||.||+|++.++||..... ++++|+++.|+|..
T Consensus 243 ~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~-~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh 321 (491)
T PRK13806 243 ADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGD-RLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVH 321 (491)
T ss_pred hhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhc-cCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEE
Confidence 99999999999999999997 4 37999999999999998875 89999999999722
Q ss_pred ------ccccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 861 ------DKLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 861 ------i~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
..++.+|.+.+++||+|+|+|+++|++++||+|++++
T Consensus 322 ~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~ 364 (491)
T PRK13806 322 VSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364 (491)
T ss_pred HHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence 2334566678999999999999999999999999763
No 41
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.2e-17 Score=173.24 Aligned_cols=225 Identities=18% Similarity=0.236 Sum_probs=170.9
Q ss_pred hcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCC-eEEEEEEEecCccccccccCCCCCCceeEEEEEEeeCCCCc
Q 002487 444 VEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGE-TQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSV 522 (916)
Q Consensus 444 l~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~-TqVl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~~fpP~s~ 522 (916)
.+..+|.|||...++|||.+++|+||+++|||.+..|+ |-++++|+. +.. +.+.. ...++.+.+.+.+.|-+.
T Consensus 17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKa---Evg-~~~~~--~p~egk~~~~VD~S~sas 90 (288)
T KOG1612|consen 17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKA---EVG-SPDDE--TPVEGKYLFFVDCSPSAS 90 (288)
T ss_pred cCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEee---ecc-Ccccc--CCCCCeEEEEEEecCCcC
Confidence 35789999999999999999999999999999999999 999999962 221 11111 123556888999999888
Q ss_pred ccccCCCCCChhhHHHHHHHHHHhcc---------ccCCCCCCCeEEEEEEEEEecCCCcchhHHhHHHHHHHhcCCCcc
Q 002487 523 GEVGRIGAPSRREIGHGTLAERALEP---------VLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIK 593 (916)
Q Consensus 523 ~e~~r~g~~~rrei~~~~l~eraL~~---------vip~~~~fp~tI~V~~~VLesdGs~~~Asv~aaslAL~dAGIP~~ 593 (916)
+++..+| .+.-.-++...++|+|.. +... +.|.|.|.|++-||++|||.++|.-.|+.+||.+.-+|--
T Consensus 91 p~f~gRg-gde~~~eltsaLq~~l~~~~sgv~ls~L~lt-~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv 168 (288)
T KOG1612|consen 91 PQFQGRG-GDELVEELTSALQRVLNSLGSGVDLSKLQLT-PGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKV 168 (288)
T ss_pred ccccCCC-hhhHHHHHHHHHHHHHhCcCcccchhheecc-CCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCcc
Confidence 8776443 445556788889999876 3333 5699999999999999999999999999999999999821
Q ss_pred cce-------------------------eEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEEEe
Q 002487 594 CSI-------------------------AGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQM 648 (916)
Q Consensus 594 ~~V-------------------------agvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~ 648 (916)
... ..+-+.+.+-| +.+|+|||.+|+......+.|.-+..|++-+--
T Consensus 169 ~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG--------~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r 240 (288)
T KOG1612|consen 169 IVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIG--------TNMLVDPTAEEESVANSGLLISVSAGGIVSCTR 240 (288)
T ss_pred ccccccCCceeeccCcccchhhhhhcccCCEEEEEEeec--------ceEEccCCccHHHhhhcceEEEEecCcceEEEE
Confidence 100 11111221111 257889999999999888988877777665433
Q ss_pred eccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCC
Q 002487 649 DIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPP 684 (916)
Q Consensus 649 d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~ 684 (916)
....|++..+...++++++++-...+...+.+.+.+
T Consensus 241 ~VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~ 276 (288)
T KOG1612|consen 241 SVGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLEN 276 (288)
T ss_pred EecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhh
Confidence 333455899999999999998888877777776654
No 42
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.76 E-value=1.5e-18 Score=207.27 Aligned_cols=167 Identities=22% Similarity=0.314 Sum_probs=139.8
Q ss_pred CceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC
Q 002487 726 VEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK 804 (916)
Q Consensus 726 v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~ 804 (916)
+.+++++ +.+++.++.+...... ..+.+..++..+++|++++| +|+++.+||+||+++ |++||+|+|+++|.++.+
T Consensus 164 ~~V~~~d~~~~~i~lS~k~~~~~~-~~~~~~~~~~~l~~G~iv~g-~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~ 240 (565)
T PRK06299 164 FKVIKLDKKRNNIVVSRRAVLEEE-RAEEREELLENLEEGQVVEG-VVKNITDYGAFVDLG-GVDGLLHITDISWKRVNH 240 (565)
T ss_pred EEEEEEECCCCEEEEEhHHhhhhh-hhhHHHHHHhcCCCCCEEEE-EEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCC
Confidence 3356776 4567777766543221 22345566678899999999 999999999999998 999999999999999999
Q ss_pred ccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc----------------------
Q 002487 805 AEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD---------------------- 861 (916)
Q Consensus 805 ~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i---------------------- 861 (916)
+.+.|++||.|+|+|+++|. ++++.||+|.+.++||..... .|++|+++.|+|..+
T Consensus 241 ~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~-~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel 319 (565)
T PRK06299 241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEK-KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM 319 (565)
T ss_pred HhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHh-hCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHc
Confidence 99999999999999999998 899999999999999998775 799999999997332
Q ss_pred ---cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCC
Q 002487 862 ---KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 862 ---~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
....+|...+++||.|.|+|+++|+++++|+|+++
T Consensus 320 ~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k 357 (565)
T PRK06299 320 SWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357 (565)
T ss_pred CccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehH
Confidence 12344556789999999999999999999999975
No 43
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.76 E-value=3.6e-18 Score=195.13 Aligned_cols=169 Identities=24% Similarity=0.353 Sum_probs=139.4
Q ss_pred eeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 728 AIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 728 ~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
+++++ +++++.+|.+...... ....+..+...+++|++++| +|+++.++|+||++. +++||||+|+++|.++.++.
T Consensus 157 Vl~~d~~~~~i~lS~k~~~~~~-~~~~~~~~~~~~~~G~~v~g-~V~~v~~~G~fV~l~-~v~g~v~~sels~~~~~~~~ 233 (390)
T PRK06676 157 IIELDPEKNRVILSRRAVVEEE-RAAKKEELLSSLKEGDVVEG-TVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPS 233 (390)
T ss_pred EEEEECCCCEEEEEeHHHhhhh-hhhHHHHHHhhCCCCCEEEE-EEEEEecceEEEEeC-CeEEEEEHHHcCccccCCHH
Confidence 45666 4677888776432211 12334455667899999999 999999999999995 89999999999999999999
Q ss_pred ccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc------------------------
Q 002487 807 DVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD------------------------ 861 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i------------------------ 861 (916)
+.|++||.|+|+|+++|. +++|.||+|++.++||..... .+++|+++.|+|..+
T Consensus 234 ~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~-~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~ 312 (390)
T PRK06676 234 EVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE-KLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISH 312 (390)
T ss_pred HhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchh-hhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCc
Confidence 999999999999999998 899999999999999988875 899999999997332
Q ss_pred cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCCCC
Q 002487 862 KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYS 900 (916)
Q Consensus 862 ~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~~~ 900 (916)
.++.++...|++||+|+|+|+++|++++||+|+++++..
T Consensus 313 ~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~ 351 (390)
T PRK06676 313 KHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351 (390)
T ss_pred cccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEeccc
Confidence 123344567899999999999999999999999875444
No 44
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=7.1e-19 Score=164.64 Aligned_cols=82 Identities=37% Similarity=0.696 Sum_probs=78.3
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeecCCCC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEA 839 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p 839 (916)
.+++|++++| +|++|++|||||+|.+|..|||||||+.+.|++++++.+++||+|.|||+++|++|+|+||+|+++..|
T Consensus 2 ~~kvG~~l~G-kItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~p 80 (129)
T COG1098 2 SMKVGSKLKG-KITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEP 80 (129)
T ss_pred CccccceEEE-EEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCc
Confidence 4689999999 999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred CCC
Q 002487 840 DAE 842 (916)
Q Consensus 840 ~~~ 842 (916)
...
T Consensus 81 e~~ 83 (129)
T COG1098 81 EKQ 83 (129)
T ss_pred ccc
Confidence 654
No 45
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.74 E-value=5.7e-18 Score=202.28 Aligned_cols=170 Identities=18% Similarity=0.248 Sum_probs=143.4
Q ss_pred CceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc-c
Q 002487 726 VEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL-A 803 (916)
Q Consensus 726 v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v-~ 803 (916)
+.+++++ +++++.++.+... .+.|..+...+++|+++.| +|+++.++|+||+|.++++||+|+|+++|.+. .
T Consensus 340 v~V~~id~~~~~i~ls~k~~~-----~~p~~~~~~~~~~G~~v~g-~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~ 413 (565)
T PRK06299 340 VMVLEIDEEKRRISLGLKQCK-----ENPWEEFAEKYPVGDVVEG-KVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGE 413 (565)
T ss_pred EEEEEEcCCCCEEEEehHHhc-----cchhhhHHHhCCCCCEEEE-EEEEEecceEEEECCCCCEEEEEHHHcCcccccc
Confidence 4456776 4678888765432 2345555567899999999 99999999999999889999999999999887 8
Q ss_pred CccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc---------------------
Q 002487 804 KAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--------------------- 861 (916)
Q Consensus 804 ~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--------------------- 861 (916)
++.+.|++||.|+|+|+++|. +++|.||+|.+..+||..... .+++|+++.|+|..+
T Consensus 414 ~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~-~~~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se 492 (565)
T PRK06299 414 EAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAK-KHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASE 492 (565)
T ss_pred ChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHh-hcCCCCEEEEEEEEEecCceEEecCCCcEEEEEHHH
Confidence 889999999999999999998 899999999999999988875 789999999997332
Q ss_pred ---cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCCCCcc
Q 002487 862 ---KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSNK 902 (916)
Q Consensus 862 ---~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~~~~~ 902 (916)
.++.++.+.+++||.|+++|+++|.+++||+|+++......
T Consensus 493 ~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~~~~~ 536 (565)
T PRK06299 493 LSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAE 536 (565)
T ss_pred hcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeehhhhh
Confidence 23445677899999999999999999999999998655543
No 46
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.73 E-value=9.9e-18 Score=162.75 Aligned_cols=125 Identities=28% Similarity=0.275 Sum_probs=104.9
Q ss_pred CeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCC-CC-CCCc--cccceeecccccccCCCCCcccCCCCCchh
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSE-PS-DFFP--LNVNYQERFSAAGRTSGGFFKREGRTKDHE 173 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~-~~-~f~p--L~v~y~ek~~A~g~iPg~f~kReg~p~~~e 173 (916)
-|++.+++|.+ .+||||+++++|+|+|+|+|+++.++++ .. +..+ +++++.-..++.+++ +++|++++.+
T Consensus 2 ~R~i~i~~~~~-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~-----~~~~~~~~~~ 75 (132)
T PF01138_consen 2 LRPISIETGVL-PRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSF-----RRGGRPDEEE 75 (132)
T ss_dssp BEEEEEEESSS-SSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSS-----SSSSSTHHHH
T ss_pred CccEEEEeCCC-CCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEecccccccc-----ccccccchhH
Confidence 38999999999 8999999999999999999999865521 22 4445 888888777666653 6668999999
Q ss_pred hhHHHHhcCccccccc--CCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCC
Q 002487 174 VLVCRLIDRPLRPTLI--KGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVP 229 (916)
Q Consensus 174 il~sRlIdR~LRplfp--~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP 229 (916)
.+++++|++.|++.+. ..+++.++|+++||+.|| .....+|+|||++||++++||
T Consensus 76 ~~l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG-~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 76 RELSSLLERALRSSILLEGYPRWQIHVDVQVLSDDG-GNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSS-SSHHHHHHHHHHHHHHHHTCS
T ss_pred HHHHHHHhhhccccccccccCceEEEEEEEEEecCC-CCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999655 444689999999999998 234489999999999999998
No 47
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.72 E-value=2.3e-17 Score=199.50 Aligned_cols=173 Identities=24% Similarity=0.334 Sum_probs=141.6
Q ss_pred CceeccCC-Ccc-eeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCccccc
Q 002487 726 VEAIDTED-DGT-VKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLA 803 (916)
Q Consensus 726 v~~Idi~d-~g~-v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~ 803 (916)
+.++++++ +++ +.++.+...... ..+.+...+..+++|++|.| +|+++.+||+||++ ++++||+|+|+++|.++.
T Consensus 439 v~Vl~vd~e~~~~l~lS~k~~~~~~-~~~~~~~~~~~l~~G~iV~g-~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~ 515 (647)
T PRK00087 439 VKIIEFNRKRRKKVVLSRKAILEEE-KEKKKEETWNSLEEGDVVEG-EVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVE 515 (647)
T ss_pred EEEEEEEcCCCcEEEEEeHHHhhhh-hhhHHHHHHHhCCCCCEEEE-EEEEEeCCcEEEEE-CCEEEEEEHHHcCccccC
Confidence 44467774 455 666665432111 12334455566899999999 99999999999999 699999999999999999
Q ss_pred CccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc---------------------
Q 002487 804 KAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--------------------- 861 (916)
Q Consensus 804 ~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--------------------- 861 (916)
++.+.|++||.|+|+|+++|+ +++|.||+|.+.++||..... ++++|+++.|+|..+
T Consensus 516 ~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~-~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~se 594 (647)
T PRK00087 516 KPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEE-KYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQ 594 (647)
T ss_pred CHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhh-hccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhh
Confidence 999999999999999999998 899999999999999998775 789999999997332
Q ss_pred ---cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCCCCcc
Q 002487 862 ---KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSNK 902 (916)
Q Consensus 862 ---~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~~~~~ 902 (916)
.++.++...|++||+|+|+|+++|++++||+|+++++..++
T Consensus 595 l~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 595 ISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred cCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 22345556899999999999999999999999988665544
No 48
>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=99.72 E-value=2.1e-17 Score=195.45 Aligned_cols=165 Identities=19% Similarity=0.256 Sum_probs=137.7
Q ss_pred CCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc-
Q 002487 725 GVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL- 802 (916)
Q Consensus 725 ~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v- 802 (916)
.+.+++++ +++++.++.+... .+.|..+...+++|+++.| +|+++.+||+||+|.+|++||+|+++|+|.+.
T Consensus 325 ~v~V~~id~~~~~i~lS~k~~~-----~~p~~~~~~~~~~G~~v~g-~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~ 398 (516)
T TIGR00717 325 EVMILDIDPERRRLSLGLKQCK-----ANPWEQFEEKHPVGDRVTG-KIKKITDFGAFVELEGGIDGLIHLSDISWDKDG 398 (516)
T ss_pred EEEEEEEcCCCCEEEEEehhcc-----cCcHHHHHHhCCCCCEEEE-EEEEEecceEEEECCCCCEEEEEHHHCcCcccC
Confidence 34456777 4678888765432 2345555566799999999 99999999999999999999999999999764
Q ss_pred cCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc--------------------
Q 002487 803 AKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD-------------------- 861 (916)
Q Consensus 803 ~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i-------------------- 861 (916)
.++...|++||.|.++|+++|. +++|.||+|.+.++||..... .+++|+++.|+|..+
T Consensus 399 ~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~-~~~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s 477 (516)
T TIGR00717 399 READHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAA-KYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNS 477 (516)
T ss_pred CCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhh-ccCcceEEEEEEEEEecceEEEEcCCCeEEEEEHH
Confidence 4567889999999999999998 899999999999999988764 889999999997332
Q ss_pred ----cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCC
Q 002487 862 ----KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 862 ----~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
.++.++.+.|++||+++++|+++|.+++||+|+++
T Consensus 478 ~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 478 ELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred HcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 22344667899999999999999999999999864
No 49
>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=99.71 E-value=3.3e-17 Score=193.73 Aligned_cols=166 Identities=24% Similarity=0.304 Sum_probs=139.0
Q ss_pred CCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcc-cc
Q 002487 725 GVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSN-WL 802 (916)
Q Consensus 725 ~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~-~v 802 (916)
.+.++.+| +++++.++.+... .+.|+.+...+++|+++.| +|+++.+||+||++.++++||+|+|+++|. ..
T Consensus 238 ~v~Vl~~d~~~~~i~lS~k~~~-----~~p~~~~~~~~~~G~i~~g-~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~ 311 (516)
T TIGR00717 238 KVKVIKFDKEKGRISLSLKQLG-----EDPWEAIEKKFPVGDKITG-RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKN 311 (516)
T ss_pred EEEEEEEECCCCcEEEEEEecc-----hhHHHHHHhhccCCCEEEE-EEEEeeCCcEEEEeCCCCEEEEEHHHcCCcccc
Confidence 34456676 4678888877543 2456666667899999999 999999999999999999999999999986 46
Q ss_pred cCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc--------------------
Q 002487 803 AKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD-------------------- 861 (916)
Q Consensus 803 ~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i-------------------- 861 (916)
.++.+.|++||.|+|+|+++|. ++++.||+|++..+||..+.. ++++|+++.|+|.++
T Consensus 312 ~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~-~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s 390 (516)
T TIGR00717 312 SHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEE-KHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLS 390 (516)
T ss_pred CCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHH-hCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHH
Confidence 6777889999999999999998 899999999999999988765 789999999997332
Q ss_pred -----cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 862 -----KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 862 -----~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
.....+...+++||.|.++|+++|++++||.|+++.
T Consensus 391 ~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~ 431 (516)
T TIGR00717 391 DISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ 431 (516)
T ss_pred HCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence 112234568999999999999999999999999774
No 50
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.67 E-value=6.9e-17 Score=176.94 Aligned_cols=98 Identities=22% Similarity=0.370 Sum_probs=93.0
Q ss_pred CCCCcEEEccEEEEEecceEEEEEC--CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCC
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIA--PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLP 837 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~--~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~ 837 (916)
|++|+++.| +|++|.+|||||+|. +|++||||+|||+|+|+.++.++|++||+|.|+|+++|+ +|+|.||+|++.+
T Consensus 15 P~~GdvV~g-~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~ 93 (319)
T PTZ00248 15 PEEDDLVMV-KVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP 93 (319)
T ss_pred CCCCCEEEE-EEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc
Confidence 458999999 999999999999996 689999999999999999999999999999999999998 9999999999999
Q ss_pred CCCCCCCCCCCCCCCcEEEeecc
Q 002487 838 EADAENPPVKLPTGDPTKDAAAS 860 (916)
Q Consensus 838 ~p~~~~~~~~~~~G~vv~g~Vs~ 860 (916)
+||..+.. +|+.|+++.++|.+
T Consensus 94 ~pw~~~~e-~~~~g~~v~~~V~~ 115 (319)
T PTZ00248 94 EDIEACEE-KFSKSKKVHSIMRH 115 (319)
T ss_pred chHHHHHH-hCcCCCEEEEEEEE
Confidence 99999986 99999999999844
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.63 E-value=1.2e-15 Score=169.41 Aligned_cols=157 Identities=17% Similarity=0.255 Sum_probs=126.0
Q ss_pred eeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 728 AIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 728 ~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
+++++ ++|++.+|.+.... .+.|+.+....+.|++++| +|+++.++|+||++. |++||||+|+|+|.+..
T Consensus 86 Vi~~~~~~~~i~lS~k~~~~----~~~w~~l~~~~~~~~~V~g-~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~~--- 156 (318)
T PRK07400 86 ILSDENEDGQLTLSIRRIEY----MRAWERVRQLQKEDATVRS-EVFATNRGGALVRIE-GLRGFIPGSHISTRKPK--- 156 (318)
T ss_pred EEEEeCCCCeEEEehhhhhh----hhHHHHHHHhccCCCEEEE-EEEEEECCeEEEEEC-CEEEEEEHHHcCccCCc---
Confidence 45555 46888888776422 2446666666678999999 999999999999995 99999999999986543
Q ss_pred ccccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc-----------------------c
Q 002487 807 DVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD-----------------------K 862 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i-----------------------~ 862 (916)
+.+ +|+.|.++|+++|+ +++|.||+|.+..++ .. .++++|+++.|+|..+ .
T Consensus 157 ~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~-~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~ 231 (318)
T PRK07400 157 EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KM-NRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHE 231 (318)
T ss_pred ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hh-ccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccc
Confidence 334 99999999999999 899999999766432 23 3789999999997332 2
Q ss_pred ccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCC
Q 002487 863 LVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRP 898 (916)
Q Consensus 863 ~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~ 898 (916)
++.++...|++||.|+|+|+++|.++++|+|++++.
T Consensus 232 ~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l 267 (318)
T PRK07400 232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQL 267 (318)
T ss_pred cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEecc
Confidence 345667789999999999999999999999997643
No 52
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.59 E-value=1.3e-15 Score=177.24 Aligned_cols=161 Identities=18% Similarity=0.275 Sum_probs=129.6
Q ss_pred CceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC
Q 002487 726 VEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK 804 (916)
Q Consensus 726 v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~ 804 (916)
+.++.++ ++|++.++.+.... . ..|+.+-..++.|++++| +|+++.++|+||+| |++||||.|++++.++.+
T Consensus 88 ~~V~~~~~~~g~liLS~k~~~~-~---~~w~~ie~~~e~g~~V~G-~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~ 160 (486)
T PRK07899 88 ALVLQKEDKEGRLILSKKRAQY-E---RAWGTIEKIKEKDGVVTG-TVIEVVKGGLILDI--GLRGFLPASLVEMRRVRD 160 (486)
T ss_pred EEEEEEECCCCeEEEEehhhcc-c---chHHHHHHHhcCCCEEEE-EEEEEECCeEEEEE--CCEEEEEhhHhcccccCC
Confidence 3346665 46788888775332 1 234544444578999999 99999999999999 689999999999998888
Q ss_pred ccccccCCCEEEEEEEEEcC-CCceEEEEeecCC----CCCCCCCCCCCCCCCcEEEeeccc------------------
Q 002487 805 AEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLP----EADAENPPVKLPTGDPTKDAAASD------------------ 861 (916)
Q Consensus 805 ~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~----~p~~~~~~~~~~~G~vv~g~Vs~i------------------ 861 (916)
+.. .+||+|+|+|+++|. ++++.||+|.++. .+|..+.. .+++|+++.|+|..+
T Consensus 161 ~~~--~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~-~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~ 237 (486)
T PRK07899 161 LQP--YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLN-QLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHV 237 (486)
T ss_pred hhh--cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHH-hccCCCEEEEEEEEEECCeEEEEECCEEEEEEH
Confidence 766 389999999999998 8899999997643 56666654 789999999997332
Q ss_pred -----cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCC
Q 002487 862 -----KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 862 -----~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
.++.+|.+.|++||+|+|+|+++|++++||+||++
T Consensus 238 Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK 277 (486)
T PRK07899 238 SELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277 (486)
T ss_pred HHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEe
Confidence 34556677899999999999999999999999976
No 53
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.57 E-value=1.1e-13 Score=143.33 Aligned_cols=205 Identities=19% Similarity=0.208 Sum_probs=160.0
Q ss_pred eeEEEEeCccccCCCceEEEEeCCeEEEEEEEecC-CC---CCCCCCCccccceeecccccccCCCCCcccCCCCCchhh
Q 002487 99 RQILVETGHMGRQASGAVTVTDGETIIYTSVCLAD-VP---SEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEV 174 (916)
Q Consensus 99 R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~-e~---~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~ei 174 (916)
|.++++.|+. -||+.+++|+|+|||.|+..- +| ++..+.+.+.+++.+..+.+. --|++++.+.
T Consensus 33 R~lei~fGke----~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~telsPmA~~sf--------E~Gr~~~~~v 100 (291)
T KOG1614|consen 33 RDLEIEFGKE----YGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASPSF--------EPGRKGESEV 100 (291)
T ss_pred hceEEEeccc----cccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeecccccccccc--------CCCCccchHH
Confidence 7789999988 399999999999999999852 22 222233344455443332211 1188999999
Q ss_pred hHHHHhcCcccc----------cccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCC-----------------
Q 002487 175 LVCRLIDRPLRP----------TLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSE----------------- 227 (916)
Q Consensus 175 l~sRlIdR~LRp----------lfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~----------------- 227 (916)
+++|+|++.+|- .......|.+.|+..+|+.||+.- -||..||.+||+-=+
T Consensus 101 ~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlv--DaA~iAviaaL~hFrrPdvTv~g~ev~ihp~e 178 (291)
T KOG1614|consen 101 ELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLV--DAACIAVIAALMHFRRPDVTVGGEEVIIHPVE 178 (291)
T ss_pred HHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCee--hhHHHHHHHHHHhcCCCCcccccceeEecChh
Confidence 999999999996 233444778999999999999755 577888999998654
Q ss_pred ------CCCCCceEEEEEEEEC--CEEEECCChHHHhhCCeeEEEEeecCe-EEEEEecCCC-CCHHHHHHHHHHHHHHH
Q 002487 228 ------VPNSKVIAGVRVGLVG--DKFIVNPTTQEMEDSQLDLLLAGSDDA-ILMIEGYCDF-LSEEMLIQAVQVGQDAV 297 (916)
Q Consensus 228 ------IP~~~~VaaV~vg~i~--g~~ildPt~~E~~~s~~dl~vagt~~~-i~mie~~~~~-~~e~~l~~al~~a~~~~ 297 (916)
+-++....+++.|..| +-.|+|||..|+...|.-++|+.+++. |+.++..|++ +.+.+++.+...|..-+
T Consensus 179 Er~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~a 258 (291)
T KOG1614|consen 179 EREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGGEILDESVIERCYKLAKDRA 258 (291)
T ss_pred ccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecCCCccccHHHHHHHHHHHHHHH
Confidence 3356777889999885 557999999999999999999999885 8888887655 77999999999999999
Q ss_pred HHHHHHHHHHHHHhCCCCcc
Q 002487 298 REISNEVKALVEMCGKPKML 317 (916)
Q Consensus 298 ~~i~~~~~~~~~~~gk~k~~ 317 (916)
..+...+.+.+++..+++..
T Consensus 259 ~~vt~ii~e~l~~d~~~r~~ 278 (291)
T KOG1614|consen 259 VEVTGIILEALEEDQRERSA 278 (291)
T ss_pred HHHHHHHHHHHHHHHHHhhh
Confidence 99999999998877665543
No 54
>PRK08582 hypothetical protein; Provisional
Probab=99.57 E-value=1.1e-14 Score=143.40 Aligned_cols=83 Identities=34% Similarity=0.624 Sum_probs=78.7
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeecCCCC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEA 839 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p 839 (916)
.+++|++|.| +|++|++||+||+|.++.+||||+|+++|+++.++.+.|++||.|+|+|+++|.+|+|.||+|++.++|
T Consensus 2 ~~kvG~iv~G-~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~ 80 (139)
T PRK08582 2 SIEVGSKLQG-KVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80 (139)
T ss_pred CCcCCCEEEE-EEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCc
Confidence 4689999999 999999999999999999999999999999999999999999999999999998899999999999999
Q ss_pred CCCC
Q 002487 840 DAEN 843 (916)
Q Consensus 840 ~~~~ 843 (916)
|.+.
T Consensus 81 ~~~~ 84 (139)
T PRK08582 81 KRQH 84 (139)
T ss_pred hhhc
Confidence 8754
No 55
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.56 E-value=9.4e-15 Score=162.42 Aligned_cols=141 Identities=18% Similarity=0.223 Sum_probs=118.3
Q ss_pred HhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 755 SNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 755 ~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
+.+...++.|++++| +|+++.++|+||+|+.+.+|+||.+|++|.++.++.+.|++||+|+|+|+++|. ++++.||+|
T Consensus 23 e~~~~~~~~G~iv~G-~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k 101 (318)
T PRK07400 23 DKYDYHFKPGDIVNG-TVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIR 101 (318)
T ss_pred HhhHhhcCCCCEEEE-EEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehh
Confidence 333345799999999 999999999999998789999999999999999999999999999999999988 899999999
Q ss_pred ecC-CCCCCCCCCCCCCCCCcEEEeeccc---------------------cccCCCCCCCCCCCcEEEeEeeecCCCCcc
Q 002487 834 ALL-PEADAENPPVKLPTGDPTKDAAASD---------------------KLVGSPKPKGSSSEDTVLPHKKVKVFKRPA 891 (916)
Q Consensus 834 ~~~-~~p~~~~~~~~~~~G~vv~g~Vs~i---------------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~rI 891 (916)
.+. .++|..... .+..|++++|+|..+ .. ..+. ...+|+++.++|+++|++++||
T Consensus 102 ~~~~~~~w~~l~~-~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~-~~~~-~~~vG~~i~~kVl~id~~~~~i 178 (318)
T PRK07400 102 RIEYMRAWERVRQ-LQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHIST-RKPK-EELVGEELPLKFLEVDEERNRL 178 (318)
T ss_pred hhhhhhHHHHHHH-hccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCc-cCCc-cccCCCEEEEEEEEEEcccCEE
Confidence 986 478887765 667789999986322 11 1122 2359999999999999999999
Q ss_pred cCCCCCCC
Q 002487 892 SPAKDRPY 899 (916)
Q Consensus 892 sL~~~~~~ 899 (916)
.||.+...
T Consensus 179 ~lS~K~~~ 186 (318)
T PRK07400 179 VLSHRRAL 186 (318)
T ss_pred EEEhhHhh
Confidence 99987443
No 56
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.52 E-value=2.1e-14 Score=164.25 Aligned_cols=161 Identities=20% Similarity=0.308 Sum_probs=128.7
Q ss_pred eeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 728 AIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 728 ~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
++.++ +++.+.++.+... ....|+.+...++.|+++.| +|+++.++|+||++. |++||||++++++.+..++.
T Consensus 73 V~~v~~~~~~i~lS~k~~~----~~~~~~~~~~~~~~G~~v~g-~V~~v~~~G~~V~~~-G~~gflp~~el~~~~~~~~~ 146 (390)
T PRK06676 73 VLKVEDGEGNLLLSKRRLE----AEKAWDKLEEKFEEGEVVEV-KVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFS 146 (390)
T ss_pred EEEEECCCCCEEEEHHHhh----hhhhHHHHHHhccCCCEEEE-EEEEEECCeEEEEEC-CEEEEEEHHHcCCccCCChH
Confidence 45665 4566777766432 22346666666799999999 999999999999995 88999999999999888876
Q ss_pred ccccCCCEEEEEEEEEcC-CCceEEEEeecCCC----CCCCCCCCCCCCCCcEEEeeccc--------------------
Q 002487 807 DVVKVGDLVDVKLIEVND-KGQLRLSRRALLPE----ADAENPPVKLPTGDPTKDAAASD-------------------- 861 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~----p~~~~~~~~~~~G~vv~g~Vs~i-------------------- 861 (916)
+. +||.|.|+|+++|. ++++.||+|.+... +|..... .+++|+++.|+|..+
T Consensus 147 ~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~-~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~se 223 (390)
T PRK06676 147 DF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLS-SLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISE 223 (390)
T ss_pred Hc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHh-hCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHH
Confidence 64 89999999999998 89999999997653 4444443 688999999997332
Q ss_pred ---cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 862 ---KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 862 ---~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
.++.+|.+.+++||.|+++|+++|++++||.||+++
T Consensus 224 ls~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~ 262 (390)
T PRK06676 224 LSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD 262 (390)
T ss_pred cCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 233455567899999999999999999999999763
No 57
>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=99.52 E-value=3.1e-14 Score=124.69 Aligned_cols=71 Identities=25% Similarity=0.425 Sum_probs=67.2
Q ss_pred CCCCcEEEccEEEEEec-ceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEe
Q 002487 761 PTVGDIYRNCEIKSIAP-YGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRR 833 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~-fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K 833 (916)
+++|++|.| +|++|.+ ||+||+|.++.+|++|+|+++|+++.++.+.|++||.|+|+|+++|. +++.||+|
T Consensus 1 l~~G~iv~G-~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLG-MVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR 72 (72)
T ss_pred CCCCCEEEE-EEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence 368999999 9999986 99999999999999999999999999999999999999999999986 99999986
No 58
>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=99.50 E-value=5.4e-14 Score=123.87 Aligned_cols=70 Identities=21% Similarity=0.409 Sum_probs=65.1
Q ss_pred CCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCc---cccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKA---EDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~---~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
+++|+++.| +|+++++||+||+|.++++|+||+++|+|.++.++ .+.|++||.|+++|+++|+ +++|.||
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 IKEGQLLRG-YVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEE-EEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 478999999 99999999999999999999999999999997775 5899999999999999998 8899886
No 59
>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=99.49 E-value=1.1e-13 Score=121.43 Aligned_cols=71 Identities=37% Similarity=0.597 Sum_probs=65.2
Q ss_pred CCCCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSR 832 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~ 832 (916)
+++|++|+| +|++|.+||+||+|.+ +.+||+|+|+++|.++.++.+.|++||+|+|+|+++|..+++.||+
T Consensus 1 ~~~g~~~~g-~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 1 PALYQIFKG-EVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CcCCCEEEE-EEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 468999999 9999999999999943 2699999999999999999999999999999999999966999986
No 60
>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=99.43 E-value=3.8e-13 Score=117.47 Aligned_cols=68 Identities=25% Similarity=0.411 Sum_probs=64.5
Q ss_pred CcEEE-ccEEEEE-ecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 764 GDIYR-NCEIKSI-APYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 764 G~i~~-G~~V~~I-~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
|++|+ | +|+++ .+||+||+|.+|++||+|+|++++.++.++.+.|++||.++++|+++|+ +++|.||+
T Consensus 1 G~v~~~g-~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSV-KVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeee-EEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 6 99999 6999999999999999999999999999999999999999999999998 88999985
No 61
>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=99.42 E-value=4.5e-13 Score=115.99 Aligned_cols=69 Identities=28% Similarity=0.432 Sum_probs=66.3
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
|++|.| +|+++.+||+||++.++.+||+|+|+|+++++.++.+.|++||.|+|+|+++|. ++++.||+|
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 GLKTHG-TIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEE-EEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789998 999999999999999899999999999999999999999999999999999999 899999986
No 62
>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=99.41 E-value=4.9e-13 Score=120.02 Aligned_cols=74 Identities=30% Similarity=0.409 Sum_probs=69.9
Q ss_pred hcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 758 TMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 758 ~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
+.++++|++|.| +|+++.+||+||+|.++.+||+|+++++++++.++.+.|++||+|+|+|+++|. +++|.||+
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 FSDLKPGMVVHG-YVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HHhCCCCCEEEE-EEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 345799999999 999999999999999899999999999999999999999999999999999998 89999985
No 63
>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=99.41 E-value=8.2e-13 Score=116.00 Aligned_cols=73 Identities=36% Similarity=0.535 Sum_probs=68.3
Q ss_pred CCCCcEEEccEEEEEecceEEEEEC--CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEee
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIA--PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRA 834 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~--~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~ 834 (916)
|++|++|.| +|+++.+||+||+|. ++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|+
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 PEEGELVVV-TVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEE-EEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 468999999 999999999999996 369999999999999999999999999999999999998 8999999974
No 64
>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=99.41 E-value=9.8e-13 Score=115.00 Aligned_cols=73 Identities=40% Similarity=0.682 Sum_probs=69.5
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
++++|+++.| +|+++.++|+||+|..+.+||||.+++++.+..++.+.+++||.|+|+|+++|. ++++.||+|
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 KLKEGDIVEG-KVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEE-EEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEE-EEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 3689999999 999999999999999899999999999999999999999999999999999999 889999986
No 65
>PRK05807 hypothetical protein; Provisional
Probab=99.40 E-value=1.1e-12 Score=128.91 Aligned_cols=75 Identities=32% Similarity=0.625 Sum_probs=71.6
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeecC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALL 836 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~ 836 (916)
.+++|++|+| +|++|.+||+||+| ++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+++|.||+|.+.
T Consensus 2 ~~~vG~vv~G-~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEG-TVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEE-EEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 4689999999 99999999999999 589999999999999999999999999999999999998899999999986
No 66
>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=99.40 E-value=1.1e-12 Score=116.68 Aligned_cols=74 Identities=39% Similarity=0.656 Sum_probs=68.8
Q ss_pred CcEEEccEEEEEecceEEEEEC---CCeeeEEeccccCcccc-cCccccccCCCEEEEEEEEEcCCCceEEEEeecCCCC
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIA---PGREGLCHISELSSNWL-AKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEA 839 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~---~g~eGlvhiSels~~~v-~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p 839 (916)
|++|.| +|++|.+||+||+|. ++.+||+|+++++|++. .++.+.|++||.|+|+|+++| ++++.||+|++.++.
T Consensus 1 G~~~~g-~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~~~~ 78 (79)
T cd05684 1 GKIYKG-KVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKDVDQDT 78 (79)
T ss_pred CCEEEE-EEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEecccCC
Confidence 789998 999999999999998 46899999999999986 899999999999999999999 999999999987653
No 67
>PRK07252 hypothetical protein; Provisional
Probab=99.40 E-value=1.4e-12 Score=125.38 Aligned_cols=77 Identities=35% Similarity=0.673 Sum_probs=73.1
Q ss_pred CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCCCC
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLPEA 839 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p 839 (916)
++|++|.| +|++|.+||+||+|.++.+||+|+|+|+++++.++.+.|++||.|+|+|+++|. ++++.||+|.+.+++
T Consensus 2 kvG~iv~G-~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~ 79 (120)
T PRK07252 2 KIGDKLKG-TITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK 79 (120)
T ss_pred CCCCEEEE-EEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 57999999 999999999999999899999999999999999999999999999999999999 899999999998744
No 68
>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=99.39 E-value=1.4e-12 Score=113.94 Aligned_cols=71 Identities=21% Similarity=0.306 Sum_probs=67.6
Q ss_pred CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
++|++|.| +|+++.+||+||+|.++++|++|++++++++..++.+.|++||.|+++|+++|. ++++.||+|
T Consensus 2 ~~G~iv~g-~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 2 KVGDILPG-RVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCEEEE-EEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 68999998 999999999999999999999999999999988888999999999999999998 899999975
No 69
>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=99.39 E-value=9.3e-13 Score=115.71 Aligned_cols=69 Identities=25% Similarity=0.397 Sum_probs=65.5
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCccc--ccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNW--LAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~--v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
|++++| +|+++.+||+||+|.++++|+||+++|+|.+ .+++.+.|++||.|+++|+++|. +++|.||+|
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 GQEVTG-FVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEE-EEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 789998 9999999999999999999999999999864 88999999999999999999998 899999987
No 70
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.39 E-value=5.5e-13 Score=161.65 Aligned_cols=161 Identities=19% Similarity=0.273 Sum_probs=129.1
Q ss_pred eeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCcc
Q 002487 728 AIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAE 806 (916)
Q Consensus 728 ~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~ 806 (916)
++.++ ++|++.++.+.... ...|+.+...++.|+++.| +|+++.++|+||+++ |++||||.|++++.++.++.
T Consensus 357 V~~vd~~~g~i~LS~k~~~~----~~~~~~l~~~~~~G~iv~g-~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d~~ 430 (647)
T PRK00087 357 VLKLEDEDGYVVLSKKEADR----EKAWKELEEAFENGEPVKG-KVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLS 430 (647)
T ss_pred EEEEECCCCcEEEEeehhcc----hhHHHHHHHHhhCCCEEEE-EEEEEECCeEEEEEC-CEEEEEEHHHhCccccCCHH
Confidence 45665 57888888776542 2335555556799999999 999999999999998 69999999999999888876
Q ss_pred ccccCCCEEEEEEEEEcC-CCc-eEEEEeecCC----CCCCCCCCCCCCCCCcEEEeeccc-------------------
Q 002487 807 DVVKVGDLVDVKLIEVND-KGQ-LRLSRRALLP----EADAENPPVKLPTGDPTKDAAASD------------------- 861 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~-~gk-I~LS~K~~~~----~p~~~~~~~~~~~G~vv~g~Vs~i------------------- 861 (916)
.. +||.|.|+|+++|. +++ +.||+|.+.. .++..... .+++|+++.|+|..+
T Consensus 431 ~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~-~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~s 507 (647)
T PRK00087 431 EY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWN-SLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVS 507 (647)
T ss_pred Hh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHH-hCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHH
Confidence 53 89999999999998 778 9999999853 34444443 678999999997332
Q ss_pred ----cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 862 ----KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 862 ----~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
.++.+|.+.|++||.++++|+++|+++++|.||+++
T Consensus 508 els~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~ 547 (647)
T PRK00087 508 EISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 (647)
T ss_pred HcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence 223445567999999999999999999999999764
No 71
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.38 E-value=1.2e-12 Score=113.30 Aligned_cols=68 Identities=25% Similarity=0.438 Sum_probs=65.0
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
|++|+| +|++|.+||+||+|.++++||+|+++++|.+..++.+.|++||.++++|+++|. ++++.||+
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 GQVVKG-TIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEE-EEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789998 999999999999999899999999999999999999999999999999999998 89999985
No 72
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.35 E-value=1.6e-12 Score=112.08 Aligned_cols=67 Identities=34% Similarity=0.620 Sum_probs=64.2
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|++|.| +|++|.+||+||+|.++++||+|++++++++..++.+.|++||.|+|+|+++|+ +++|.||
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 GDVVRG-FVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEE-EEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999 999999999999999999999999999999999999999999999999999999 8899875
No 73
>PHA02945 interferon resistance protein; Provisional
Probab=99.35 E-value=3.1e-12 Score=113.89 Aligned_cols=75 Identities=24% Similarity=0.487 Sum_probs=69.2
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEE--CCCeeeEEecccc--CcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEI--APGREGLCHISEL--SSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel--~~g~eGlvhiSel--s~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
.-|++|+++.| +|+. .+||+||.| .+|.+||+|+|++ +..|+++ ++.+ +||+|.+|||.+|+ +|.|.||+|
T Consensus 7 ~~P~~Gelvig-tV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK 82 (88)
T PHA02945 7 SLPNVGDVLKG-KVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYK 82 (88)
T ss_pred cCCCCCcEEEE-EEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence 34799999998 9999 999999999 4699999999965 9999999 9999 99999999999999 999999999
Q ss_pred ecCC
Q 002487 834 ALLP 837 (916)
Q Consensus 834 ~~~~ 837 (916)
.+.+
T Consensus 83 ~V~~ 86 (88)
T PHA02945 83 RMCR 86 (88)
T ss_pred Eccc
Confidence 8754
No 74
>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=99.34 E-value=4.4e-12 Score=110.28 Aligned_cols=71 Identities=30% Similarity=0.484 Sum_probs=67.9
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeec
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRAL 835 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~ 835 (916)
|++|.| +|+++.++|+||+|.++++|++|+++++++++.++.+.|++||.|+++|+++|. ++++.||+|.+
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 GSIVTG-KVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEE-EEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789998 999999999999999899999999999999999999999999999999999998 78999999976
No 75
>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=99.34 E-value=2.4e-12 Score=110.90 Aligned_cols=67 Identities=28% Similarity=0.587 Sum_probs=62.4
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCc-ccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSS-NWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~-~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|++|.| +|++|++||+||+|.++++||+|+++++| .+..++.+.|++||.|+|+|+++|. +++|.|+
T Consensus 1 G~~~~g-~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSG-KIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEE-EEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 789998 99999999999999999999999999997 5788888999999999999999998 8898874
No 76
>PRK08059 general stress protein 13; Validated
Probab=99.32 E-value=5.8e-12 Score=121.73 Aligned_cols=80 Identities=35% Similarity=0.622 Sum_probs=75.8
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCC
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLP 837 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~ 837 (916)
.++++|++|.| +|+++.+||+||+|.++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|.+..
T Consensus 3 ~~~k~G~iv~G-~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 3 SQYEVGSVVTG-KVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred ccCCCCCEEEE-EEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 45789999999 999999999999999999999999999999999999999999999999999998 8999999999988
Q ss_pred CC
Q 002487 838 EA 839 (916)
Q Consensus 838 ~p 839 (916)
+|
T Consensus 82 ~~ 83 (123)
T PRK08059 82 AP 83 (123)
T ss_pred Cc
Confidence 77
No 77
>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=99.31 E-value=7.2e-12 Score=106.97 Aligned_cols=69 Identities=33% Similarity=0.705 Sum_probs=65.9
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K 833 (916)
|++|.| +|+++.+||+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|.++++.||+|
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 GSVVEG-TVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEE-EEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 789998 999999999999999899999999999999999999999999999999999998889999986
No 78
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.31 E-value=1e-11 Score=109.44 Aligned_cols=70 Identities=21% Similarity=0.287 Sum_probs=64.7
Q ss_pred CCCCcEEEccEEEEEecceEEEEEC-CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCC
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIA-PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLP 837 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~-~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~ 837 (916)
+++|+++.| +|++|.+||+||+++ +|++||+|.++++|. +.+++||.+.++|+++|+ ++++.||+|++.+
T Consensus 2 l~~G~~v~g-~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 2 LVEGMVLSG-CVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCEEEE-EEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 578999999 999999999999996 689999999999987 789999999999999998 8999999998754
No 79
>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=99.31 E-value=8.7e-12 Score=109.43 Aligned_cols=73 Identities=34% Similarity=0.642 Sum_probs=68.4
Q ss_pred CCCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeec
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRAL 835 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~ 835 (916)
++|++|.| +|+++.+||+||+|.+ +.+||+|++++++++..++.+.|++||.|+|+|+++|. ++++.||+|..
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 KVGQKIDG-TVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEE-EEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 46999999 9999999999999984 79999999999999998899999999999999999998 89999999875
No 80
>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=99.30 E-value=7.3e-12 Score=109.09 Aligned_cols=70 Identities=29% Similarity=0.546 Sum_probs=63.1
Q ss_pred CCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcc-cccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSN-WLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~-~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
+.+|++|.| +|++|++||+||+|.++.+||+|+++++|. +..++.+.|++||.|+|+|+++|. ++++.|+
T Consensus 1 ~~~g~~~~g-~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFG-KVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEE-EEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999998 999999999999999899999999999975 555777899999999999999998 7888764
No 81
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.29 E-value=2.2e-12 Score=135.67 Aligned_cols=78 Identities=37% Similarity=0.708 Sum_probs=73.9
Q ss_pred CCCCCcEEEccEEEEEecceEEEEE--CCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEI--APGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel--~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
-|++|+++-| +|++|.+|||||.| ++|++||+|+||++..|++++++++++||.+-+|||++|+ +|.|.||+|.+.
T Consensus 8 ~PeeGEiVv~-tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~ 86 (269)
T COG1093 8 YPEEGEIVVG-TVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT 86 (269)
T ss_pred CCCCCcEEEE-EEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence 3799999998 99999999999999 5799999999999999999999999999999999999999 999999999986
Q ss_pred CC
Q 002487 837 PE 838 (916)
Q Consensus 837 ~~ 838 (916)
++
T Consensus 87 ~~ 88 (269)
T COG1093 87 EH 88 (269)
T ss_pred HH
Confidence 54
No 82
>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=99.26 E-value=1.7e-11 Score=106.26 Aligned_cols=69 Identities=41% Similarity=0.608 Sum_probs=66.0
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
|++|.| +|.++.++|+||+|..+.+|++|.+++++.+..++.+.|++||.++++|+++|+ ++++.||+|
T Consensus 1 G~iv~g-~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKG-TVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEE-EEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999 999999999999998889999999999999999999999999999999999996 789999986
No 83
>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....
Probab=99.22 E-value=5.5e-11 Score=107.04 Aligned_cols=83 Identities=43% Similarity=0.615 Sum_probs=70.8
Q ss_pred hHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccC
Q 002487 326 ELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDE 405 (916)
Q Consensus 326 ~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 405 (916)
||.+.|++++.++|.+|+++++|++|++++++|++++.+.|.++. ++. ++
T Consensus 1 el~~~v~~~~~~~l~~a~~~~~K~eR~~a~~~i~~~~~~~~~~~~------------------~e~--~~---------- 50 (83)
T PF03726_consen 1 ELKEAVKELAGEKLKEALQIPDKQEREEALDAIKEEVIEELEEEY------------------EEE--DE---------- 50 (83)
T ss_dssp HHHHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHHCCC------------------HHS--TT----------
T ss_pred CHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHhh------------------ccc--ch----------
Confidence 588999999999999999999999999999999999999997520 000 00
Q ss_pred CccccCCCCCCCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 002487 406 GDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRF 454 (916)
Q Consensus 406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~ 454 (916)
....+|+.+|+.+.++.||++||++|+|+|||+
T Consensus 51 ----------------~~~~~i~~~~~~l~k~~vR~~Il~~~~R~DGR~ 83 (83)
T PF03726_consen 51 ----------------EDEKEIKEAFEELEKKIVREMILEEGIRIDGRK 83 (83)
T ss_dssp ----------------SHHHHHHHHHHHHHHHHHHHHHHCTSBTTTS-B
T ss_pred ----------------hhHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence 235689999999999999999999999999995
No 84
>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=99.22 E-value=2.4e-11 Score=103.54 Aligned_cols=67 Identities=34% Similarity=0.766 Sum_probs=63.6
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|++|.| +|+++.+||+||++.++.+||+|.++++++++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 g~~~~g-~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEG-VVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEE-EEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789998 999999999999999999999999999999998999999999999999999998 8899875
No 85
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.21 E-value=4e-11 Score=102.59 Aligned_cols=68 Identities=56% Similarity=0.951 Sum_probs=64.4
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSR 832 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~ 832 (916)
|++|.| +|+++.+||+||+|.++.+||+|+++++++++.++.+.|++||.|+|+|+++|.++++.||+
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 GKIYEG-KVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEE-EEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 789998 99999999999999989999999999999999899899999999999999999888999885
No 86
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.21 E-value=3.6e-11 Score=108.53 Aligned_cols=75 Identities=21% Similarity=0.337 Sum_probs=68.4
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCc----ccccCccccccCCCEEEEEEEEEcCCCceEEEEeec
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSS----NWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~----~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
.|++|+++.| +|+++.++|+||+|.++.+|++|+|++++ .+..+..+.|++||.|.++|+++|+++++.||+|..
T Consensus 3 ~p~~GdiV~g-~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 3 IPEVGDVVIG-RVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred cCCCCCEEEE-EEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 3689999999 99999999999999989999999999996 455677788999999999999998889999999864
No 87
>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=99.19 E-value=5.7e-11 Score=108.20 Aligned_cols=72 Identities=29% Similarity=0.494 Sum_probs=62.9
Q ss_pred CCCCCcEEEccEEEEEecc--eEEEEECCCeeeEEeccccCc---ccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 760 VPTVGDIYRNCEIKSIAPY--GVFVEIAPGREGLCHISELSS---NWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~f--GaFVel~~g~eGlvhiSels~---~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
.+++|++|.| +|++|.+| ||||+|.+|.+||||+||++| .++.++.+.+++||.|.|+|++... ..--.|+.
T Consensus 4 ~~~~G~iy~g-~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 4 EPIVGNIYLG-RVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred cCCCCCEEEE-EEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence 4689999999 99999997 999999999999999999999 6788889999999999999999865 33334444
No 88
>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=99.14 E-value=1.1e-10 Score=100.48 Aligned_cols=65 Identities=17% Similarity=0.289 Sum_probs=59.2
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|++++| +|+++.+||+||+|.++++|++|.++++..+.. .+.|++||+|++||+++|+ +++|.||
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 GMLVNA-RVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEE-EEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789998 999999999999998899999999999866554 7789999999999999998 7888876
No 89
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.14 E-value=1.2e-10 Score=126.07 Aligned_cols=79 Identities=34% Similarity=0.626 Sum_probs=73.4
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECC--CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAP--GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~--g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
-|++|++|.| +|++|.+||+||+|.. |++||+|+|+++++++.++.+.|++||.|.|+|+++|. +++|.||+|.+.
T Consensus 5 ~P~~GdiV~G-~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~ 83 (262)
T PRK03987 5 WPEEGELVVG-TVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVN 83 (262)
T ss_pred CCCCCCEEEE-EEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecc
Confidence 3689999999 9999999999999964 89999999999999999999999999999999999998 899999999887
Q ss_pred CCC
Q 002487 837 PEA 839 (916)
Q Consensus 837 ~~p 839 (916)
++.
T Consensus 84 ~~e 86 (262)
T PRK03987 84 EHQ 86 (262)
T ss_pred cch
Confidence 543
No 90
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.14 E-value=8.1e-11 Score=139.98 Aligned_cols=114 Identities=31% Similarity=0.451 Sum_probs=90.5
Q ss_pred CCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeE
Q 002487 712 SGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGL 791 (916)
Q Consensus 712 ~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGl 791 (916)
.|-.|+++|+.+...+.-|..++-.--++..+ ...++ ++++|.++.| +|+++++||+||+|+-+.+||
T Consensus 618 ~gl~Tl~dIi~eL~kp~rdpR~~f~~~~~~~~-------v~~i~----dLk~Gm~leg-~Vrnv~~fgafVdIgv~qDgl 685 (780)
T COG2183 618 FGLPTLEDIILELEKPGRDPRDEFHTPTLDEG-------VESIT----DLKPGMILEG-TVRNVVDFGAFVDIGVHQDGL 685 (780)
T ss_pred cCCchHHHHHHHhhcCCCCCcccccccchhhh-------hhhHh----hccCCCEEEE-EEEEeeeccceEEecccccee
Confidence 34467888887776654444333222222221 11122 5699999999 999999999999999899999
Q ss_pred EeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecCC
Q 002487 792 CHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALLP 837 (916)
Q Consensus 792 vhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~ 837 (916)
||+|++++.++.+|.+++++||.|+|+|+++|. +++|.||++....
T Consensus 686 vHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~ 732 (780)
T COG2183 686 VHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEE 732 (780)
T ss_pred eeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence 999999999999999999999999999999999 8999999997654
No 91
>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=99.13 E-value=1.7e-10 Score=99.26 Aligned_cols=66 Identities=24% Similarity=0.444 Sum_probs=60.9
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
|++|+| +|+++.++|+||++ +|++||+|.|++++.+..++.+. +||.++|+|+++|. +++|.||+|
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 GEIVEG-KVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEE-EEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 789998 99999999999999 69999999999999888777663 89999999999998 899999986
No 92
>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=99.12 E-value=2.3e-10 Score=102.00 Aligned_cols=69 Identities=28% Similarity=0.615 Sum_probs=61.5
Q ss_pred CCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCccccc-----------CccccccCCCEEEEEEEEEcC-CCceE
Q 002487 763 VGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWLA-----------KAEDVVKVGDLVDVKLIEVND-KGQLR 829 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v~-----------~~~~~~kvGd~V~VKVi~iD~-~gkI~ 829 (916)
+|++|+| +|++|++||+||+|.+ +.+|++|.++++++++. +..+.|++||.|+|+|+++|. ++++.
T Consensus 1 ~g~~~~g-~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 1 VGEEFDG-VISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEE-EEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEE
Confidence 4899998 9999999999999998 89999999999876432 455789999999999999998 89999
Q ss_pred EEE
Q 002487 830 LSR 832 (916)
Q Consensus 830 LS~ 832 (916)
|++
T Consensus 80 ~~l 82 (83)
T cd04471 80 FEL 82 (83)
T ss_pred EEE
Confidence 986
No 93
>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=99.11 E-value=1.9e-10 Score=98.27 Aligned_cols=67 Identities=36% Similarity=0.715 Sum_probs=63.0
Q ss_pred CCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 763 VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
+|++|.| +|+++.++|+||++. +.+|++|.+++++.++.++.+.|++||.|+|+|+++|. ++++.||
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 EGDVVEG-TVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEE-EEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899998 999999999999997 79999999999999998999999999999999999998 8898875
No 94
>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=99.10 E-value=1.5e-10 Score=107.90 Aligned_cols=74 Identities=23% Similarity=0.425 Sum_probs=66.3
Q ss_pred CCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc-------------------cCccccccCCCEEEEEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL-------------------AKAEDVVKVGDLVDVKLIE 821 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v-------------------~~~~~~~kvGd~V~VKVi~ 821 (916)
+++|+++.| +|++|.++|+||+|++|++|++|+++++|.+. .++.+.|++||.|+++|++
T Consensus 1 L~~G~vV~G-~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 1 LSEGMLVLG-QVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEE-EEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 368999999 99999999999999999999999999998763 3477889999999999999
Q ss_pred EcC----CCceEEEEeec
Q 002487 822 VND----KGQLRLSRRAL 835 (916)
Q Consensus 822 iD~----~gkI~LS~K~~ 835 (916)
+|. +++|.||+|..
T Consensus 80 ~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 80 LDKSKSGKKRIELSLEPE 97 (100)
T ss_pred ccCCcCCCcEEEEEecHH
Confidence 998 47999999853
No 95
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=1.6e-08 Score=106.01 Aligned_cols=200 Identities=21% Similarity=0.225 Sum_probs=134.4
Q ss_pred CeeEEEEeCccccCCCceEEEEeCC-eEEEEEEEecCC----CCCCCCCCccccceeecccccccCCCCCcccCCCCCch
Q 002487 98 DRQILVETGHMGRQASGAVTVTDGE-TIIYTSVCLADV----PSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDH 172 (916)
Q Consensus 98 ~R~i~~etG~la~qAdGSa~v~~G~-T~Vl~tV~~~~e----~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~ 172 (916)
=|+|.+|||++ .++||||.|++|+ |-|+++|...-. ..+.....-+.||+.... . ..|--|+| .+-
T Consensus 31 ~Rpi~vetdVl-p~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~sa--s----p~f~gRgg--de~ 101 (288)
T KOG1612|consen 31 FRPIEVETDVL-PGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPSA--S----PQFQGRGG--DEL 101 (288)
T ss_pred cceEEEEeccc-cCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCCc--C----ccccCCCh--hhH
Confidence 38999999999 8999999999999 999999987421 111112222355543221 1 12333433 222
Q ss_pred hhhHHHHhcCcccc----------cccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCC-------------
Q 002487 173 EVLVCRLIDRPLRP----------TLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVP------------- 229 (916)
Q Consensus 173 eil~sRlIdR~LRp----------lfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP------------- 229 (916)
..+++..+.|.|.. .|-++|.|.+.|++.|++.||+ ..| |--.|+.+||..--+|
T Consensus 102 ~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn-~~d-AiS~Ai~~AL~~T~lPkv~v~~dd~~~~~ 179 (288)
T KOG1612|consen 102 VEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGN-LLD-AISIAIYAALNNTRLPKVIVAFDDDGEVE 179 (288)
T ss_pred HHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCC-HHH-HHHHHHHHHHhcccCCccccccccCCcee
Confidence 33344444555554 4556799999999999999984 334 3446888888866555
Q ss_pred -------C-------CCceEEEEEEEECCEEEECCChHHHhhCCeeEEEEeecCeEE-EEEe-cCCCCCHHHHHHHHHHH
Q 002487 230 -------N-------SKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAIL-MIEG-YCDFLSEEMLIQAVQVG 293 (916)
Q Consensus 230 -------~-------~~~VaaV~vg~i~g~~ildPt~~E~~~s~~dl~vagt~~~i~-mie~-~~~~~~e~~l~~al~~a 293 (916)
. .-+..=+++..++..++||||.+|++.+...|.|+-+..+++ .+-. +.+.+..+-..++|+.|
T Consensus 180 i~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~l~~s~i~~mle~~ 259 (288)
T KOG1612|consen 180 ILLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGDLDPSSIPEMLEQG 259 (288)
T ss_pred eccCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcceEEEEEecCCCCChhhHHHHHHHH
Confidence 1 112234778889999999999999999888888887666533 3333 33347777788888888
Q ss_pred HHHHHHHHHHHHHHH
Q 002487 294 QDAVREISNEVKALV 308 (916)
Q Consensus 294 ~~~~~~i~~~~~~~~ 308 (916)
.+-.+.+.....+.+
T Consensus 260 ~~~~e~l~~~l~k~L 274 (288)
T KOG1612|consen 260 KAVVETLAPDLVKSL 274 (288)
T ss_pred HHHHHhhhHHHHHHh
Confidence 888877766655544
No 96
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.06 E-value=5.9e-10 Score=95.06 Aligned_cols=71 Identities=44% Similarity=0.767 Sum_probs=66.4
Q ss_pred CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
++|+++.| +|+++.++|+||++.++.+|++|.+++.+.+..++.+.|++||.|.|+|+++|. ++++.||++
T Consensus 1 ~~G~~v~g-~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEG-TVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEE-EEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 36999998 999999999999999899999999999998888888899999999999999998 699999975
No 97
>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=99.00 E-value=1.3e-09 Score=97.52 Aligned_cols=74 Identities=20% Similarity=0.212 Sum_probs=69.5
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEee
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRA 834 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~ 834 (916)
.|++|+++.| +|+++.+.|++|++..+.+|++|+++++..+..+..+.|++||.|.++|+++|..+++.||++.
T Consensus 3 ~p~~GdiV~G-~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 3 LPDVGDIVIG-IVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCCCEEEE-EEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 3689999999 9999999999999988999999999999888888899999999999999999887899999986
No 98
>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=98.98 E-value=2.5e-09 Score=94.86 Aligned_cols=65 Identities=32% Similarity=0.560 Sum_probs=58.9
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEE
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSR 832 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~ 832 (916)
.++++|++|.| +|+++++||+||++.++.+||+|+|++. +.+++||.++|+|.++..++++.||+
T Consensus 12 ~~~~~G~~~~g-~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 12 EDLEVGKLYKG-KVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred hhCCCCCEEEE-EEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 45789999999 9999999999999998999999999973 46999999999999994489999985
No 99
>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=98.96 E-value=1.7e-09 Score=93.98 Aligned_cols=62 Identities=26% Similarity=0.479 Sum_probs=57.8
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCccc--ccCccccccCCCEEEEEEEEEcCCC
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNW--LAKAEDVVKVGDLVDVKLIEVNDKG 826 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~--v~~~~~~~kvGd~V~VKVi~iD~~g 826 (916)
|+++.| +|+++.++|+||++.++++|++|++++++++ ..++.+.|++||.|+++|+++|..+
T Consensus 1 G~iV~g-~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKA-KVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEE-EEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 789998 9999999999999999999999999999885 7888899999999999999998743
No 100
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.88 E-value=3.4e-09 Score=90.02 Aligned_cols=60 Identities=58% Similarity=0.874 Sum_probs=56.9
Q ss_pred CeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHH
Q 002487 694 PLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAII 754 (916)
Q Consensus 694 P~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i 754 (916)
|++.+++|++++++.+||+||++|++|+++||++ |+++++|.|.|++.+.++++.|+++|
T Consensus 1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~-I~i~~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVK-IDIEDDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred CeEEEEEeChhheeeeECCCchHHHHHHHHHCCE-EEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence 7899999999999999999999999999999997 99999999999999888999998776
No 101
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.87 E-value=4.5e-09 Score=87.91 Aligned_cols=64 Identities=48% Similarity=0.804 Sum_probs=59.2
Q ss_pred EEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 767 YRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 767 ~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|.| +|+++.++|+||++.++.+|++|.+++++.+..++.+.|++||.|+++|+++|. ++++.||
T Consensus 1 v~g-~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTG-KVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEE-EEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 467 999999999999999899999999999999888888999999999999999998 8888875
No 102
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=98.85 E-value=5.8e-09 Score=128.44 Aligned_cols=143 Identities=19% Similarity=0.192 Sum_probs=117.8
Q ss_pred hcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 758 TMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 758 ~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
..+++.|+++.| .|.++.+.|+|+.+.+++++++++|++++.+...++..|.+||.|.++|+++++ .+++.|++|...
T Consensus 1157 ~eDlk~g~iv~G-~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~ 1235 (1710)
T KOG1070|consen 1157 IEDLKIGDIVRG-FVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSD 1235 (1710)
T ss_pred hhhcccCceeEE-EEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccc
Confidence 345799999999 999999999999999999999999999999999999999999999999999999 789999999864
Q ss_pred CC-C-CCCCCCCCCCCCCcEEEeeccc--------------------------cccCCCCCCCCCCCcEEEeEeeecCCC
Q 002487 837 PE-A-DAENPPVKLPTGDPTKDAAASD--------------------------KLVGSPKPKGSSSEDTVLPHKKVKVFK 888 (916)
Q Consensus 837 ~~-p-~~~~~~~~~~~G~vv~g~Vs~i--------------------------~~v~~p~~~~k~Gd~V~v~I~~id~ek 888 (916)
.. + ......+.+.+|+...|+|... .+...-...+..|+.|.+.+++++.++
T Consensus 1236 ~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek 1315 (1710)
T KOG1070|consen 1236 IKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEK 1315 (1710)
T ss_pred cCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchh
Confidence 32 1 1112224668888888876221 111222357899999999999999999
Q ss_pred CcccCCCCCCCCc
Q 002487 889 RPASPAKDRPYSN 901 (916)
Q Consensus 889 ~rIsL~~~~~~~~ 901 (916)
+||+++.+..|..
T Consensus 1316 ~rIsl~~k~s~~~ 1328 (1710)
T KOG1070|consen 1316 KRISLGLKSSYLS 1328 (1710)
T ss_pred hhhhhhhhhhccC
Confidence 9999998877763
No 103
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=98.84 E-value=2.2e-08 Score=104.21 Aligned_cols=195 Identities=16% Similarity=0.200 Sum_probs=129.6
Q ss_pred eeEEEEeCccccCCCceEEEEeCCeEEEEEEEec-CCCCCCC-CCCccccceeecccccccCCC--CCcccCCCCCchhh
Q 002487 99 RQILVETGHMGRQASGAVTVTDGETIIYTSVCLA-DVPSEPS-DFFPLNVNYQERFSAAGRTSG--GFFKREGRTKDHEV 174 (916)
Q Consensus 99 R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~-~e~~~~~-~f~pL~v~y~ek~~A~g~iPg--~f~kReg~p~~~ei 174 (916)
|.+.++.|-+ ..||||++++.|+|.|+|++.+. -+|..+. +--.+..+|. .|. .-.-|-|+|++.+.
T Consensus 47 Rdt~in~g~I-sTangSal~K~G~ttvi~~Ik~ei~epstdapdeg~Iv~n~~--------lpplcs~r~RpG~p~dea~ 117 (298)
T KOG1613|consen 47 RDTAINAGNI-STANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDIVPNYA--------LPPLCSSRFRPGPPTDEAQ 117 (298)
T ss_pred hhhheecCce-eccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcceeeccc--------CCcccccCCCCCCCchHHH
Confidence 6678899999 89999999999999999999985 1222111 1111222221 121 11236699999987
Q ss_pred hHHHHhcCcccc----------cccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCC---CCc--------
Q 002487 175 LVCRLIDRPLRP----------TLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPN---SKV-------- 233 (916)
Q Consensus 175 l~sRlIdR~LRp----------lfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~---~~~-------- 233 (916)
-+|.-+..+|.. ++++.+.|....++.+|++||..- -+|.+|+.+||..-.+|. +.-
T Consensus 118 viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~f--Da~w~al~aAlknvklP~a~ide~~~~~~~t~ 195 (298)
T KOG1613|consen 118 VISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVF--DACWNALMAALKNVKLPRAFIDERASDLRMTI 195 (298)
T ss_pred HHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHH--HHHHHHHHHHHhcCCCceeeecccchhhhhhH
Confidence 777665443332 788889999999999999999654 689999999998766662 110
Q ss_pred ---eE---------------EE-------EEE-EECCEEE-ECCChHHHhhCCeeEEEEee-cCeEEEE-EecCCC-CCH
Q 002487 234 ---IA---------------GV-------RVG-LVGDKFI-VNPTTQEMEDSQLDLLLAGS-DDAILMI-EGYCDF-LSE 283 (916)
Q Consensus 234 ---Va---------------aV-------~vg-~i~g~~i-ldPt~~E~~~s~~dl~vagt-~~~i~mi-e~~~~~-~~e 283 (916)
++ ++ +-. ..|+.++ .|||-+|+...+..+.|... .++++-+ -.+|.. .+.
T Consensus 196 e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvldss~n~v~l~k~GG~al~~~ 275 (298)
T KOG1613|consen 196 EEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVLDSSGNYVQLTKVGGGALITP 275 (298)
T ss_pred HHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEEcCCCCEEEEEecCcccccCH
Confidence 00 11 111 1234444 89999999987777766553 3344433 334434 555
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 002487 284 EMLIQAVQVGQDAVREISNEV 304 (916)
Q Consensus 284 ~~l~~al~~a~~~~~~i~~~~ 304 (916)
+.+-.+|++|..-.+++-+.+
T Consensus 276 ~~iK~c~elar~Rakelk~~~ 296 (298)
T KOG1613|consen 276 EMIKRCLELARVRAKELKTRF 296 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 888899999988887765543
No 104
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=98.83 E-value=8.5e-09 Score=89.09 Aligned_cols=65 Identities=28% Similarity=0.402 Sum_probs=51.6
Q ss_pred CceEEEEEEEECCEEEECCChHHHhhCCeeEEEE--eecCeEEEEEecCCC-CCHHHHHHHHHHHHHH
Q 002487 232 KVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLA--GSDDAILMIEGYCDF-LSEEMLIQAVQVGQDA 296 (916)
Q Consensus 232 ~~VaaV~vg~i~g~~ildPt~~E~~~s~~dl~va--gt~~~i~mie~~~~~-~~e~~l~~al~~a~~~ 296 (916)
++++|||+|++||++|+|||.+|+..++.+|+++ ++.+.+.|.+.++.. +++++|.+||++|+++
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 5899999999999999999999988766555555 455566777766644 9999999999999986
No 105
>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=98.77 E-value=2.1e-08 Score=93.20 Aligned_cols=77 Identities=25% Similarity=0.446 Sum_probs=65.5
Q ss_pred cEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC-----------ccccccCCCEEEEEEEEEcC-C-----Cc
Q 002487 765 DIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK-----------AEDVVKVGDLVDVKLIEVND-K-----GQ 827 (916)
Q Consensus 765 ~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~-----------~~~~~kvGd~V~VKVi~iD~-~-----gk 827 (916)
++|.| +|++|.+||+||+|. +++||+|+++++++++.. +...|++||.|+|+|.++|. + ++
T Consensus 1 ~vv~g-~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEG-EVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEE-EEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence 47898 999999999999998 599999999999876543 35789999999999999997 2 58
Q ss_pred eEEEEeecCCCCCCCC
Q 002487 828 LRLSRRALLPEADAEN 843 (916)
Q Consensus 828 I~LS~K~~~~~p~~~~ 843 (916)
+.||+|+....||.-.
T Consensus 79 i~ls~k~~~~g~~~~~ 94 (99)
T cd04460 79 IGLTMRQPGLGKLEWI 94 (99)
T ss_pred EEEEEecCCCCcHHHh
Confidence 9999998876666543
No 106
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.74 E-value=3.1e-08 Score=121.93 Aligned_cols=81 Identities=25% Similarity=0.516 Sum_probs=69.6
Q ss_pred HHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCcccc-----------cCccccccCCCEEEEE
Q 002487 751 KAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWL-----------AKAEDVVKVGDLVDVK 818 (916)
Q Consensus 751 ~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v-----------~~~~~~~kvGd~V~VK 818 (916)
..++...+.+.++|++|+| +|++|++||+||+|.+ +++||||+|+|+++++ ++....|++||.|+|+
T Consensus 615 ~~~~~~~yl~~~iG~~~~g-~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vk 693 (709)
T TIGR02063 615 NDWKKAEYMSEKIGEEFEG-VISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVR 693 (709)
T ss_pred HHHHHHHhhhccCCcEEEE-EEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEE
Confidence 4455555566789999999 9999999999999987 8999999999997653 3455789999999999
Q ss_pred EEEEcC-CCceEEEE
Q 002487 819 LIEVND-KGQLRLSR 832 (916)
Q Consensus 819 Vi~iD~-~gkI~LS~ 832 (916)
|.++|. +++|.|++
T Consensus 694 v~~vd~~~~~I~~~l 708 (709)
T TIGR02063 694 VVKADLDTGKIDFEL 708 (709)
T ss_pred EEEEecccCeEEEEE
Confidence 999998 89999986
No 107
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.74 E-value=1.8e-08 Score=104.58 Aligned_cols=78 Identities=24% Similarity=0.411 Sum_probs=69.6
Q ss_pred HHhhhcCCCCCcEEEccEEEEEecceEEEEEC----------CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEc
Q 002487 754 ISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIA----------PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 754 i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~----------~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD 823 (916)
|......+++|+++.| +|++|.++|+||+|. ++.+|++|++++++.+..++.+.|++||.|.++|++++
T Consensus 55 ~~~~~~~~~~GdiV~G-kV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 55 FKKTPPLLKKGDIVYG-RVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CcCCCCCCCCCCEEEE-EEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 3333456799999999 999999999999994 36889999999999988889999999999999999998
Q ss_pred CCCceEEEEee
Q 002487 824 DKGQLRLSRRA 834 (916)
Q Consensus 824 ~~gkI~LS~K~ 834 (916)
+++.||+|+
T Consensus 134 --~~i~LS~k~ 142 (189)
T PRK09521 134 --DPLQLSTKG 142 (189)
T ss_pred --CcEEEEEec
Confidence 899999985
No 108
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.73 E-value=1e-08 Score=105.63 Aligned_cols=84 Identities=27% Similarity=0.536 Sum_probs=76.6
Q ss_pred CeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeEE---ecccccHHHHHHHHHhhhc--CCC-----
Q 002487 694 PLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKIT---AKDLSSLEKSKAIISNLTM--VPT----- 762 (916)
Q Consensus 694 P~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I~---~~~~~~~~~a~~~i~~l~~--~~~----- 762 (916)
..+.++.||+++++.+||+||++|+.|++++|++ |+++++ |.|.|+ +.+..++++|+++|+.+.. +++
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~-I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l 80 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVK-LEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRL 80 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcE-EEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHH
Confidence 3567889999999999999999999999999996 999976 999999 8999999999999999887 566
Q ss_pred CCcEEEccEEEEEecce
Q 002487 763 VGDIYRNCEIKSIAPYG 779 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fG 779 (916)
+|+.|.+ .|.++.+|+
T Consensus 81 ~gd~y~~-~Vi~i~~~~ 96 (180)
T PRK13763 81 LDDDYVL-EVIDLSDYG 96 (180)
T ss_pred hCCCceE-EEEEhhhcc
Confidence 8999998 999999984
No 109
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.69 E-value=4.2e-08 Score=105.16 Aligned_cols=74 Identities=19% Similarity=0.331 Sum_probs=69.1
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc----cCccccccCCCEEEEEEEEEcCCCceEEEEee
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL----AKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRA 834 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v----~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~ 834 (916)
.|++|+++.| +|+++.++|+||+|..+.+|+||++++++.++ .++.+.|++||.|.+||++++..+++.||+|+
T Consensus 60 ~P~vGDiViG-~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~ 137 (235)
T PRK04163 60 IPKVGDLVIG-KVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG 137 (235)
T ss_pred cCCCCCEEEE-EEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence 4799999999 99999999999999988999999999999987 78888999999999999999987789999974
No 110
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.65 E-value=1.6e-08 Score=103.50 Aligned_cols=79 Identities=32% Similarity=0.615 Sum_probs=72.1
Q ss_pred EeeccceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeE--EecccccHHHHHHHHHhhhc--CCC-----CCcEEE
Q 002487 699 MKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKI--TAKDLSSLEKSKAIISNLTM--VPT-----VGDIYR 768 (916)
Q Consensus 699 ~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I--~~~~~~~~~~a~~~i~~l~~--~~~-----vG~i~~ 768 (916)
+.||+++|+.+||+||++|+.|++++|++ |+++++ |.|.| ...+..++.+|+++|+.+.. .++ +|+.|.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~-I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y~ 80 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVK-LDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYM 80 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcE-EEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcce
Confidence 57999999999999999999999999996 999966 99999 88889999999999999877 466 899999
Q ss_pred ccEEEEEecce
Q 002487 769 NCEIKSIAPYG 779 (916)
Q Consensus 769 G~~V~~I~~fG 779 (916)
+ .|.+|.+|+
T Consensus 81 ~-~Vi~I~~~~ 90 (172)
T TIGR03665 81 L-EVIDLKEYG 90 (172)
T ss_pred E-EEEEhhhcc
Confidence 8 999999984
No 111
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.58 E-value=8.4e-08 Score=99.35 Aligned_cols=103 Identities=25% Similarity=0.504 Sum_probs=79.2
Q ss_pred eccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCccccc-----
Q 002487 729 IDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLA----- 803 (916)
Q Consensus 729 Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~----- 803 (916)
+|+.+-+.-.|...+......+. ++.+...|.+|+++.| +|+++.++|+||+++ ..+|++|.+++.+++..
T Consensus 49 ~di~~i~~g~i~~gdg~~~~~v~--f~~lvf~P~~GEVv~g-~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~ 124 (187)
T PRK08563 49 LDVKVIGEGKIVPGDGATYHEVE--FDALVFKPELQEVVEG-EVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKN 124 (187)
T ss_pred EEeEEecccEEecCCCCcEEEEE--EEEEEEeccCCCEEEE-EEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEcccc
Confidence 45554444455555554444443 5667778999999999 999999999999998 49999999999876432
Q ss_pred ------CccccccCCCEEEEEEEEEcC-C-----CceEEEEeec
Q 002487 804 ------KAEDVVKVGDLVDVKLIEVND-K-----GQLRLSRRAL 835 (916)
Q Consensus 804 ------~~~~~~kvGd~V~VKVi~iD~-~-----gkI~LS~K~~ 835 (916)
+....+++||.|++||++++. . .+|.||+|+-
T Consensus 125 ~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~ 168 (187)
T PRK08563 125 GRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQP 168 (187)
T ss_pred ceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCC
Confidence 345689999999999999986 2 3788999874
No 112
>PRK11642 exoribonuclease R; Provisional
Probab=98.57 E-value=3.4e-07 Score=113.49 Aligned_cols=79 Identities=25% Similarity=0.470 Sum_probs=66.9
Q ss_pred hhcCCCCCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCccccc-----------CccccccCCCEEEEEEEEEcC
Q 002487 757 LTMVPTVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWLA-----------KAEDVVKVGDLVDVKLIEVND 824 (916)
Q Consensus 757 l~~~~~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v~-----------~~~~~~kvGd~V~VKVi~iD~ 824 (916)
.+++-++|++|+| +|++|++||+||+|.+ +++||||+++|.++|.. +....|++||.|+|+|.++|.
T Consensus 637 ~~m~~~iGe~f~G-~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~ 715 (813)
T PRK11642 637 DFMLDQVGNVFKG-VISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNM 715 (813)
T ss_pred hhhhccCCcEEEE-EEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeec
Confidence 3344589999999 9999999999999976 49999999999876421 345789999999999999998
Q ss_pred -CCceEEEEeecC
Q 002487 825 -KGQLRLSRRALL 836 (916)
Q Consensus 825 -~gkI~LS~K~~~ 836 (916)
+++|.|++-...
T Consensus 716 ~~rkI~f~l~~~~ 728 (813)
T PRK11642 716 DERKIDFSLISSE 728 (813)
T ss_pred CCCeEEEEEeccc
Confidence 899999985443
No 113
>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=98.55 E-value=2.2e-07 Score=113.21 Aligned_cols=81 Identities=31% Similarity=0.519 Sum_probs=68.2
Q ss_pred HHHHHhhhcCCCCCcEEEccEEEEEecceEEEEEC-CCeeeEEeccccCcccc-----------cCccccccCCCEEEEE
Q 002487 751 KAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIA-PGREGLCHISELSSNWL-----------AKAEDVVKVGDLVDVK 818 (916)
Q Consensus 751 ~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~-~g~eGlvhiSels~~~v-----------~~~~~~~kvGd~V~VK 818 (916)
..++...+.+-++|++|+| +|++|++||+||+|. .+++||||+++|.+++. ++....|++||.|+|+
T Consensus 560 ~~~~~~~yl~~~iG~~~~g-~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vk 638 (654)
T TIGR00358 560 ADWLKCRYLLDKVGTEFSG-EISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVK 638 (654)
T ss_pred HHHHHHHhhhhCCCcEEEE-EEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEE
Confidence 3444444555688999999 999999999999997 78999999999998741 3345789999999999
Q ss_pred EEEEcC-CCceEEEE
Q 002487 819 LIEVND-KGQLRLSR 832 (916)
Q Consensus 819 Vi~iD~-~gkI~LS~ 832 (916)
|+++|. +++|.|++
T Consensus 639 i~~vd~~~~~I~f~l 653 (654)
T TIGR00358 639 LTEVNMETRSIIFEL 653 (654)
T ss_pred EEEEecccCeEEEEE
Confidence 999998 89999875
No 114
>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=98.53 E-value=2.5e-07 Score=95.28 Aligned_cols=80 Identities=25% Similarity=0.533 Sum_probs=67.4
Q ss_pred hhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCccccc-----------CccccccCCCEEEEEEEEEc-
Q 002487 756 NLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLA-----------KAEDVVKVGDLVDVKLIEVN- 823 (916)
Q Consensus 756 ~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~-----------~~~~~~kvGd~V~VKVi~iD- 823 (916)
.++..+.+|++++| +|++++++|+||+++ ..+|++|.+++.+++.. +....++.||.|+|||+++|
T Consensus 74 ~i~f~p~~gEvv~G-~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 151 (179)
T TIGR00448 74 ALVFKPELGEIVEG-EVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSL 151 (179)
T ss_pred EEEEeccCCCEEEE-EEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEc
Confidence 45567889999999 999999999999996 59999999999866432 24468999999999999998
Q ss_pred ----C-CCceEEEEeecCC
Q 002487 824 ----D-KGQLRLSRRALLP 837 (916)
Q Consensus 824 ----~-~gkI~LS~K~~~~ 837 (916)
+ ..+|.||+|+..-
T Consensus 152 ~~~~~~~~~I~lt~k~~~L 170 (179)
T TIGR00448 152 KDRRPEGSKIGLTMRQPLL 170 (179)
T ss_pred cCCCCCcceEEEEeccCcC
Confidence 3 5789999998643
No 115
>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=98.49 E-value=4.2e-07 Score=78.47 Aligned_cols=63 Identities=24% Similarity=0.322 Sum_probs=55.1
Q ss_pred CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC---CCceEEEE
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND---KGQLRLSR 832 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~---~gkI~LS~ 832 (916)
..|++++| +|.++.++|+||+++ +.+|+||.+|++ +.+.|++||.|+|.|++++. .++|.||+
T Consensus 2 ~~g~iV~G-~V~~~~~~~~~vdig-~~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTG-IVKRVDRGNVIVDLG-KVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEE-EEEEEcCCCEEEEcC-CeEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 46999999 999999999999996 599999999997 34578999999999999986 35788874
No 116
>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=98.41 E-value=7e-07 Score=82.16 Aligned_cols=74 Identities=23% Similarity=0.336 Sum_probs=66.2
Q ss_pred CCCCCcEEEccEEEEEecceEEEEE--------CCCeeeEEeccccCccccc--CccccccCCCEEEEEEEEEcCCCceE
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEI--------APGREGLCHISELSSNWLA--KAEDVVKVGDLVDVKLIEVNDKGQLR 829 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel--------~~g~eGlvhiSels~~~v~--~~~~~~kvGd~V~VKVi~iD~~gkI~ 829 (916)
.|++|+++.| +|++++...|+|+| .....|++|+|++...+.. ++.+.|++||.|++||++.+....+.
T Consensus 3 ~P~~GDiVig-~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~ 81 (92)
T cd05791 3 LPKVGSIVIA-RVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYY 81 (92)
T ss_pred CCCCCCEEEE-EEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcE
Confidence 3689999999 99999999999999 6678899999999877776 67889999999999999998767799
Q ss_pred EEEee
Q 002487 830 LSRRA 834 (916)
Q Consensus 830 LS~K~ 834 (916)
||++.
T Consensus 82 Lst~~ 86 (92)
T cd05791 82 LSTAE 86 (92)
T ss_pred EEecC
Confidence 99875
No 117
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.34 E-value=7.3e-07 Score=90.58 Aligned_cols=86 Identities=26% Similarity=0.476 Sum_probs=70.1
Q ss_pred HhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc----------cC-ccccccCCCEEEEEEEEEc
Q 002487 755 SNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL----------AK-AEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 755 ~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v----------~~-~~~~~kvGd~V~VKVi~iD 823 (916)
+.++..|..|++++| .|+++.+||+||.|+ -.+||+|+|++.++++ .+ ....+++||.|++||++++
T Consensus 73 ~al~fkP~~gEVV~G-eVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s 150 (183)
T COG1095 73 RALVFKPFRGEVVEG-EVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVS 150 (183)
T ss_pred EEEEEEeccccEEEE-EEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEe
Confidence 446677899999999 999999999999998 5999999999998742 22 4448999999999999997
Q ss_pred C-C-----CceEEEEeecC--CCCCCC
Q 002487 824 D-K-----GQLRLSRRALL--PEADAE 842 (916)
Q Consensus 824 ~-~-----gkI~LS~K~~~--~~p~~~ 842 (916)
. . .+|.|++|+.. .-+|..
T Consensus 151 ~~~~~~~~~~I~lTmrq~~LGklew~~ 177 (183)
T COG1095 151 LKSRRPRESKIGLTMRQPGLGKLEWIE 177 (183)
T ss_pred cccCccccceEEEEeccccCCcchhhh
Confidence 6 2 57889998853 344544
No 118
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=98.32 E-value=1.5e-06 Score=107.88 Aligned_cols=140 Identities=20% Similarity=0.181 Sum_probs=114.7
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEECCC-eeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEIAPG-REGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel~~g-~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
.++++|+.+.| +|..+++-|+.|.+.+| +.|+++.++|++.+..-|...|++|-.++.||+.++. .|++.|++|..+
T Consensus 505 nDI~iG~~V~~-~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~sl 583 (1710)
T KOG1070|consen 505 NDIEIGQLVPG-VIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSL 583 (1710)
T ss_pred ccccccceeee-EEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEechhh
Confidence 34799999998 99999999999999766 9999999999999888888888898888889999998 899999998875
Q ss_pred CCCCCCCCC--CCCCCCCcEEEeeccc------------------------cccCCCCCCCCCCCcEEEeEeeecCCCCc
Q 002487 837 PEADAENPP--VKLPTGDPTKDAAASD------------------------KLVGSPKPKGSSSEDTVLPHKKVKVFKRP 890 (916)
Q Consensus 837 ~~p~~~~~~--~~~~~G~vv~g~Vs~i------------------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~r 890 (916)
-+....... +...+|.++.|++-.+ .++..+...|.+||+|.++|.++|++++|
T Consensus 584 v~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~r 663 (1710)
T KOG1070|consen 584 VNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRR 663 (1710)
T ss_pred hcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhce
Confidence 433211111 2346899999986221 35566678999999999999999999999
Q ss_pred ccCCCCCCC
Q 002487 891 ASPAKDRPY 899 (916)
Q Consensus 891 IsL~~~~~~ 899 (916)
|-+|.+...
T Consensus 664 m~l~~r~s~ 672 (1710)
T KOG1070|consen 664 MPLGLRASS 672 (1710)
T ss_pred eehhhhhhh
Confidence 999987554
No 119
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.17 E-value=4e-06 Score=74.46 Aligned_cols=71 Identities=18% Similarity=0.394 Sum_probs=65.0
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEECC-CeeeEEe-ccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCH-ISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvh-iSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
.-|++|+++.| |+.+.+.|+||.|.. +.+|++. .||++.+++++..+.+ +|-.+.|+|+.+|+ +|-|.||.
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 VFPNINEVTKG--IVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred ecCCCCeEEEE--EEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 45899999985 999999999999943 6999998 9999999999999999 99999999999999 99999985
No 120
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.16 E-value=1.9e-06 Score=100.67 Aligned_cols=71 Identities=23% Similarity=0.280 Sum_probs=63.2
Q ss_pred hhhcCCC--CCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CC--ceEE
Q 002487 756 NLTMVPT--VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KG--QLRL 830 (916)
Q Consensus 756 ~l~~~~~--vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~g--kI~L 830 (916)
.++..|+ +|++++| +|+++.++|+||+|+ |++||||.|+++ |.+.|++||.|+|+|++++. ++ +|.|
T Consensus 125 ~i~~eyk~~~GeIV~G-~V~ri~~~giiVDLg-gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIil 196 (470)
T PRK09202 125 RVYEEYKDRVGEIITG-VVKRVERGNIIVDLG-RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIIL 196 (470)
T ss_pred HHHHHHHhhcCCEEEE-EEEEEecCCEEEEEC-CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEE
Confidence 4556675 9999999 999999999999995 899999999985 77889999999999999998 44 8999
Q ss_pred EEee
Q 002487 831 SRRA 834 (916)
Q Consensus 831 S~K~ 834 (916)
|++.
T Consensus 197 SRt~ 200 (470)
T PRK09202 197 SRTH 200 (470)
T ss_pred EeCc
Confidence 9965
No 121
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.05 E-value=7.1e-06 Score=79.12 Aligned_cols=61 Identities=30% Similarity=0.371 Sum_probs=54.3
Q ss_pred cceeeeeecCCchhHHHHHHHhCCceeccCCC-----------------------cceeEEecc--cccHHHHHHHHHhh
Q 002487 703 PEKINLIIGSGGKKVKSIIEETGVEAIDTEDD-----------------------GTVKITAKD--LSSLEKSKAIISNL 757 (916)
Q Consensus 703 ~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-----------------------g~v~I~~~~--~~~~~~a~~~i~~l 757 (916)
..+|+.+|||||+|+|.|+++||++ |+|.++ +.|.|++.+ .+++++|.++|+.+
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~k-I~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~l 92 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAK-ISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEEL 92 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCE-EEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence 3579999999999999999999997 999876 899999999 89999999999998
Q ss_pred hcCCCCC
Q 002487 758 TMVPTVG 764 (916)
Q Consensus 758 ~~~~~vG 764 (916)
+..+..+
T Consensus 93 l~~~~~~ 99 (120)
T cd02395 93 LKPAIEG 99 (120)
T ss_pred hccCCCc
Confidence 8765443
No 122
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=98.02 E-value=1.2e-05 Score=69.51 Aligned_cols=66 Identities=18% Similarity=0.220 Sum_probs=50.1
Q ss_pred cceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEE--ecCCceeEEEeeccccCCCHHHHHHHHHHHHhh
Q 002487 594 CSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVA--GNEDGITAFQMDIKVGGITLPVMKKALQQAKDG 670 (916)
Q Consensus 594 ~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Va--gt~~gItalq~d~K~ggis~e~l~eaL~~A~~a 670 (916)
+++++++++++.+ .+++||+.+|+..++.+|+++ ++.+.++.+++.+. .+++.+.+.+|++.|++|
T Consensus 1 ~~~~avt~~~i~~----------~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~-~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDG----------ELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGG-SELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETT----------EEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEES-SEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECC----------EEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCC-CCCCHHHHHHHHHHHhcC
Confidence 5789999999954 277899999999888777776 44555677777631 129999999999999875
No 123
>PRK05054 exoribonuclease II; Provisional
Probab=97.84 E-value=6.1e-05 Score=91.95 Aligned_cols=79 Identities=27% Similarity=0.298 Sum_probs=61.3
Q ss_pred HHHhhhcCCCCCc--EEEccEEEEEecceEEEEEC-CCeeeEEeccccCccc--c----c------CccccccCCCEEEE
Q 002487 753 IISNLTMVPTVGD--IYRNCEIKSIAPYGVFVEIA-PGREGLCHISELSSNW--L----A------KAEDVVKVGDLVDV 817 (916)
Q Consensus 753 ~i~~l~~~~~vG~--i~~G~~V~~I~~fGaFVel~-~g~eGlvhiSels~~~--v----~------~~~~~~kvGd~V~V 817 (916)
++...+.+-.+|+ .|.| .|++|++||+||+|. .+++||||++.|.+++ . + .-+..|++||.|+|
T Consensus 549 ~~~~~y~~~~~G~~~~f~g-~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V 627 (644)
T PRK05054 549 WLYARYLKDKAGTDTRFAA-EIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDV 627 (644)
T ss_pred HHHHHHHhhccCCCeEEEE-EEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEE
Confidence 3333344446764 9999 999999999999995 4799999999996531 1 0 11247999999999
Q ss_pred EEEEEcC-CCceEEEE
Q 002487 818 KLIEVND-KGQLRLSR 832 (916)
Q Consensus 818 KVi~iD~-~gkI~LS~ 832 (916)
+|.++|. +++|.+++
T Consensus 628 ~v~~vd~~~~~i~~~~ 643 (644)
T PRK05054 628 TLAEVRMETRSIIARP 643 (644)
T ss_pred EEEEEccccCeEEEEE
Confidence 9999998 88988764
No 124
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.77 E-value=1.4e-05 Score=84.55 Aligned_cols=83 Identities=30% Similarity=0.503 Sum_probs=75.4
Q ss_pred CCCCCcEEEccEEEEEecceEEEEE--CCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEI--APGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel--~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
-|++++++-+ .|.+|.+-|+||.| +++++||+-.||||.+|++++....++|-.=.|.|+.+|+ +|.|.||.+.+.
T Consensus 13 yPev~e~Vmv-nV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916|consen 13 YPEVEEIVMV-NVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CCCcccEEEE-EeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCC
Confidence 3799999998 99999999999999 4689999999999999999999999999999999999999 999999999987
Q ss_pred CCCCCCC
Q 002487 837 PEADAEN 843 (916)
Q Consensus 837 ~~p~~~~ 843 (916)
++...+.
T Consensus 92 ~ed~~kC 98 (304)
T KOG2916|consen 92 PEDKEKC 98 (304)
T ss_pred HHHHHHH
Confidence 6544433
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.66 E-value=0.00019 Score=76.11 Aligned_cols=89 Identities=27% Similarity=0.402 Sum_probs=75.4
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccc----cCccccccCCCEEEEEEEEEcCCCceEEEEeec
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL----AKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v----~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
.|++||++.| +|..+...++.|+|.....+++|+|++-++.+ .+.+..|++||.|.+||..+|..+...|++|..
T Consensus 61 iP~~gD~VIG-~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~ 139 (239)
T COG1097 61 IPEVGDVVIG-KIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDE 139 (239)
T ss_pred cCCCCCEEEE-EEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecC
Confidence 4799999999 99999999999999978999999999976653 456779999999999999999999999999643
Q ss_pred CCCCCCCCCCCCCCCCCcEEEe
Q 002487 836 LPEADAENPPVKLPTGDPTKDA 857 (916)
Q Consensus 836 ~~~p~~~~~~~~~~~G~vv~g~ 857 (916)
. ..+++-|.++...
T Consensus 140 ~--------~GkL~~G~iv~i~ 153 (239)
T COG1097 140 G--------LGKLKNGQIVKIP 153 (239)
T ss_pred C--------CccccCCEEEEEc
Confidence 2 1366677766655
No 126
>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=97.65 E-value=7.4e-05 Score=86.44 Aligned_cols=61 Identities=25% Similarity=0.485 Sum_probs=53.4
Q ss_pred CCCCcEEEccEEEEEecc--eEEEEECCCeeeEEeccccCcc------------cccCccccccCCCEEEEEEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPY--GVFVEIAPGREGLCHISELSSN------------WLAKAEDVVKVGDLVDVKLIEV 822 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~f--GaFVel~~g~eGlvhiSels~~------------~v~~~~~~~kvGd~V~VKVi~i 822 (916)
..+|++|.| +|++|.++ ||||+|+.+..||+|++++.+. +..++.+.+++||+|.|+|..-
T Consensus 23 ~~vGnIY~G-rV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 23 QLKGNIYKG-RVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred CCCCCEEEE-EEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence 468999999 99999999 9999999999999999999753 2345567899999999999993
No 127
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.63 E-value=9.9e-05 Score=83.26 Aligned_cols=73 Identities=23% Similarity=0.339 Sum_probs=61.9
Q ss_pred HhhhcCC--CCCcEEEccEEEEEecce-EEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC---CCce
Q 002487 755 SNLTMVP--TVGDIYRNCEIKSIAPYG-VFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND---KGQL 828 (916)
Q Consensus 755 ~~l~~~~--~vG~i~~G~~V~~I~~fG-aFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~---~gkI 828 (916)
+.++.+| ++|++++| +|.++.+.| +||+|+ +.+|++|.+|+. +.+.|++||.|+|.|++++. ..+|
T Consensus 121 e~i~~ey~~k~GeiV~G-~V~~v~~~g~v~VdiG-~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qI 192 (341)
T TIGR01953 121 ERVYDEFSSKEGEIISG-TVKRVNRRGNLYVELG-KTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQI 192 (341)
T ss_pred HHHHHHHHhhcCCEEEE-EEEEEecCCcEEEEEC-CeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeE
Confidence 4455556 69999999 999999988 699996 899999999987 45669999999999999985 3589
Q ss_pred EEEEeec
Q 002487 829 RLSRRAL 835 (916)
Q Consensus 829 ~LS~K~~ 835 (916)
.||++..
T Consensus 193 ivSRt~~ 199 (341)
T TIGR01953 193 ILSRTHP 199 (341)
T ss_pred EEEeCcH
Confidence 9999653
No 128
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.59 E-value=8.6e-05 Score=62.87 Aligned_cols=56 Identities=34% Similarity=0.522 Sum_probs=47.8
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCceeccCC----CcceeEEecccccHHHHHHHH
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED----DGTVKITAKDLSSLEKSKAII 754 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d----~g~v~I~~~~~~~~~~a~~~i 754 (916)
..+.||+++++.+||++|.+|+.|.+++|+. |++.+ ++.|.|.+. .+....|.+++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~-I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVK-IRFPDPGSKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCE-EEcCCCCCCCCEEEEEcC-HHHHHHHHHHh
Confidence 4678999999999999999999999999996 88876 789999998 45666666543
No 129
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.52 E-value=0.00016 Score=82.03 Aligned_cols=69 Identities=23% Similarity=0.250 Sum_probs=59.3
Q ss_pred hhcCC--CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC--C-CceEEE
Q 002487 757 LTMVP--TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND--K-GQLRLS 831 (916)
Q Consensus 757 l~~~~--~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~--~-gkI~LS 831 (916)
++.+| ++|++++| +|.++.++|+||+|+ +++|+||.+++. +++.|++||.|+|.|++++. + .+|.||
T Consensus 126 v~~ef~~k~GeiV~G-~V~~~~~~~~~Vdlg-~vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivS 197 (362)
T PRK12327 126 IYNEFSEREGDIVTG-VVQRRDNRFVYVNLG-KIEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVS 197 (362)
T ss_pred HHHHHHHhcCCEEEE-EEEEEeCCcEEEEeC-CeEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 34456 99999999 999999999999996 799999988874 36789999999999999996 2 378898
Q ss_pred Ee
Q 002487 832 RR 833 (916)
Q Consensus 832 ~K 833 (916)
+.
T Consensus 198 Rt 199 (362)
T PRK12327 198 RT 199 (362)
T ss_pred eC
Confidence 83
No 130
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.50 E-value=0.00027 Score=87.41 Aligned_cols=80 Identities=29% Similarity=0.539 Sum_probs=65.3
Q ss_pred HHHhhhcCCCCCcEEEccEEEEEecceEEEEECC-CeeeEEeccccCcccc-----------cCccccccCCCEEEEEEE
Q 002487 753 IISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWL-----------AKAEDVVKVGDLVDVKLI 820 (916)
Q Consensus 753 ~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v-----------~~~~~~~kvGd~V~VKVi 820 (916)
++..-+..-.+|++++| .|++++.||+||+|.+ +++|+||++.|..++. .+....+++||.|+|+|.
T Consensus 612 ~~~~~~m~~~vg~~f~g-~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~ 690 (706)
T COG0557 612 LLKAEYMKKRVGEEFDG-VVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVT 690 (706)
T ss_pred HHHHHHHHHhcCCEEEE-EEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEE
Confidence 33333445589999999 9999999999999965 5899999999996432 334557999999999999
Q ss_pred EEcC-CCceEEEEe
Q 002487 821 EVND-KGQLRLSRR 833 (916)
Q Consensus 821 ~iD~-~gkI~LS~K 833 (916)
++|. .++|.+++-
T Consensus 691 ~v~~~~~~i~~~~v 704 (706)
T COG0557 691 SVDLDERKIDFELV 704 (706)
T ss_pred EEcccccceEEEec
Confidence 9998 888988763
No 131
>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=97.48 E-value=0.00031 Score=85.71 Aligned_cols=79 Identities=23% Similarity=0.264 Sum_probs=60.2
Q ss_pred HHHHhhhcCCCCC--cEEEccEEEEEecceEEEEE-CCCeeeEEeccccCc--ccc---c-C----c--cccccCCCEEE
Q 002487 752 AIISNLTMVPTVG--DIYRNCEIKSIAPYGVFVEI-APGREGLCHISELSS--NWL---A-K----A--EDVVKVGDLVD 816 (916)
Q Consensus 752 ~~i~~l~~~~~vG--~i~~G~~V~~I~~fGaFVel-~~g~eGlvhiSels~--~~v---~-~----~--~~~~kvGd~V~ 816 (916)
+++...+..-++| +.|.| .|+++++||+||+| ..|++||||++.|.+ ++. . . . ...|++||.|+
T Consensus 544 ~~~~~~yl~~~~g~~~~f~g-~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~ 622 (639)
T TIGR02062 544 DWLYARFLADKAAKNTRFAA-EIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVID 622 (639)
T ss_pred HHHHHHHHhhccCCCcEEEE-EEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEE
Confidence 3444434444675 49998 99999999999999 568999999999965 221 1 1 1 12699999999
Q ss_pred EEEEEEcC-CCceEEE
Q 002487 817 VKLIEVND-KGQLRLS 831 (916)
Q Consensus 817 VKVi~iD~-~gkI~LS 831 (916)
|+|.++|. +++|.+.
T Consensus 623 V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 623 VVLTEVRMETRSIIAR 638 (639)
T ss_pred EEEEEeccccCcEeee
Confidence 99999998 8888763
No 132
>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=97.46 E-value=0.00057 Score=62.19 Aligned_cols=74 Identities=20% Similarity=0.172 Sum_probs=63.9
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeec
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
.|++||.+-| +|+++....++|+|.....|++|.+++... .++.+..|++||.|-++|..+|+.....||....
T Consensus 3 ~P~~gD~VIG-~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 3 VPAKGDHVIG-IVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred cCCCCCEEEE-EEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 3789999999 999999999999998788999999887543 4445668999999999999999888899998763
No 133
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.39 E-value=0.00028 Score=82.08 Aligned_cols=71 Identities=28% Similarity=0.462 Sum_probs=62.2
Q ss_pred cCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeecC
Q 002487 759 MVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRALL 836 (916)
Q Consensus 759 ~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~~ 836 (916)
.+++.|..|.| +|.++..||+||+|...+.||+|-++++.. .-+.+||++-|++..+-+ +|.|.|....+.
T Consensus 118 ~Dve~g~~Y~g-~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 118 EDVEAGKYYKG-IVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hhcccceeeec-cccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 45799999999 999999999999999999999999999852 247899999999999988 698888776554
No 134
>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=0.00086 Score=61.34 Aligned_cols=60 Identities=18% Similarity=0.212 Sum_probs=49.1
Q ss_pred CCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccC-----------ccccccCCCEEEEEEEEEcC
Q 002487 763 VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAK-----------AEDVVKVGDLVDVKLIEVND 824 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~-----------~~~~~kvGd~V~VKVi~iD~ 824 (916)
+|++++| +|+++.++|+||.++ .+++|+|.+.+..+..-+ -...++.|+.|++||+++..
T Consensus 1 kgEVi~g-~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 71 (88)
T cd04462 1 KGEVVDA-IVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV 71 (88)
T ss_pred CCcEEEE-EEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE
Confidence 4899999 999999999999997 589999999986543221 23468899999999998854
No 135
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.26 E-value=0.00024 Score=76.44 Aligned_cols=62 Identities=27% Similarity=0.422 Sum_probs=57.5
Q ss_pred EEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhcC
Q 002487 698 IMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMV 760 (916)
Q Consensus 698 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~ 760 (916)
.++|++++++.+||++|++|+.|.++++++ |++.++|.|.|++.+.+.+++|.++|+.+-.+
T Consensus 148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~-I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 148 IVEIKPVKVPRVIGKKGSMINMLKEETGCD-IIVGQNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEECHHHHHhhcCCCChhHhhhhhhhCcE-EEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 569999999999999999999999999996 99999999999999999999999999887544
No 136
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=97.16 E-value=0.0009 Score=60.35 Aligned_cols=61 Identities=26% Similarity=0.403 Sum_probs=42.7
Q ss_pred CCCCcEEEccEEEEEecceEEEEECC------------------CeeeEEeccccCcccccC--ccccccCCCEEEEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAP------------------GREGLCHISELSSNWLAK--AEDVVKVGDLVDVKLI 820 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~------------------g~eGlvhiSels~~~v~~--~~~~~kvGd~V~VKVi 820 (916)
|++|+++.| +|++|++--|+++|.- ...|++|.+++......+ +.+.|++||.|+++|+
T Consensus 2 P~vGdiV~~-rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 2 PKVGDIVIA-RVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp --TT-EEEE-EEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCEEEE-EEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 689999998 9999999999999831 346999999987665554 4788999999999999
Q ss_pred EE
Q 002487 821 EV 822 (916)
Q Consensus 821 ~i 822 (916)
++
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 74
No 137
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=97.15 E-value=0.00034 Score=58.81 Aligned_cols=56 Identities=38% Similarity=0.560 Sum_probs=47.9
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCC---cceeEEecccccHHHHHHHH
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDD---GTVKITAKDLSSLEKSKAII 754 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~---g~v~I~~~~~~~~~~a~~~i 754 (916)
..+.||.+.++.+||++|.+|+.|.+++|+. |.+.++ ..+.|.+ +.+..++|+++|
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~-I~i~~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVK-IQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSE-EEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeE-EEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 4678999999999999999999999999996 888764 5788888 777788887654
No 138
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.08 E-value=0.0013 Score=67.65 Aligned_cols=78 Identities=12% Similarity=0.219 Sum_probs=60.0
Q ss_pred HhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCccc-----------c-cCccccccCCCEEEEEEEEE
Q 002487 755 SNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNW-----------L-AKAEDVVKVGDLVDVKLIEV 822 (916)
Q Consensus 755 ~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~-----------v-~~~~~~~kvGd~V~VKVi~i 822 (916)
+.+...|-.|++++| +|+++.++|+||.+++ .++++|.++|.++. . ++-+..++.|+.|++||.++
T Consensus 73 raivFrPf~gEVv~g-~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v 150 (176)
T PTZ00162 73 QAIVFKPFKDEVLDA-IVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGV 150 (176)
T ss_pred EEEEEecCCCCEEEE-EEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEE
Confidence 346678899999999 9999999999999985 66999999997431 1 12245799999999999988
Q ss_pred cC---CCceEEEEee
Q 002487 823 ND---KGQLRLSRRA 834 (916)
Q Consensus 823 D~---~gkI~LS~K~ 834 (916)
.. +.++-.|+|+
T Consensus 151 ~~~~~~~~~i~T~~~ 165 (176)
T PTZ00162 151 RYDASNLFAIATINS 165 (176)
T ss_pred EecCCCcEEEEEecC
Confidence 54 2334455554
No 139
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.04 E-value=0.0016 Score=66.74 Aligned_cols=73 Identities=22% Similarity=0.443 Sum_probs=62.6
Q ss_pred hcCCCCCcEEEccEEEEEecceEEEEECC----------CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCc
Q 002487 758 TMVPTVGDIYRNCEIKSIAPYGVFVEIAP----------GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQ 827 (916)
Q Consensus 758 ~~~~~vG~i~~G~~V~~I~~fGaFVel~~----------g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gk 827 (916)
..-++.|+++-| +|+++..-.+.|++.. ...|-+|+|+....++++..+.|++||.|+++|++.- -.
T Consensus 59 ~~~~K~GdiV~g-rV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~ 135 (188)
T COG1096 59 PPLPKGGDIVYG-RVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DP 135 (188)
T ss_pred CCCCCCCCEEEE-EEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CC
Confidence 345799999998 9999999999999851 1457899999999999999999999999999999974 45
Q ss_pred eEEEEe
Q 002487 828 LRLSRR 833 (916)
Q Consensus 828 I~LS~K 833 (916)
+.||.+
T Consensus 136 ~~Lst~ 141 (188)
T COG1096 136 IQLSTK 141 (188)
T ss_pred eEEEec
Confidence 777775
No 140
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.97 E-value=0.0022 Score=69.04 Aligned_cols=75 Identities=25% Similarity=0.335 Sum_probs=62.8
Q ss_pred HHHhhhcCCCC---CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceE
Q 002487 753 IISNLTMVPTV---GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLR 829 (916)
Q Consensus 753 ~i~~l~~~~~v---G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~ 829 (916)
.++++....-. ++.+.| +|.++..-|.||-+.++.-||||-||.. ...+.|+.++++|+++.++|+|.
T Consensus 142 ~l~~l~~~~~~~l~nq~v~~-tVYr~~~~G~fv~~e~~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~ln 212 (287)
T COG2996 142 ILENLATPAYNNLKNQEVDA-TVYRLLESGTFVITENGYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLN 212 (287)
T ss_pred HHHhcCCccchhhhcCeeee-EEEEEeccceEEEEcCCeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeee
Confidence 34445444444 899998 9999999999999999999999999864 24578999999999998899999
Q ss_pred EEEeecC
Q 002487 830 LSRRALL 836 (916)
Q Consensus 830 LS~K~~~ 836 (916)
||++-..
T Consensus 213 LSl~p~~ 219 (287)
T COG2996 213 LSLRPRA 219 (287)
T ss_pred ccccccc
Confidence 9997653
No 141
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=96.95 E-value=0.0014 Score=55.28 Aligned_cols=55 Identities=36% Similarity=0.537 Sum_probs=43.6
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCceeccCC------CcceeEEecccccHHHHHHH
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED------DGTVKITAKDLSSLEKSKAI 753 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d------~g~v~I~~~~~~~~~~a~~~ 753 (916)
..+.||.+.++.+||++|++|+.|.+++|+. |.+.+ +..+.|.+. .+..+.|..+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~-I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~ 62 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAK-IKIPDSGSGSEERIVTITGT-PEAVEKAKEL 62 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCE-EEEcCCCCCCCceEEEEEcC-HHHHHHHHHH
Confidence 3578999999999999999999999999996 88764 456777777 3455555543
No 142
>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=96.84 E-value=0.0043 Score=54.78 Aligned_cols=67 Identities=10% Similarity=-0.015 Sum_probs=46.9
Q ss_pred ccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cc---cCCCCCCCCCCCcEEEeE
Q 002487 809 VKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KL---VGSPKPKGSSSEDTVLPH 881 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~---v~~p~~~~k~Gd~V~v~I 881 (916)
+++||.|.++|.++...| +-+++. .-+.|.+ +++ .+ ..++.+.|++||.++++|
T Consensus 1 ~k~G~~V~g~V~~i~~~G-~fV~l~------------------~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kV 61 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQG-VFFRLS------------------SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKV 61 (74)
T ss_pred CCCCCEEEEEEEEEeCCc-EEEEeC------------------CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEE
Confidence 578999999999997654 333331 1133443 111 12 223457899999999999
Q ss_pred eeecCCCCcccCC
Q 002487 882 KKVKVFKRPASPA 894 (916)
Q Consensus 882 ~~id~ek~rIsL~ 894 (916)
+++|++++||.||
T Consensus 62 l~id~~~~~i~LS 74 (74)
T cd05705 62 LSVNSEKNLVELS 74 (74)
T ss_pred EEEECCCCEEecC
Confidence 9999999999986
No 143
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=96.69 E-value=0.0009 Score=64.02 Aligned_cols=79 Identities=11% Similarity=0.100 Sum_probs=54.0
Q ss_pred cccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 808 VVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
.+++|+.++.+|.+|-+-|-. . .+.-|..--.-+|.+ .++.+..+.+++||+|.|+|++||
T Consensus 2 ~~kvG~~l~GkItgI~~yGAF---------------V--~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAF---------------V--ELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred CccccceEEEEEEeeEecceE---------------E--EecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeec
Confidence 478999999999998653311 1 112222211123444 355666689999999999999999
Q ss_pred CCCCcccCCCCCCCCcccc
Q 002487 886 VFKRPASPAKDRPYSNKDR 904 (916)
Q Consensus 886 ~ek~rIsL~~~~~~~~~~~ 904 (916)
. +.+||||++..-..+++
T Consensus 65 e-~GKisLSIr~~~e~pe~ 82 (129)
T COG1098 65 E-NGKISLSIRKLEEEPEK 82 (129)
T ss_pred c-CCCcceehHHhhhCccc
Confidence 9 99999998766655554
No 144
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.59 E-value=0.0097 Score=50.66 Aligned_cols=61 Identities=28% Similarity=0.463 Sum_probs=36.6
Q ss_pred CCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEe
Q 002487 763 VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRR 833 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K 833 (916)
+|++.+. +|+++.++|+|++...+.+-|+|.+++. ..+++||+|.|-|-. |.++|+..|+|
T Consensus 1 iG~~~~L-~V~~~~~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~-D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTL-KVVDKNEFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYL-DKEGRLVATTK 61 (61)
T ss_dssp ---------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred CCCCcce-EEEEEeCCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEE-CCCCCEEEecC
Confidence 4888887 9999999999999887789999999875 237899999997665 66788887765
No 145
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.54 E-value=0.0064 Score=53.40 Aligned_cols=66 Identities=18% Similarity=0.339 Sum_probs=55.4
Q ss_pred CcEEEccEEEEEecceEEEEECC-CeeeEEeccccCcccccC---ccccccCCCEE-EEEEEEEcC-CCceEEEEe
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAP-GREGLCHISELSSNWLAK---AEDVVKVGDLV-DVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~-g~eGlvhiSels~~~v~~---~~~~~kvGd~V-~VKVi~iD~-~gkI~LS~K 833 (916)
|++++| +|.+-++-+++|++.+ |+.|+++.-+|++ .+++ .-..+++||++ ++-|+ |. .+.|.||.|
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 GKLVDA-RVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEE-EEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 788998 9999999999999987 8999999999998 4433 23468999999 99999 66 677888765
No 146
>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=96.45 E-value=0.0036 Score=55.07 Aligned_cols=66 Identities=12% Similarity=-0.002 Sum_probs=47.9
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc----cccCCCCCCCCCCCcEEEeEeeec
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD----KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i----~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
||.|.++|.++...| +.+++ ..| +.|.+ +++ ....++.+.|++||.|+++|+++|
T Consensus 1 G~~V~g~V~~i~~~g-~~V~l----------------~~~--i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id 61 (73)
T cd05703 1 GQEVTGFVNNVSKEF-VWLTI----------------SPD--VKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVD 61 (73)
T ss_pred CCEEEEEEEEEeCCE-EEEEe----------------CCC--cEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEe
Confidence 899999999997644 33332 011 34443 222 234567788999999999999999
Q ss_pred CCCCcccCCCC
Q 002487 886 VFKRPASPAKD 896 (916)
Q Consensus 886 ~ek~rIsL~~~ 896 (916)
++++||.||.+
T Consensus 62 ~~~~~i~Ls~k 72 (73)
T cd05703 62 KEHKLLRLSAR 72 (73)
T ss_pred CCCCEEEEEec
Confidence 99999999875
No 147
>smart00322 KH K homology RNA-binding domain.
Probab=96.37 E-value=0.01 Score=49.67 Aligned_cols=60 Identities=38% Similarity=0.597 Sum_probs=47.9
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCC----cceeEEecccccHHHHHHHHHh
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDD----GTVKITAKDLSSLEKSKAIISN 756 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~----g~v~I~~~~~~~~~~a~~~i~~ 756 (916)
....+.|+.+.++.+||++|++|+.|.+.+++. |.+..+ ..+.|.+. ....+.|..++..
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~-i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~ 66 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVK-IDIPEDGSEERVVEITGP-PENVEKAAELILE 66 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCE-EEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence 456778999999999999999999999999996 777643 67778777 5566667666654
No 148
>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=96.35 E-value=0.013 Score=50.38 Aligned_cols=64 Identities=16% Similarity=0.056 Sum_probs=43.3
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccccccCCCCCCCCCCCcEEEeEeeecCCCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASDKLVGSPKPKGSSSEDTVLPHKKVKVFKR 889 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~ 889 (916)
|+.|.++|.++...| +.+.+-. | +.|.+ +++.........|++||+++++|+.+|++++
T Consensus 1 G~~V~g~V~~i~~~G-~~v~l~~----------------~--v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~ 61 (66)
T cd05695 1 GMLVNARVKKVLSNG-LILDFLS----------------S--FTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTK 61 (66)
T ss_pred CCEEEEEEEEEeCCc-EEEEEcC----------------C--ceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCC
Confidence 789999999997766 3332210 1 23333 2221111115679999999999999999999
Q ss_pred cccCC
Q 002487 890 PASPA 894 (916)
Q Consensus 890 rIsL~ 894 (916)
||.||
T Consensus 62 ~i~LS 66 (66)
T cd05695 62 VVGLS 66 (66)
T ss_pred EEecC
Confidence 99886
No 149
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.29 E-value=0.023 Score=61.43 Aligned_cols=153 Identities=14% Similarity=0.079 Sum_probs=98.6
Q ss_pred eccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEe-cceEEEEECCCeeeEEeccccCcccccCccc
Q 002487 729 IDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIA-PYGVFVEIAPGREGLCHISELSSNWLAKAED 807 (916)
Q Consensus 729 Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~-~fGaFVel~~g~eGlvhiSels~~~v~~~~~ 807 (916)
+.+.|.=+|+|+.-....+.... ......+|+.=-+ +|+.+. +-||||+.+-..+-||+.+++...+ +-
T Consensus 44 ~evGdev~vFiY~D~~~rl~aTt-----~~p~~tvg~~g~~-~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~----~~ 113 (287)
T COG2996 44 LEVGDEVTVFIYVDSEDRLIATT-----REPKATVGEYGWL-KVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK----SL 113 (287)
T ss_pred cccCcEEEEEEEECCCCceehee-----ecceEeecceeEE-EEEEEcCCcceEEecCCCcceeeehhhccccc----cc
Confidence 44445556677655443222111 1122478998888 999998 8999999976689999999987431 12
Q ss_pred cccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCC--CCCcEEEeeccc--------------cccCCCC---
Q 002487 808 VVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLP--TGDPTKDAAASD--------------KLVGSPK--- 868 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~--~G~vv~g~Vs~i--------------~~v~~p~--- 868 (916)
-.++||.+-|.+ .+|.++||.=.++.- ..-+......+. .++.+.++|=.. .++ +++
T Consensus 114 wpq~Gd~l~v~l-~~Dkk~Ri~g~~a~~--~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI-h~sEr~ 189 (287)
T COG2996 114 WPQKGDKLLVYL-YVDKKGRIWGTLAIE--KILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI-HKSERF 189 (287)
T ss_pred CCCCCCEEEEEE-EEccCCcEEEEecch--hHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE-cchhhc
Confidence 378899999965 467888876655421 111111110111 367777776111 111 222
Q ss_pred CCCCCCCcEEEeEeeecCCCCcccCCCC
Q 002487 869 PKGSSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 869 ~~~k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
..+..|++++++|+.+.+ .++|.||.+
T Consensus 190 ~~prlG~~l~~rVi~~re-Dg~lnLSl~ 216 (287)
T COG2996 190 AEPRLGERLTARVIGVRE-DGKLNLSLR 216 (287)
T ss_pred ccccCCceEEEEEEEEcc-CCeeecccc
Confidence 467899999999999999 999999964
No 150
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.11 E-value=0.01 Score=73.55 Aligned_cols=61 Identities=25% Similarity=0.507 Sum_probs=50.8
Q ss_pred CCCcEEEccEEEEEecc--eEEEEECCCeeeEEeccccCccccc---------CccccccCCCEEEEEEEEEc
Q 002487 762 TVGDIYRNCEIKSIAPY--GVFVEIAPGREGLCHISELSSNWLA---------KAEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~f--GaFVel~~g~eGlvhiSels~~~v~---------~~~~~~kvGd~V~VKVi~iD 823 (916)
.+|.||.| +|.+|.+. +|||+|+.|..||+|++++...++. +..+.+++||.|-|+|.+-.
T Consensus 37 ~vGnIYkG-kVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 37 KKANIYKG-KITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred CccceEEE-EEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 57999999 99999774 7999999999999999999654322 23457999999999999854
No 151
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=95.98 E-value=0.00015 Score=80.54 Aligned_cols=93 Identities=18% Similarity=0.210 Sum_probs=74.6
Q ss_pred hCCceeccC-CCcceeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEec-ceEEEE------ECCCeeeEEecc
Q 002487 724 TGVEAIDTE-DDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAP-YGVFVE------IAPGREGLCHIS 795 (916)
Q Consensus 724 ~~v~~Idi~-d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~-fGaFVe------l~~g~eGlvhiS 795 (916)
..+++|.+| ++|++.+|.+... .+.|+.+...++.|+++.| +|..+.+ ||+|++ ..|..+++.|++
T Consensus 70 v~vkVl~VD~ekg~IdLS~K~v~-----~~pw~~~~e~~~~g~~v~~-~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y 143 (319)
T PTZ00248 70 EVVVVLRVDKEKGYIDLSKKRVS-----PEDIEACEEKFSKSKKVHS-IMRHIAQKHGMSVEELYTKIIWPLYKKYGHAL 143 (319)
T ss_pred EEEEEEEEeCCCCEEEEEeeecc-----cchHHHHHHhCcCCCEEEE-EEEEchhhcCCCHHHHHHHHHHHHHHhcCCHH
Confidence 445678887 6789999988654 2357777788999999998 9999955 999999 567899999999
Q ss_pred ccCcccccCcccccc---CCCEEEEEEEEE
Q 002487 796 ELSSNWLAKAEDVVK---VGDLVDVKLIEV 822 (916)
Q Consensus 796 els~~~v~~~~~~~k---vGd~V~VKVi~i 822 (916)
+.....+.++.++|+ +++.+..+++.+
T Consensus 144 ~af~~~v~~~~evl~~l~i~~ev~~~l~~~ 173 (319)
T PTZ00248 144 DALKEALTNPDNVFEGLDIPEEVKESLLQD 173 (319)
T ss_pred HHHHHHhcCchhhhccCCCCHHHHHHHHHH
Confidence 999888888877777 787776666543
No 152
>PRK11712 ribonuclease G; Provisional
Probab=95.91 E-value=0.011 Score=69.81 Aligned_cols=62 Identities=21% Similarity=0.460 Sum_probs=50.0
Q ss_pred CCCCcEEEccEEEEEecc--eEEEEECCCeeeEEeccccCcc------------cccCccccccCCCEEEEEEEEEc
Q 002487 761 PTVGDIYRNCEIKSIAPY--GVFVEIAPGREGLCHISELSSN------------WLAKAEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~f--GaFVel~~g~eGlvhiSels~~------------~v~~~~~~~kvGd~V~VKVi~iD 823 (916)
..+|.+|.| +|.+|.+- +|||+|+.+..||+|++++... ......+.+++||.|-|+|..-.
T Consensus 36 ~~vGnIY~G-~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~ 111 (489)
T PRK11712 36 GIVGNIYKG-RVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDP 111 (489)
T ss_pred cccccEEEE-EEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCC
Confidence 358999999 99999884 7999999999999999998321 01123556999999999999853
No 153
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=95.80 E-value=0.017 Score=49.60 Aligned_cols=54 Identities=33% Similarity=0.491 Sum_probs=40.6
Q ss_pred EEeeccceeeeeecCCchhHHHHHHHhCCceeccCCC-------cceeEEecccccHHHHHHH
Q 002487 698 IMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDD-------GTVKITAKDLSSLEKSKAI 753 (916)
Q Consensus 698 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-------g~v~I~~~~~~~~~~a~~~ 753 (916)
.+.|+.++++.+||.+|.+|+.|.+++|+. |.+.++ ..+.|.+. .+..+.|..+
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~tga~-I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~ 63 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREETGAK-IRVSKSVLPGSTERVVTISGK-PSAVQKALLL 63 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHHHCCE-EEEcCCCCCCCCceEEEEEeC-HHHHHHHHHh
Confidence 568999999999999999999999999996 777632 34455554 3445555544
No 154
>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=95.46 E-value=0.0091 Score=51.96 Aligned_cols=69 Identities=17% Similarity=0.138 Sum_probs=48.5
Q ss_pred ccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeee
Q 002487 809 VKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKV 884 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~i 884 (916)
+++||.+.++|.++++.| +-+.+- .-+.|-+ +++ .....+...+++||++.|+|+++
T Consensus 2 ~~~G~iv~g~V~~v~~~g-~~V~l~------------------~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~v 62 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFG-VFVDLG------------------NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKV 62 (74)
T ss_dssp SSTTSEEEEEEEEEETTE-EEEEES------------------TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEE
T ss_pred CCCCCEEEEEEEEEECCE-EEEEEC------------------CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEE
Confidence 678999999999998743 333332 0011111 111 13345678999999999999999
Q ss_pred cCCCCcccCCCC
Q 002487 885 KVFKRPASPAKD 896 (916)
Q Consensus 885 d~ek~rIsL~~~ 896 (916)
|.+++++.||.+
T Consensus 63 d~~~~~i~lS~k 74 (74)
T PF00575_consen 63 DKEKGRIRLSLK 74 (74)
T ss_dssp ETTTTEEEEEST
T ss_pred ECCCCeEEEEEC
Confidence 999999999864
No 155
>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=95.21 E-value=0.017 Score=51.80 Aligned_cols=70 Identities=14% Similarity=0.030 Sum_probs=48.8
Q ss_pred ccccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEe
Q 002487 807 DVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHK 882 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~ 882 (916)
+.+++|+.+.++|.++.+.| +-+.+- + | +.|-+ +.+ .++.++...|++||+++|+|.
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G-~fv~l~----~------------~--~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~ 70 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYG-VFVEFL----G------------G--LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVT 70 (83)
T ss_pred HhCCCCCEEEEEEEEEeece-EEEEcC----C------------C--CEEEEEHHHCCcccccCHHHhcCCCCEEEEEEE
Confidence 45899999999999997644 222220 0 0 12221 111 234467788999999999999
Q ss_pred eecCCCCcccCCC
Q 002487 883 KVKVFKRPASPAK 895 (916)
Q Consensus 883 ~id~ek~rIsL~~ 895 (916)
++|.++++|.||+
T Consensus 71 ~id~~~~~i~lsl 83 (83)
T cd04461 71 SVDEEKQRFLLSL 83 (83)
T ss_pred EEcCCCCEEEEeC
Confidence 9999999999874
No 156
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.15 E-value=0.055 Score=61.64 Aligned_cols=64 Identities=25% Similarity=0.306 Sum_probs=55.1
Q ss_pred CCCcEEEccEEEEEecc-eEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC--C--CceEEEEe
Q 002487 762 TVGDIYRNCEIKSIAPY-GVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND--K--GQLRLSRR 833 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~f-GaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~--~--gkI~LS~K 833 (916)
++|+++.| +|.++... ++||+|+ +.+|++|.++.. +.+.|++||.|+|-|.+++. + -+|-||+.
T Consensus 137 ~~Geiv~g-~V~r~~~~~~i~vdlg-~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt 205 (374)
T PRK12328 137 KVGKIVFG-TVVRVDNEENTFIEID-EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRT 205 (374)
T ss_pred hcCcEEEE-EEEEEecCCCEEEEcC-CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcC
Confidence 89999999 99999875 5999997 899999988765 56789999999999999987 3 27888873
No 157
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=95.13 E-value=0.032 Score=57.37 Aligned_cols=60 Identities=32% Similarity=0.359 Sum_probs=49.2
Q ss_pred ceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcE
Q 002487 704 EKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDI 766 (916)
Q Consensus 704 ~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i 766 (916)
..++.+||+||+|++.|++.||+. |.+.+ ..|.|.+ +.+..+.|++.++.+...-..+.+
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~-i~i~~-~~v~i~G-~~~~~~~A~~~i~~li~~~~~~~v 157 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVS-ISVYG-KTVGIIG-DPEQVQIAREAIEMLIEGAPHGTV 157 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCe-EEEcC-CEEEEEC-CHHHHHHHHHHHHHHHcCCCChhH
Confidence 368899999999999999999996 87764 7899988 778899999999988754443333
No 158
>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=95.10 E-value=0.015 Score=50.72 Aligned_cols=72 Identities=17% Similarity=0.140 Sum_probs=48.3
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
++|+.+.++|.++.+.| +-+.+.. .. +.|.+ +++ .+...+.+.|++||.|+|+|.++|
T Consensus 1 ~~g~~v~g~V~~i~~~g-~~v~l~~---~~--------------~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 1 KVGQKIDGTVRRVEDYG-VFIDIDG---TN--------------VSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred CCCCEEEEEEEEEEcce-EEEEECC---CC--------------eEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 46999999999997644 2222210 00 12221 111 122345678999999999999999
Q ss_pred CCCCcccCCCCCCC
Q 002487 886 VFKRPASPAKDRPY 899 (916)
Q Consensus 886 ~ek~rIsL~~~~~~ 899 (916)
.+++++.|++++++
T Consensus 63 ~~~~~i~ls~k~~~ 76 (77)
T cd05708 63 AEKKRISLGLKASY 76 (77)
T ss_pred CCCCEEEEEEEeec
Confidence 99999999988665
No 159
>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=94.70 E-value=0.042 Score=47.76 Aligned_cols=68 Identities=15% Similarity=0.103 Sum_probs=46.7
Q ss_pred ccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeee
Q 002487 809 VKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKV 884 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~i 884 (916)
+++|+.+.++|.++...| +.+.+ ..| ++|.+ +++ .+...+...+++||.++++|+++
T Consensus 1 ~~~G~iv~g~V~~v~~~g-i~v~l----------------~~~--~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~ 61 (73)
T cd05706 1 LKVGDILPGRVTKVNDRY-VLVQL----------------GNK--VTGPSFITDALDDYSEALPYKFKKNDIVRACVLSV 61 (73)
T ss_pred CCCCCEEEEEEEEEeCCe-EEEEe----------------CCC--cEEEEEhhhccCccccccccccCCCCEEEEEEEEE
Confidence 468999999999996543 33332 111 23332 222 12234567899999999999999
Q ss_pred cCCCCcccCCC
Q 002487 885 KVFKRPASPAK 895 (916)
Q Consensus 885 d~ek~rIsL~~ 895 (916)
|.++++|.|+.
T Consensus 62 d~~~~~i~ls~ 72 (73)
T cd05706 62 DVPNKKIALSL 72 (73)
T ss_pred eCCCCEEEEEE
Confidence 99999998875
No 160
>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=94.52 E-value=0.11 Score=45.36 Aligned_cols=32 Identities=6% Similarity=-0.208 Sum_probs=28.3
Q ss_pred cCCCCCCCCCCCcEEEeEeeecCCCCcccCCC
Q 002487 864 VGSPKPKGSSSEDTVLPHKKVKVFKRPASPAK 895 (916)
Q Consensus 864 v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~ 895 (916)
+..+.+.+++||+++++|+++|+++++|+||+
T Consensus 40 ~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 40 VPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred hcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 44566789999999999999999999999874
No 161
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=94.41 E-value=0.047 Score=68.40 Aligned_cols=74 Identities=26% Similarity=0.294 Sum_probs=63.5
Q ss_pred CCCCcEEEccEEEEEecce---EEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEeec
Q 002487 761 PTVGDIYRNCEIKSIAPYG---VFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRRAL 835 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fG---aFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K~~ 835 (916)
+.+|.++.+ +|++|+.-- +=|.+..|+.|+||.+++|+..+.+|...+++||.|.+||+++|. +=-+.||.|..
T Consensus 983 ~~~g~iV~~-~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 983 FYEGAIVPV-TVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred hccCceEEE-eeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 568999997 999997644 457788899999999999999999999999999999999999998 54566776654
No 162
>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=94.41 E-value=0.061 Score=46.57 Aligned_cols=71 Identities=14% Similarity=0.013 Sum_probs=44.3
Q ss_pred ccCCCEEEEEEEEEcCCCc-eEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 809 VKVGDLVDVKLIEVNDKGQ-LRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gk-I~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
+++|+.+.++|.++.+.|- +.|- +..+.... .-..+|-....++...+++||+++|+|.++|.+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~------~~~~Gl~~---------~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE------EGVEGLVH---------VSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC------CCCEEEEE---------EEeccCcccccCcccEeCCCCEEEEEEEEeeCC
Confidence 5789999999999976442 2220 00000000 000011112224557899999999999999999
Q ss_pred CCcccCC
Q 002487 888 KRPASPA 894 (916)
Q Consensus 888 k~rIsL~ 894 (916)
+++|.|+
T Consensus 66 ~~~i~~~ 72 (72)
T cd05689 66 RRRISLG 72 (72)
T ss_pred cCEEeCC
Confidence 9999875
No 163
>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=94.39 E-value=0.046 Score=46.73 Aligned_cols=32 Identities=13% Similarity=0.032 Sum_probs=28.1
Q ss_pred ccCCCCCCCCCCCcEEEeEeeecCCCCcccCC
Q 002487 863 LVGSPKPKGSSSEDTVLPHKKVKVFKRPASPA 894 (916)
Q Consensus 863 ~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~ 894 (916)
...++.+.|++||+|+|+|.++|.+++||+||
T Consensus 38 ~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 38 RVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred ccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 34556678999999999999999999999986
No 164
>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=94.39 E-value=0.034 Score=47.88 Aligned_cols=66 Identities=9% Similarity=0.006 Sum_probs=45.0
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
|+.+.++|.++...| +-+.+- + | +.|-+ +.+ ..+.+|.+.+++||+++++|.++|++
T Consensus 1 g~~~~g~V~~v~~~G-~~V~l~----~------------~--~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 1 GLKTHGTIVKVKPNG-CIVSFY----N------------N--VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred CCEEEEEEEEEecCc-EEEEEC----C------------C--CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCC
Confidence 789999999997643 333221 0 0 11221 111 23445677899999999999999999
Q ss_pred CCcccCCCC
Q 002487 888 KRPASPAKD 896 (916)
Q Consensus 888 k~rIsL~~~ 896 (916)
++++.|+.+
T Consensus 62 ~~~i~ls~k 70 (70)
T cd05698 62 QQRLLLSCK 70 (70)
T ss_pred CCEEEEEeC
Confidence 999998864
No 165
>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=94.32 E-value=0.036 Score=47.73 Aligned_cols=66 Identities=11% Similarity=0.113 Sum_probs=44.9
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
||.|.++|.+++.. .+.+.+- ..+.|.+ +++ ....++.+.+++||.++++|+++|++
T Consensus 1 G~iv~g~V~~i~~~-~~~v~l~------------------~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~ 61 (70)
T cd05687 1 GDIVKGTVVSVDDD-EVLVDIG------------------YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDE 61 (70)
T ss_pred CCEEEEEEEEEeCC-EEEEEeC------------------CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECC
Confidence 78999999999764 2333321 0012222 111 23445677899999999999999998
Q ss_pred CCcccCCCC
Q 002487 888 KRPASPAKD 896 (916)
Q Consensus 888 k~rIsL~~~ 896 (916)
..+|.||++
T Consensus 62 ~~~i~lS~~ 70 (70)
T cd05687 62 EGNVVLSKR 70 (70)
T ss_pred CCeEEEEeC
Confidence 889988764
No 166
>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=94.31 E-value=0.043 Score=48.49 Aligned_cols=67 Identities=22% Similarity=0.122 Sum_probs=45.6
Q ss_pred ccCCCEEEEEEEEEcCCCc-eEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 809 VKVGDLVDVKLIEVNDKGQ-LRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gk-I~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
++.|+.|.+.|.++...|- +.|.... +.|-+.. ..+.+ ...+++||++.|+|+++|++
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~~g-------------------v~Gfl~~-~~~~~-~~~~~~Gq~v~~~V~~vd~~ 60 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGIPG-------------------TTGFLPK-KDAGN-FSKLKVGQLLLCVVEKVKDD 60 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCCCC-------------------cEEEEEH-HHCCc-ccccCCCCEEEEEEEEEECC
Confidence 6789999999999977663 3331100 1222210 00000 15789999999999999999
Q ss_pred CCcccCCCC
Q 002487 888 KRPASPAKD 896 (916)
Q Consensus 888 k~rIsL~~~ 896 (916)
++++.|+.+
T Consensus 61 ~~~v~ls~k 69 (74)
T cd05694 61 GRVVSLSAD 69 (74)
T ss_pred CCEEEEEEe
Confidence 999999986
No 167
>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=94.26 E-value=0.099 Score=45.75 Aligned_cols=67 Identities=13% Similarity=0.009 Sum_probs=44.9
Q ss_pred ccCCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEee
Q 002487 809 VKVGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~ 883 (916)
+++||.+..+|.++.+ .| +-+ ++ ..| ..|-+ +++ .+..+|.+.+++||.|+|+|++
T Consensus 1 l~~G~iv~G~V~~i~~~~g-~~v---~l-------------~~~--~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~ 61 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSG-LTV---QL-------------PFG--KTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS 61 (72)
T ss_pred CCCCCEEEEEEEEeeCCcE-EEE---EC-------------CCC--CEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEE
Confidence 4689999999999854 23 211 11 112 22332 333 3455667789999999999999
Q ss_pred ecCCCCcccCCCC
Q 002487 884 VKVFKRPASPAKD 896 (916)
Q Consensus 884 id~ek~rIsL~~~ 896 (916)
+|. .||+||++
T Consensus 62 ~~~--~~i~LSl~ 72 (72)
T cd05704 62 KKD--GKYQLSLR 72 (72)
T ss_pred ecC--CEEEEEeC
Confidence 985 78888753
No 168
>PRK13763 putative RNA-processing protein; Provisional
Probab=94.12 E-value=0.04 Score=57.11 Aligned_cols=60 Identities=35% Similarity=0.428 Sum_probs=48.4
Q ss_pred eeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEE
Q 002487 705 KINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIY 767 (916)
Q Consensus 705 ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~ 767 (916)
.++.+||+||++++.|++.||+. |.+++ ..|.|.+ +.+..+.|++.++.+......+.+|
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~-i~i~~-~~v~i~G-~~~~~~~A~~~I~~li~g~~~~~~~ 164 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVD-ISVYG-KTVAIIG-DPEQVEIAREAIEMLIEGAPHGTVY 164 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcE-EEEcC-CEEEEEe-CHHHHHHHHHHHHHHHcCCCcHHHH
Confidence 57889999999999999999996 88865 4588876 6778889999999887655544443
No 169
>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=93.92 E-value=0.059 Score=46.27 Aligned_cols=64 Identities=9% Similarity=0.009 Sum_probs=45.3
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
|+.+.++|.++.+.| +-+.+-. | +.|-+ +++ .+..++...+++||.++++|+++|++
T Consensus 1 G~~v~g~V~~v~~~G-v~V~l~~----------------~--~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~ 61 (68)
T cd05707 1 GDVVRGFVKNIANNG-VFVTLGR----------------G--VDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPD 61 (68)
T ss_pred CCEEEEEEEEEECcc-EEEEeCC----------------C--CEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCC
Confidence 788999999997654 3333310 1 23333 222 23456778899999999999999999
Q ss_pred CCcccCC
Q 002487 888 KRPASPA 894 (916)
Q Consensus 888 k~rIsL~ 894 (916)
+++|.||
T Consensus 62 ~~~i~ls 68 (68)
T cd05707 62 NGRIEMT 68 (68)
T ss_pred CCEEecC
Confidence 9999875
No 170
>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=93.89 E-value=0.047 Score=47.03 Aligned_cols=65 Identities=11% Similarity=0.027 Sum_probs=44.3
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
|+.+.++|.++...| +.+.+- .| ++|-+ +++ .+..++.+.+++||+++++|+++|++
T Consensus 1 G~~v~g~V~~v~~~G-v~V~l~----------------~~--v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~ 61 (69)
T cd05697 1 GQVVKGTIRKLRPSG-IFVKLS----------------DH--IKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPE 61 (69)
T ss_pred CCEEEEEEEEEeccE-EEEEec----------------CC--cEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECC
Confidence 789999999997643 323220 11 33333 111 12334567899999999999999999
Q ss_pred CCcccCCC
Q 002487 888 KRPASPAK 895 (916)
Q Consensus 888 k~rIsL~~ 895 (916)
+++|.|++
T Consensus 62 ~~~i~ls~ 69 (69)
T cd05697 62 RKRLVLTL 69 (69)
T ss_pred CCEEEEEC
Confidence 99998763
No 171
>PRK08582 hypothetical protein; Provisional
Probab=93.85 E-value=0.058 Score=53.60 Aligned_cols=71 Identities=10% Similarity=0.098 Sum_probs=48.4
Q ss_pred cccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEee
Q 002487 808 VVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~ 883 (916)
.+++|+.+.++|.++...|-+ +.+ .. | +.|-| +++ .++.++...|++||.|+|+|++
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~f-V~L---~~-------------~--~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~ 62 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAF-VEL---PE-------------G--KTGLVHISEVADNYVKDINDHLKVGDEVEVKVLN 62 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEE-EEE---CC-------------C--CEEEEEeeccCcccccccccccCCCCEEEEEEEE
Confidence 378999999999999775422 211 10 0 12222 222 2344556789999999999999
Q ss_pred ecCCCCcccCCCCCC
Q 002487 884 VKVFKRPASPAKDRP 898 (916)
Q Consensus 884 id~ek~rIsL~~~~~ 898 (916)
+|.+ ++|.|+++++
T Consensus 63 id~~-gkI~LSlk~~ 76 (139)
T PRK08582 63 VEDD-GKIGLSIKKA 76 (139)
T ss_pred ECCC-CcEEEEEEec
Confidence 9984 8999997654
No 172
>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=93.67 E-value=0.094 Score=47.16 Aligned_cols=71 Identities=15% Similarity=0.030 Sum_probs=47.1
Q ss_pred ccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc------cccCCCCCCCCCCCcEEEe
Q 002487 809 VKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD------KLVGSPKPKGSSSEDTVLP 880 (916)
Q Consensus 809 ~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i------~~v~~p~~~~k~Gd~V~v~ 880 (916)
.++||.|.++|+++...| +.+.+ +..+.|-+ +++ .......+.+++||.+.++
T Consensus 4 p~~GdiV~g~V~~i~~~g-~~v~i------------------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~ 64 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKR-WKVDI------------------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAE 64 (86)
T ss_pred CCCCCEEEEEEEEECCCE-EEEEC------------------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEE
Confidence 478999999999997644 22211 11122332 111 1122334579999999999
Q ss_pred EeeecCCCCcccCCCCCCC
Q 002487 881 HKKVKVFKRPASPAKDRPY 899 (916)
Q Consensus 881 I~~id~ek~rIsL~~~~~~ 899 (916)
|+++|++ +++.|+++++.
T Consensus 65 V~~~~~~-~~i~LS~~~~~ 82 (86)
T cd05789 65 VQSVDSD-GSVSLHTRSLK 82 (86)
T ss_pred EEEECCC-CCEEEEeCccc
Confidence 9999987 89999988663
No 173
>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=93.65 E-value=0.075 Score=47.46 Aligned_cols=69 Identities=13% Similarity=-0.024 Sum_probs=46.0
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
++||.|.++|++++.++ +.+.+-. ...|.+ +++ ....+..+.+++||.+.|+|.++|
T Consensus 5 ~~GdiV~G~V~~v~~~~-~~V~i~~------------------~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~ 65 (82)
T cd04454 5 DVGDIVIGIVTEVNSRF-WKVDILS------------------RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLG 65 (82)
T ss_pred CCCCEEEEEEEEEcCCE-EEEEeCC------------------CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeC
Confidence 68999999999997643 3332211 112222 111 122334567999999999999999
Q ss_pred CCCCcccCCCCCC
Q 002487 886 VFKRPASPAKDRP 898 (916)
Q Consensus 886 ~ek~rIsL~~~~~ 898 (916)
.+ +++.|+++.+
T Consensus 66 ~~-~~i~LS~~~~ 77 (82)
T cd04454 66 DD-MNVLLTTADN 77 (82)
T ss_pred CC-CCEEEEECCC
Confidence 97 8899998753
No 174
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.52 E-value=0.21 Score=58.01 Aligned_cols=66 Identities=20% Similarity=0.181 Sum_probs=55.3
Q ss_pred CCCCcEEEccEEEEEecceEEEEEC---C--CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCC---C-ceEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIA---P--GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDK---G-QLRLS 831 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~---~--g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~---g-kI~LS 831 (916)
-++|+++.| +|.++...+++|+|. + +++|++|.++.. |.+.|++||.|+|-|.+|... | +|.||
T Consensus 150 ~~~GeIV~G-~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilS 222 (449)
T PRK12329 150 DLEDTVLTA-RVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVS 222 (449)
T ss_pred HhcCcEEEE-EEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEE
Confidence 389999999 999999999999993 2 389999987754 567899999999999999652 2 68888
Q ss_pred Ee
Q 002487 832 RR 833 (916)
Q Consensus 832 ~K 833 (916)
+.
T Consensus 223 Rt 224 (449)
T PRK12329 223 RA 224 (449)
T ss_pred cC
Confidence 83
No 175
>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=93.39 E-value=0.075 Score=46.54 Aligned_cols=67 Identities=7% Similarity=-0.017 Sum_probs=45.0
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
..|+.++++|.++.+.|- -+.+... + ..|-+ +++ .++.++.+.+++||+++|+|+++|
T Consensus 2 ~~g~~~~g~V~~i~~fG~-fv~l~~~---~--------------~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 2 ALYQIFKGEVASVTEYGA-FVKIPGC---R--------------KQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE 63 (73)
T ss_pred cCCCEEEEEEEEEEeeeE-EEEECCC---C--------------eEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEEC
Confidence 579999999999976442 2222110 0 11221 111 244566778999999999999999
Q ss_pred CCCCcccCCC
Q 002487 886 VFKRPASPAK 895 (916)
Q Consensus 886 ~ek~rIsL~~ 895 (916)
.++ ||+|++
T Consensus 64 ~~~-ki~ls~ 72 (73)
T cd05686 64 MKD-KMKLSL 72 (73)
T ss_pred CCC-cEEEEe
Confidence 987 888875
No 176
>PRK07252 hypothetical protein; Provisional
Probab=93.37 E-value=0.08 Score=51.31 Aligned_cols=70 Identities=13% Similarity=0.146 Sum_probs=47.6
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
++|+.+.++|.++...|- -+.+- . | +.|-+ +++ .++..+...+++||.|+|+|.++|
T Consensus 2 kvG~iv~G~V~~V~~~G~-fVei~----~------------~--~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD 62 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGA-FVALE----N------------G--TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62 (120)
T ss_pred CCCCEEEEEEEEEeCcEE-EEEEC----C------------C--CEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEe
Confidence 579999999999976542 22220 0 0 12221 111 233455678999999999999999
Q ss_pred CCCCcccCCCCCC
Q 002487 886 VFKRPASPAKDRP 898 (916)
Q Consensus 886 ~ek~rIsL~~~~~ 898 (916)
.++++|.|++++.
T Consensus 63 ~~~~ri~lSlk~~ 75 (120)
T PRK07252 63 EYTGKASLSLRTL 75 (120)
T ss_pred CCCCEEEEEEeec
Confidence 9999999986533
No 177
>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=93.29 E-value=0.052 Score=46.81 Aligned_cols=67 Identities=19% Similarity=0.152 Sum_probs=46.1
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCC
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVF 887 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~e 887 (916)
|+.+.++|.++...| +.+.+- ..+.|.+ +++ ....++.+.+++||.++++|+++|.+
T Consensus 1 G~~v~g~V~~v~~~g-~~v~l~------------------~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~ 61 (73)
T cd05691 1 GSIVTGKVTEVDAKG-ATVKLG------------------DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK 61 (73)
T ss_pred CCEEEEEEEEEECCe-EEEEeC------------------CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCC
Confidence 788999999997533 323221 0123332 121 23345667899999999999999999
Q ss_pred CCcccCCCCC
Q 002487 888 KRPASPAKDR 897 (916)
Q Consensus 888 k~rIsL~~~~ 897 (916)
++++.|++++
T Consensus 62 ~~~i~ls~k~ 71 (73)
T cd05691 62 NRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEE
Confidence 9999998764
No 178
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=93.26 E-value=0.29 Score=58.16 Aligned_cols=67 Identities=28% Similarity=0.538 Sum_probs=51.6
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC-CCc------ceeEEecccccHHHHHHHHHhhhcCCCCC
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE-DDG------TVKITAKDLSSLEKSKAIISNLTMVPTVG 764 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~-d~g------~v~I~~~~~~~~~~a~~~i~~l~~~~~vG 764 (916)
-..++|+-.+++.|||.||++||.|..+||++ |-+. ||+ .+.|... .+.++.|.+.|..++...+.|
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~K-IQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAK-IQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccCce-eEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhcc
Confidence 44568899999999999999999999999997 7765 333 4445443 456788888888887765544
No 179
>PF13014 KH_3: KH domain
Probab=93.21 E-value=0.071 Score=41.89 Aligned_cols=27 Identities=44% Similarity=0.719 Sum_probs=24.0
Q ss_pred eeeeecCCchhHHHHHHHhCCceeccCC
Q 002487 706 INLIIGSGGKKVKSIIEETGVEAIDTED 733 (916)
Q Consensus 706 i~~vIG~gGk~Ik~I~~~~~v~~Idi~d 733 (916)
++.+||++|.+|++|.+++++. |++.+
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~-I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAK-IQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcE-EEECC
Confidence 5789999999999999999996 87754
No 180
>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=93.00 E-value=0.16 Score=47.68 Aligned_cols=31 Identities=6% Similarity=-0.162 Sum_probs=27.8
Q ss_pred CCCCCCCCCCcEEEeEeeecCC---CCcccCCCC
Q 002487 866 SPKPKGSSSEDTVLPHKKVKVF---KRPASPAKD 896 (916)
Q Consensus 866 ~p~~~~k~Gd~V~v~I~~id~e---k~rIsL~~~ 896 (916)
.+.+.|++||.|.|+|+++|.+ ++||.||++
T Consensus 62 ~~~~~f~vGd~V~~kVi~~d~~~~~~~~i~LSlr 95 (100)
T cd05693 62 DLEDLFSVGQLVRCKVVSLDKSKSGKKRIELSLE 95 (100)
T ss_pred CHHHhccCCCEEEEEEEEccCCcCCCcEEEEEec
Confidence 4557899999999999999998 899999987
No 181
>PRK05807 hypothetical protein; Provisional
Probab=92.99 E-value=0.1 Score=51.64 Aligned_cols=70 Identities=7% Similarity=0.118 Sum_probs=48.0
Q ss_pred cccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEee
Q 002487 808 VVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~ 883 (916)
.+++||.|.++|.++.+.|-+ +.+ .. ..|-| +++ .++.++...+++||.|+|+|++
T Consensus 2 ~~~vG~vv~G~Vt~i~~~Gaf-V~L---~~----------------~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~ 61 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAF-VEV---EG----------------KTGLVHISEVADTYVKDIREHLKEQDKVKVKVIS 61 (136)
T ss_pred CccCCCEEEEEEEEEECCeEE-EEE---CC----------------EEEEEEhhhcccccccCccccCCCCCEEEEEEEE
Confidence 368999999999999775422 222 00 01221 111 2344556789999999999999
Q ss_pred ecCCCCcccCCCCCC
Q 002487 884 VKVFKRPASPAKDRP 898 (916)
Q Consensus 884 id~ek~rIsL~~~~~ 898 (916)
+|. +++|+|++++.
T Consensus 62 id~-~gkI~LSlk~~ 75 (136)
T PRK05807 62 IDD-NGKISLSIKQA 75 (136)
T ss_pred ECC-CCcEEEEEEec
Confidence 998 79999998653
No 182
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.77 E-value=0.46 Score=52.70 Aligned_cols=114 Identities=20% Similarity=0.359 Sum_probs=64.5
Q ss_pred ecCCceeEEEeeccccCCCHHHHHHHHHHHHhhhHHHHHHHHhcCCC---CCCCCCCCCC-eEE--EEeeccceeeeeec
Q 002487 638 GNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPP---PSNSLSKHAP-LIH--IMKVKPEKINLIIG 711 (916)
Q Consensus 638 gt~~gItalq~d~K~ggis~e~l~eaL~~A~~a~~~Il~~m~~~i~~---~r~~~~~~aP-~i~--~~~I~~~ki~~vIG 711 (916)
||.+.||++|-. .+.+...++ .|.+++++.... +..-+.+-.| |+. .+-+|-.--+.+||
T Consensus 83 GTTeRvcli~Gt-------~eai~av~e-------fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iig 148 (402)
T KOG2191|consen 83 GTTERVCLIQGT-------VEALNAVHE-------FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIG 148 (402)
T ss_pred CccceEEEEecc-------HHHHHHHHH-------HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceec
Confidence 788899999843 344444443 345555443322 2222222222 223 23446667789999
Q ss_pred CCchhHHHHHHHhCCceeccC--C-------CcceeEEecccccHHHH-HHHHHhhhcCCCCCcEE
Q 002487 712 SGGKKVKSIIEETGVEAIDTE--D-------DGTVKITAKDLSSLEKS-KAIISNLTMVPTVGDIY 767 (916)
Q Consensus 712 ~gGk~Ik~I~~~~~v~~Idi~--d-------~g~v~I~~~~~~~~~~a-~~~i~~l~~~~~vG~i~ 767 (916)
+||-+||.|+|+.+.- |.|. + +..|.++. +.+...+| ..++..+..+++-|..+
T Consensus 149 kggAtiK~~~Eqsga~-iqisPqkpt~~sLqervvt~sg-e~e~~~~A~~~IL~Ki~eDpqs~scl 212 (402)
T KOG2191|consen 149 KGGATIKAIQEQSGAW-IQISPQKPTGISLQERVVTVSG-EPEQNMKAVSLILQKIQEDPQSGSCL 212 (402)
T ss_pred CCcchHHHHHHhhCcc-eEecccCCCCccceeEEEEecC-CHHHHHHHHHHHHHHhhcCCccccee
Confidence 9999999999999884 5554 1 22333443 33444444 44445566666655543
No 183
>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=92.67 E-value=0.16 Score=44.24 Aligned_cols=71 Identities=18% Similarity=0.142 Sum_probs=47.9
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
+.|+.+.++|.++...| +-+.+-.. + | +.|-+ +++ .++.++...+++||.|+|+|.++|
T Consensus 2 ~~G~~~~g~V~~v~~~g-~~v~l~~~---~-----------~--~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 2 EEGELVVVTVKSIADMG-AYVSLLEY---G-----------N--IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred CCCCEEEEEEEEEEccE-EEEEEcCC---C-----------C--eEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEE
Confidence 57999999999997644 22222110 0 0 22222 222 334456678999999999999999
Q ss_pred CCCCcccCCCCC
Q 002487 886 VFKRPASPAKDR 897 (916)
Q Consensus 886 ~ek~rIsL~~~~ 897 (916)
.+++++.|++++
T Consensus 65 ~~~~~i~ls~k~ 76 (76)
T cd04452 65 KEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEcC
Confidence 999999998763
No 184
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=92.45 E-value=0.13 Score=43.51 Aligned_cols=64 Identities=14% Similarity=0.116 Sum_probs=43.4
Q ss_pred CCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecC
Q 002487 811 VGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKV 886 (916)
Q Consensus 811 vGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~ 886 (916)
+|+.+.++|.+++..| +.+.+- .. .|.+ +++ .+...+.+.++.||.++|+|.++|.
T Consensus 1 ~g~~~~g~V~~v~~~g-~~v~l~-----~~--------------~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 1 EGDVVEGTVKSITDFG-AFVDLG-----GV--------------DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred CCCEEEEEEEEEEeee-EEEEEC-----Ce--------------EEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEEC
Confidence 4899999999997654 222221 01 1111 000 2334566789999999999999999
Q ss_pred CCCcccCC
Q 002487 887 FKRPASPA 894 (916)
Q Consensus 887 ek~rIsL~ 894 (916)
+++++.||
T Consensus 61 ~~~~i~ls 68 (68)
T cd05688 61 ERKRISLG 68 (68)
T ss_pred CCCEEecC
Confidence 99999875
No 185
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.08 E-value=0.16 Score=60.52 Aligned_cols=62 Identities=24% Similarity=0.510 Sum_probs=52.7
Q ss_pred CCCCcEEEccEEEEEecc--eEEEEECCCeeeEEeccccCcccccCc-----cccccCCCEEEEEEEEEcC
Q 002487 761 PTVGDIYRNCEIKSIAPY--GVFVEIAPGREGLCHISELSSNWLAKA-----EDVVKVGDLVDVKLIEVND 824 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~f--GaFVel~~g~eGlvhiSels~~~v~~~-----~~~~kvGd~V~VKVi~iD~ 824 (916)
..+|.+|.| +|++|.+. .|||+++....||+|.+++.+ +.+.+ ...++.||.+-|.|+.-..
T Consensus 35 ~~~gniy~g-rv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~ 103 (487)
T COG1530 35 QIVGNIYKG-RVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPR 103 (487)
T ss_pred eeecCceEE-EecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecC
Confidence 468999999 99999886 589999989999999999998 54433 3589999999999998754
No 186
>PRK08059 general stress protein 13; Validated
Probab=92.01 E-value=0.11 Score=50.39 Aligned_cols=72 Identities=17% Similarity=0.055 Sum_probs=48.8
Q ss_pred cccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEee
Q 002487 808 VVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~ 883 (916)
.+++|+.+.++|.++...| +.+.+ . +. +.|-+ +++ .++.++...+++||.|.|+|.+
T Consensus 4 ~~k~G~iv~G~V~~i~~~G-~fV~i---~-~~--------------~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~ 64 (123)
T PRK08059 4 QYEVGSVVTGKVTGIQPYG-AFVAL---D-EE--------------TQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLS 64 (123)
T ss_pred cCCCCCEEEEEEEEEecce-EEEEE---C-CC--------------CEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEE
Confidence 3789999999999998744 22222 0 00 11211 111 1233455679999999999999
Q ss_pred ecCCCCcccCCCCCC
Q 002487 884 VKVFKRPASPAKDRP 898 (916)
Q Consensus 884 id~ek~rIsL~~~~~ 898 (916)
+|.+++++.|++++.
T Consensus 65 id~~~~~i~lslk~~ 79 (123)
T PRK08059 65 VDEEKGKISLSIRAT 79 (123)
T ss_pred EECCCCeEEEEEEEc
Confidence 999999999997654
No 187
>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=91.70 E-value=0.16 Score=42.81 Aligned_cols=29 Identities=10% Similarity=-0.039 Sum_probs=25.7
Q ss_pred CCCCCCCCCCcEEEeEeeecCCCCcccCC
Q 002487 866 SPKPKGSSSEDTVLPHKKVKVFKRPASPA 894 (916)
Q Consensus 866 ~p~~~~k~Gd~V~v~I~~id~ek~rIsL~ 894 (916)
++...+++||.++|+|.++|++++++.||
T Consensus 40 ~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 40 HPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 45567999999999999999999999875
No 188
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=91.51 E-value=0.12 Score=63.29 Aligned_cols=55 Identities=11% Similarity=0.045 Sum_probs=45.4
Q ss_pred CCCCCCCcEEEeeccc------------------------cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCCCC
Q 002487 846 VKLPTGDPTKDAAASD------------------------KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYS 900 (916)
Q Consensus 846 ~~~~~G~vv~g~Vs~i------------------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~~~ 900 (916)
+.+++|.++.|+|.++ +++.+|.+++++||.|+|+|+++|..++||+|++..+-.
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~ 732 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEE 732 (780)
T ss_pred hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence 4667788888876442 678889999999999999999999999999999864433
No 189
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=91.43 E-value=0.023 Score=67.05 Aligned_cols=104 Identities=11% Similarity=0.098 Sum_probs=68.3
Q ss_pred eEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEE-EeecCCCCCC-----CCCCCCCC--CCCcEEEeeccc
Q 002487 790 GLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLS-RRALLPEADA-----ENPPVKLP--TGDPTKDAAASD 861 (916)
Q Consensus 790 GlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS-~K~~~~~p~~-----~~~~~~~~--~G~vv~g~Vs~i 861 (916)
+.+++++... ....+++||.|.+.|...+. ||+.++ .|+.....|. ... ..|+ +|++++|+|..+
T Consensus 73 ~eI~L~eAk~-----~~~~~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~-~eyk~~~GeIV~G~V~ri 145 (470)
T PRK09202 73 KEISLEEARK-----IDPDAEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVY-EEYKDRVGEIITGVVKRV 145 (470)
T ss_pred ceeeHHHHhh-----hCccccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcCCEEEEEEEEE
Confidence 4555555421 12347899999999988774 444333 3443222222 233 3565 899999998432
Q ss_pred -----------------cccCCCCCCCCCCCcEEEeEeeecCCCC--cccCCCCCCCC
Q 002487 862 -----------------KLVGSPKPKGSSSEDTVLPHKKVKVFKR--PASPAKDRPYS 900 (916)
Q Consensus 862 -----------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~--rIsL~~~~~~~ 900 (916)
+.-..|...|++||+++|.|++|+.+++ +|-||...|-+
T Consensus 146 ~~~giiVDLggvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~ 203 (470)
T PRK09202 146 ERGNIIVDLGRAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEF 203 (470)
T ss_pred ecCCEEEEECCeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcHHH
Confidence 1112477899999999999999999988 88888766543
No 190
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=91.42 E-value=0.43 Score=49.80 Aligned_cols=110 Identities=14% Similarity=0.093 Sum_probs=62.9
Q ss_pred cceEEEEEC---CCeeeEEeccc----cCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCC
Q 002487 777 PYGVFVEIA---PGREGLCHISE----LSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLP 849 (916)
Q Consensus 777 ~fGaFVel~---~g~eGlvhiSe----ls~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~ 849 (916)
..|.|++=. ..+-|++.+.. ++..........+++||.|.++|.++...+ +.+.+=..... . ..+.
T Consensus 23 G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g-~~V~I~~~~~~--~----~~l~ 95 (189)
T PRK09521 23 GEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQR-ALVRIVSIEGS--E----RELA 95 (189)
T ss_pred CCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCe-EEEEEEEeccc--c----cccC
Confidence 357777521 13457777643 223333443456789999999999997643 33333221100 0 0111
Q ss_pred CCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeecCCCCcccCCCCCC
Q 002487 850 TGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRP 898 (916)
Q Consensus 850 ~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~~ 898 (916)
.+ ..|-+ +++ ....++.+.+++||.|.|+|++++ +++.|+++++
T Consensus 96 ~~--~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~~ 143 (189)
T PRK09521 96 TS--KLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKGK 143 (189)
T ss_pred CC--ceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEecC
Confidence 11 22322 222 122345678999999999999999 6888887653
No 191
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=90.80 E-value=0.93 Score=41.34 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=50.8
Q ss_pred EEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 766 IYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 766 i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
.++| +|+.+.+.+-| |+|.+|.+-+.|+|= +...-.-.+-+||.|.|.+-..|. +|+|..-.|
T Consensus 8 e~~G-~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 8 ELDG-IVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEE-EEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 4788 99999999987 699999999999873 222222246789999999999998 899998777
No 192
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=90.79 E-value=0.93 Score=52.83 Aligned_cols=89 Identities=27% Similarity=0.347 Sum_probs=60.3
Q ss_pred hhHHHHHHHHhcCCCCCCCCCCCCCe---EEEEeec------cceeeeeecCCchhHHHHHHHhCCceeccCC-------
Q 002487 670 GRRHILAEMLKCSPPPSNSLSKHAPL---IHIMKVK------PEKINLIIGSGGKKVKSIIEETGVEAIDTED------- 733 (916)
Q Consensus 670 a~~~Il~~m~~~i~~~r~~~~~~aP~---i~~~~I~------~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d------- 733 (916)
.+..+++.+.+.+..- +...+|-|- -..+-|+ -..|+-|||+-|.|.|.++++||++ |-|..
T Consensus 111 er~e~I~~~lk~nP~f-kpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAK-I~IRGkgSvkEg 188 (554)
T KOG0119|consen 111 ERHEIIEEILKLNPGF-KPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAK-IAIRGKGSVKEG 188 (554)
T ss_pred HHHHHHHHHHHhCcCC-CCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCe-EEEecccccccc
Confidence 3344555555555442 334455442 1122333 3468999999999999999999997 65542
Q ss_pred ---------------CcceeEEecccccHHHHHHHHHhhhcC
Q 002487 734 ---------------DGTVKITAKDLSSLEKSKAIISNLTMV 760 (916)
Q Consensus 734 ---------------~g~v~I~~~~~~~~~~a~~~i~~l~~~ 760 (916)
+-...|++.+.+++++|.+.|+.++.+
T Consensus 189 k~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 189 KGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred ccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 224568888899999999999999875
No 193
>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=89.43 E-value=1.4 Score=38.60 Aligned_cols=59 Identities=27% Similarity=0.364 Sum_probs=46.3
Q ss_pred EEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceE
Q 002487 766 IYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLR 829 (916)
Q Consensus 766 i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~ 829 (916)
.+.| +|++..+.|.| |.+.+|.+-+.|+|- +...-.-.+.+||.|.|.+-..|. +|+|.
T Consensus 6 e~~G-~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEG-KVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEE-EEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 4678 99999999987 699999999999873 222223357789999999888887 78775
No 194
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=89.27 E-value=0.57 Score=48.80 Aligned_cols=72 Identities=24% Similarity=0.366 Sum_probs=59.8
Q ss_pred CCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC-CCcceeEEec----ccccHHHHHHHHHhhhcCCCCCc
Q 002487 693 APLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE-DDGTVKITAK----DLSSLEKSKAIISNLTMVPTVGD 765 (916)
Q Consensus 693 aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~-d~g~v~I~~~----~~~~~~~a~~~i~~l~~~~~vG~ 765 (916)
.+.+..+.||+++++-+||+.|++.+.|.+.++++ +.+| ++|.|.|... |..+..+|++.++.+-.-+.+.+
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~-~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVK-LRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeE-EEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 35567789999999999999999999999999996 8888 6799999877 66788899999988865544433
No 195
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=88.97 E-value=0.27 Score=41.32 Aligned_cols=67 Identities=16% Similarity=0.106 Sum_probs=43.4
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEeeec
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
++|+.+.++|.++...| +.+.+-. -+.|.+ +++ ....++...+++||.+.++|.+++
T Consensus 1 ~~G~~v~g~V~~v~~~g-~~v~i~~------------------~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 1 EVGDVVEGTVTEITPFG-AFVDLGN------------------GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61 (72)
T ss_pred CCCCEEEEEEEEEEccE-EEEEeCC------------------CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEe
Confidence 36999999999997643 3332210 011221 111 112233457999999999999999
Q ss_pred CCCCcccCCC
Q 002487 886 VFKRPASPAK 895 (916)
Q Consensus 886 ~ek~rIsL~~ 895 (916)
.+++++.++.
T Consensus 62 ~~~~~i~ls~ 71 (72)
T smart00316 62 EEKGRIILSL 71 (72)
T ss_pred CCCCEEEEEe
Confidence 9999988765
No 196
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=88.11 E-value=1.6 Score=44.60 Aligned_cols=72 Identities=24% Similarity=0.275 Sum_probs=54.7
Q ss_pred CCCCcEEEccEEEEEecceEEEEEC--------CCeeeEEeccccCccc--ccCccccccCCCEEEEEEEEEcCCCceEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIA--------PGREGLCHISELSSNW--LAKAEDVVKVGDLVDVKLIEVNDKGQLRL 830 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~--------~g~eGlvhiSels~~~--v~~~~~~~kvGd~V~VKVi~iD~~gkI~L 830 (916)
|.+|+++.. +|.++..-=|=|+|. ....|+||..++-..- --++-+.|++||.|.+||++.+.....-|
T Consensus 66 P~~G~IVta-rV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~L 144 (193)
T KOG3409|consen 66 PFVGAIVTA-RVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLL 144 (193)
T ss_pred CccCcEEEE-EEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEE
Confidence 689999996 999998877777774 2457999988875421 12355679999999999999766666677
Q ss_pred EEe
Q 002487 831 SRR 833 (916)
Q Consensus 831 S~K 833 (916)
+.-
T Consensus 145 TtA 147 (193)
T KOG3409|consen 145 TTA 147 (193)
T ss_pred EEe
Confidence 653
No 197
>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=87.82 E-value=0.58 Score=39.49 Aligned_cols=30 Identities=7% Similarity=-0.018 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCcEEEeEeeecCCCCcccCCC
Q 002487 865 GSPKPKGSSSEDTVLPHKKVKVFKRPASPAK 895 (916)
Q Consensus 865 ~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~ 895 (916)
.++...|+.||.+.|+|.++|+ ++++.+|+
T Consensus 39 ~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 39 EKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred cCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 3455679999999999999999 88888764
No 198
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=87.77 E-value=1.4 Score=44.50 Aligned_cols=66 Identities=21% Similarity=0.321 Sum_probs=45.8
Q ss_pred hhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEec----cccCcccccC-------ccccccCCCEEEEEEEEEc
Q 002487 756 NLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHI----SELSSNWLAK-------AEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 756 ~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhi----Sels~~~v~~-------~~~~~kvGd~V~VKVi~iD 823 (916)
.++..+-.|++++| .|+.+..-|+|++++| ++-++-. .++.....++ -..++++|.+|++||++..
T Consensus 74 av~FkpfKGEVvdg-vV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 74 AVTFKPFKGEVVDG-VVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred EEEEeecCCcEEEE-EEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 34556778999999 9999999999999986 4444321 2221111112 1236899999999999874
No 199
>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=87.15 E-value=0.49 Score=39.81 Aligned_cols=31 Identities=6% Similarity=-0.035 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCcEEEeEeeecCCCCcccCCCC
Q 002487 865 GSPKPKGSSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 865 ~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
.++.+.+++||.+.++|.++|. ++++.|+++
T Consensus 39 ~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 39 KDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 3455679999999999999999 888887753
No 200
>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=86.97 E-value=0.77 Score=40.66 Aligned_cols=64 Identities=9% Similarity=0.070 Sum_probs=41.6
Q ss_pred ccccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecC
Q 002487 807 DVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKV 886 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~ 886 (916)
..+++|+.+.++|.++.+.|-. +.+ . +. ..|-+ +.......++.||+++++|.++ .
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~f-V~l---~-~~--------------~~Glv----~~se~~~~~~iGd~v~v~I~~i-~ 67 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVF-VDL---N-DH--------------VRGLI----HRSNLLRDYEVGDEVIVQVTDI-P 67 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEE-EEE---C-CC--------------cEEEE----EchhccCcCCCCCEEEEEEEEE-C
Confidence 4588899999999998654421 111 1 00 11222 1111235699999999999999 8
Q ss_pred CCCcccCC
Q 002487 887 FKRPASPA 894 (916)
Q Consensus 887 ek~rIsL~ 894 (916)
++++|.++
T Consensus 68 e~~~i~l~ 75 (77)
T cd04473 68 ENGNIDLI 75 (77)
T ss_pred CCCcEEEE
Confidence 89998875
No 201
>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=85.57 E-value=1.5 Score=37.51 Aligned_cols=25 Identities=0% Similarity=-0.052 Sum_probs=22.5
Q ss_pred CCCCcEEEeEeeecCCCCcccCCCC
Q 002487 872 SSSEDTVLPHKKVKVFKRPASPAKD 896 (916)
Q Consensus 872 k~Gd~V~v~I~~id~ek~rIsL~~~ 896 (916)
.+||.++|+|+++|.++++|.||.+
T Consensus 43 ~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 43 YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 4899999999999999999988753
No 202
>PHA02945 interferon resistance protein; Provisional
Probab=84.94 E-value=0.77 Score=41.93 Aligned_cols=29 Identities=14% Similarity=0.001 Sum_probs=26.5
Q ss_pred CCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 868 KPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 868 ~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
++.+ +||++.|+|+++|+.++.|-||+|+
T Consensus 55 rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 55 RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 5678 9999999999999999999999874
No 203
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=84.75 E-value=0.79 Score=50.36 Aligned_cols=74 Identities=18% Similarity=0.117 Sum_probs=50.5
Q ss_pred ccccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--cccCCCCCCCCCCCcEEEeEe
Q 002487 807 DVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--KLVGSPKPKGSSSEDTVLPHK 882 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~~v~~p~~~~k~Gd~V~v~I~ 882 (916)
...++||.|.++|.++...| +.+.+-+. + | +.|-+ +++ .++..+.+.+++||.|.|+|+
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G-~fV~L~e~--~------------g--ieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi 66 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFG-AFVTLDEY--P------------G--KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVI 66 (262)
T ss_pred CCCCCCCEEEEEEEEEECCE-EEEEECCC--C------------C--cEEEEEHHHcCcccccCHHHhCCCCCEEEEEEE
Confidence 34578999999999997644 22222110 0 1 12332 222 234456678999999999999
Q ss_pred eecCCCCcccCCCCC
Q 002487 883 KVKVFKRPASPAKDR 897 (916)
Q Consensus 883 ~id~ek~rIsL~~~~ 897 (916)
++|.++++|.|++++
T Consensus 67 ~VD~~k~~I~LSlK~ 81 (262)
T PRK03987 67 RVDPRKGHIDLSLKR 81 (262)
T ss_pred EEecccCeEEEEEEe
Confidence 999999999999863
No 204
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=84.69 E-value=2.4 Score=50.75 Aligned_cols=60 Identities=28% Similarity=0.499 Sum_probs=46.0
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCC--------CcceeEEecccccHHHHHHHHHhh
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED--------DGTVKITAKDLSSLEKSKAIISNL 757 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d--------~g~v~I~~~~~~~~~~a~~~i~~l 757 (916)
...+.|+.+|-+-+||+||.|||.|..++|+- +.+.. +.++.|. -+...++-|+.+|+..
T Consensus 319 ~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~-~el~r~~p~~~~~ektf~Ir-G~~~QIdhAk~LIr~k 386 (600)
T KOG1676|consen 319 QFYMKVPADKCGLVIGRGGETIKQINQQSGAR-CELSRQPPNGNPKEKTFVIR-GDKRQIDHAKQLIRDK 386 (600)
T ss_pred eEEEeccccccccccCCCccchhhhcccCCcc-ccccCCCCCCCccceEEEEe-cCcccchHHHHHHHHH
Confidence 56789999999999999999999999999985 54431 2344444 4556688888888764
No 205
>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=83.42 E-value=9.2 Score=32.63 Aligned_cols=56 Identities=30% Similarity=0.398 Sum_probs=38.7
Q ss_pred EEccEEEEEec---ceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCce
Q 002487 767 YRNCEIKSIAP---YGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQL 828 (916)
Q Consensus 767 ~~G~~V~~I~~---fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI 828 (916)
.+| +|+...+ ||....-..+.+-++|+|++.... -..++.||.|...+.. +.+|..
T Consensus 1 ~~G-~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g~~ 59 (66)
T PF00313_consen 1 MTG-TVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKGPQ 59 (66)
T ss_dssp EEE-EEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTSEE
T ss_pred CeE-EEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCCCE
Confidence 367 8888864 665444444458999999998664 3468899999999998 545533
No 206
>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=83.37 E-value=1.7 Score=37.54 Aligned_cols=63 Identities=17% Similarity=0.041 Sum_probs=42.3
Q ss_pred CCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccc--c--ccCCCCCCCCCCCcEEEeEeeec
Q 002487 812 GDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASD--K--LVGSPKPKGSSSEDTVLPHKKVK 885 (916)
Q Consensus 812 Gd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i--~--~v~~p~~~~k~Gd~V~v~I~~id 885 (916)
|+.|.++|.+++..+ +.+.+- .-++|.+ +++ . ...+|.+.|++||.+.++|+++|
T Consensus 1 G~iV~g~V~~i~~~g-i~v~l~------------------~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 1 GDLVKAKVKSVKPTQ-LNVQLA------------------DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGH 61 (70)
T ss_pred CCEEEEEEEEEECCc-EEEEeC------------------CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEe
Confidence 789999999997643 333331 1133333 222 1 24456678999999999999999
Q ss_pred CCCCcccC
Q 002487 886 VFKRPASP 893 (916)
Q Consensus 886 ~ek~rIsL 893 (916)
.++..-+|
T Consensus 62 ~~~~~~~~ 69 (70)
T cd05702 62 DAKTHRFL 69 (70)
T ss_pred CccccccC
Confidence 98875443
No 207
>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=83.32 E-value=1.5 Score=38.72 Aligned_cols=31 Identities=6% Similarity=0.048 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCcEEEeEeeecCCCCcccCCCCC
Q 002487 865 GSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDR 897 (916)
Q Consensus 865 ~~p~~~~k~Gd~V~v~I~~id~ek~rIsL~~~~ 897 (916)
.++...|+.||+|+|+|.++| ++++.++.++
T Consensus 43 ~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~ 73 (79)
T cd05684 43 ANPSDVVKRGQKVKVKVISIQ--NGKISLSMKD 73 (79)
T ss_pred CChhheeCCCCEEEEEEEEEe--CCEEEEEEEe
Confidence 455678999999999999999 7888888653
No 208
>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=81.77 E-value=3.4 Score=35.46 Aligned_cols=58 Identities=10% Similarity=0.119 Sum_probs=37.8
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecCCCC
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVFKR 889 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~ 889 (916)
+.|+.|+++|.+++.++ +-+.+ |. ++|-++.-.. .|.+.+++||++++.|.+++.+++
T Consensus 2 ~~g~iV~G~V~~~~~~~-~~vdi------------------g~-~eg~lp~~e~--~~~~~~~~Gd~v~v~v~~v~~~~~ 59 (67)
T cd04455 2 REGEIVTGIVKRVDRGN-VIVDL------------------GK-VEAILPKKEQ--IPGESYRPGDRIKAYVLEVRKTSK 59 (67)
T ss_pred CCCCEEEEEEEEEcCCC-EEEEc------------------CC-eEEEeeHHHC--CCCCcCCCCCEEEEEEEEEecCCC
Confidence 46999999999998754 22322 11 2233211111 144678999999999999997664
No 209
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=81.47 E-value=5 Score=37.83 Aligned_cols=66 Identities=20% Similarity=0.305 Sum_probs=50.4
Q ss_pred CCCCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
.++.|+++ | +|+.....+.| |++.+|..-|+|++- +++. .-.++.||.|.|.....|. +|+|..-+
T Consensus 17 ~p~e~e~~-g-~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~ 84 (100)
T PRK04012 17 MPEEGEVF-G-VVEQMLGANRVRVRCMDGVERMGRIPG----KMKK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred CCCCCEEE-E-EEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 35677766 6 89999999987 688889999999873 3333 3468899999999888876 66665543
No 210
>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=79.07 E-value=0.21 Score=56.71 Aligned_cols=92 Identities=12% Similarity=0.099 Sum_probs=53.7
Q ss_pred cccccCCCEEEEEEEEEcCCCceE-EEEeecC-----CCCCCCCCCCCC--CCCCcEEEeeccccc--------------
Q 002487 806 EDVVKVGDLVDVKLIEVNDKGQLR-LSRRALL-----PEADAENPPVKL--PTGDPTKDAAASDKL-------------- 863 (916)
Q Consensus 806 ~~~~kvGd~V~VKVi~iD~~gkI~-LS~K~~~-----~~p~~~~~~~~~--~~G~vv~g~Vs~i~~-------------- 863 (916)
...+++||.|.+.+..-+. ||+. .+.|+.. ...++.... .| +.|++++|+|..+..
T Consensus 81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~-ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~ 158 (341)
T TIGR01953 81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYD-EFSSKEGEIISGTVKRVNRRGNLYVELGKTEGI 158 (341)
T ss_pred ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhcCCEEEEEEEEEecCCcEEEEECCeEEE
Confidence 3457778888877754332 3322 2233321 122222222 44 478888888733210
Q ss_pred ----cCCCCCCCCCCCcEEEeEeeecCCC--CcccCCCCCCC
Q 002487 864 ----VGSPKPKGSSSEDTVLPHKKVKVFK--RPASPAKDRPY 899 (916)
Q Consensus 864 ----v~~p~~~~k~Gd~V~v~I~~id~ek--~rIsL~~~~~~ 899 (916)
-..|.+.|++||+++|.|++++.++ ..|-||++.|-
T Consensus 159 LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~ 200 (341)
T TIGR01953 159 LPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPE 200 (341)
T ss_pred ecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcHH
Confidence 0134567999999999999999665 45777776553
No 211
>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=78.96 E-value=8.5 Score=37.56 Aligned_cols=62 Identities=18% Similarity=0.155 Sum_probs=43.7
Q ss_pred CCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcc-c-----------c-cCccccccCCCEEEEEEEEEcC
Q 002487 762 TVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSN-W-----------L-AKAEDVVKVGDLVDVKLIEVND 824 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~-~-----------v-~~~~~~~kvGd~V~VKVi~iD~ 824 (916)
-+|+++.| +|++-..-|+.|.|+=--+=+|+-+.|... + . ..-.-.+..|+.|++||.++.-
T Consensus 2 F~gEvl~g-~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 2 FVGEVLTG-KIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp -TT-EEEE-EEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCCEEEE-EEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 47999999 999999999999996445677887777531 1 1 3333468999999999999853
No 212
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=78.83 E-value=2.9 Score=35.58 Aligned_cols=36 Identities=28% Similarity=0.405 Sum_probs=31.2
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceecc
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDT 731 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi 731 (916)
....+.++++.++..||.+|.+|+.+...++.. ||+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~-I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEK-IDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCC-eEE
Confidence 556678899999999999999999999999875 664
No 213
>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=78.31 E-value=6.2 Score=35.86 Aligned_cols=74 Identities=14% Similarity=0.077 Sum_probs=35.5
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEee--ccccccC----CCCCCCCCCCcEEEeEee
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAA--ASDKLVG----SPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V--s~i~~v~----~p~~~~k~Gd~V~v~I~~ 883 (916)
++||.|.+||..+.. ....+.+-.++..++..........++...|.+ +.++..+ .+.+-|++||-|.++|++
T Consensus 3 ~vGdiV~~rVtrv~~-~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 3 KVGDIVIARVTRVNP-RQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp -TT-EEEEEEEEE-S-SEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred CCCCEEEEEEEEEec-cEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence 579999999999965 566777777755444333222233344444554 2332111 234679999999999987
Q ss_pred e
Q 002487 884 V 884 (916)
Q Consensus 884 i 884 (916)
+
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 4
No 214
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=77.36 E-value=0.83 Score=49.53 Aligned_cols=78 Identities=12% Similarity=0.022 Sum_probs=49.6
Q ss_pred cccCCCEEEEEEEEEcCCC-ceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecC
Q 002487 808 VVKVGDLVDVKLIEVNDKG-QLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKV 886 (916)
Q Consensus 808 ~~kvGd~V~VKVi~iD~~g-kI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~ 886 (916)
.=.+|+.|-++|-.|-.-| .+.| ++-| ... .-....++.+|+|.+ -.+.+++||+|-|+|+++|+
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L-----~EY~--g~E-g~ihiSEvas~wVkn------Ird~vkegqkvV~kVlrVd~ 73 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVEL-----DEYP--GKE-GFIHISEVASGWVKN------IRDYVKEGQKVVAKVLRVDP 73 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEe-----eccC--Cee-eeEEHHHHHHHHHHH------HHHHhhcCCeEEEEEEEEcC
Confidence 3478999999999996644 2322 1111 111 011222233333333 34678999999999999999
Q ss_pred CCCcccCCCCCCC
Q 002487 887 FKRPASPAKDRPY 899 (916)
Q Consensus 887 ek~rIsL~~~~~~ 899 (916)
+++.|-||+++=-
T Consensus 74 ~rg~IDLSlkrV~ 86 (269)
T COG1093 74 KRGHIDLSLKRVT 86 (269)
T ss_pred CCCeEeeehhhCC
Confidence 9999999987433
No 215
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=76.48 E-value=12 Score=33.38 Aligned_cols=66 Identities=29% Similarity=0.405 Sum_probs=49.1
Q ss_pred CCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 762 TVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
+.+++ .| +|.+.-+-|-| |++.+|..-+-|+|-= .+.-.-.+.+||.|.|..-..|. +|+|..-.+
T Consensus 5 d~~e~-~g-~V~e~L~~~~f~v~~edg~~~~ahI~GK----mr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 5 DEIEM-EG-TVIEMLPNGRFRVELENGHERLAHISGK----MRKNRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred cccEE-EE-EEEEecCCCEEEEEecCCcEEEEEccCc----chheeEEeCCCCEEEEEecccccccccEEEEec
Confidence 34554 47 89999998876 9999999999998732 22112247789999999999986 888876544
No 216
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=76.38 E-value=9.9 Score=34.59 Aligned_cols=65 Identities=23% Similarity=0.294 Sum_probs=48.3
Q ss_pred CCCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
++.|+++ | +|+.....+.| |++.+|..-++|++- +.++ .--++.||.|.|.....+. +|+|..-+
T Consensus 2 p~e~q~~-g-~V~~~lG~~~~~V~~~dG~~~la~ipg----K~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r~ 68 (83)
T smart00652 2 KEDGQEI-A-QVVKMLGNGRLEVMCADGKERLARIPG----KMRK-KVWIRRGDIVLVDPWDFQDVKADIIYKY 68 (83)
T ss_pred CCCCcEE-E-EEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEecCCCCCEEEEEEEe
Confidence 4567766 6 89999999987 688889999999863 2332 3358899999998877665 66665443
No 217
>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=75.82 E-value=2 Score=35.11 Aligned_cols=29 Identities=14% Similarity=0.023 Sum_probs=25.3
Q ss_pred CCCCCCCCCCcEEEeEeeecCCCCcccCC
Q 002487 866 SPKPKGSSSEDTVLPHKKVKVFKRPASPA 894 (916)
Q Consensus 866 ~p~~~~k~Gd~V~v~I~~id~ek~rIsL~ 894 (916)
++...+++||.|.++|.++|++++++.|+
T Consensus 37 ~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 37 DPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 45567999999999999999999988775
No 218
>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=73.99 E-value=4.2 Score=42.02 Aligned_cols=34 Identities=6% Similarity=-0.095 Sum_probs=29.7
Q ss_pred CCCCCCCCCcEEEeEeeec-----CCCCcccCCCCCCCC
Q 002487 867 PKPKGSSSEDTVLPHKKVK-----VFKRPASPAKDRPYS 900 (916)
Q Consensus 867 p~~~~k~Gd~V~v~I~~id-----~ek~rIsL~~~~~~~ 900 (916)
....++.||+|+++|.+++ ++..+|.+++++||-
T Consensus 132 ~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k~~~L 170 (179)
T TIGR00448 132 TKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQPLL 170 (179)
T ss_pred CCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEeccCcC
Confidence 3467999999999999998 677899999999886
No 219
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=70.52 E-value=16 Score=44.22 Aligned_cols=64 Identities=20% Similarity=0.346 Sum_probs=49.5
Q ss_pred eEEEEeecc-ceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeEEecccccHHHHHHHHHhhhc
Q 002487 695 LIHIMKVKP-EKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKITAKDLSSLEKSKAIISNLTM 759 (916)
Q Consensus 695 ~i~~~~I~~-~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I~~~~~~~~~~a~~~i~~l~~ 759 (916)
.+.++.+|. +--|.+||..|.|||.+..-|||. |=|||. +.|.||+-|..--+-|+..++.+..
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd-~iiddtp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVD-LIIDDTPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCce-EEEcCCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 455667777 456899999999999999999997 667775 5778888788766666666666654
No 220
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=69.59 E-value=12 Score=37.98 Aligned_cols=65 Identities=25% Similarity=0.400 Sum_probs=49.3
Q ss_pred CCCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
++.|++| | +|+.....|.| |.+.+|..-|+|++-= .+. .-.+..||.|.|..-..+. +++|..-+
T Consensus 29 ~eegq~~-g-~V~~~LGn~~f~V~c~dG~~rLa~I~GK----mRK-~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 29 KEEGQEY-A-QVLRMLGNGRLEAYCFDGVKRLCHIRGK----MRK-RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred CCCCcEE-E-EEEEEcCCCEEEEEECCCCEEEEEeecc----cee-eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 4679988 5 89999999987 7888899999998742 222 2358899999998766665 67776654
No 221
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=69.13 E-value=3.2 Score=47.53 Aligned_cols=62 Identities=23% Similarity=0.362 Sum_probs=41.9
Q ss_pred HHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 666 QAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 666 ~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
.+-+||..||+.|.+.-.... +..-.|+ .+.-.-..++.+||..|.++|+|..+||.+ |.|.
T Consensus 255 g~s~Ac~~ILeimqkEA~~~k--~~~e~pL--k~lAHN~lvGRLIGKeGrnlKkIeq~TgTk-ITis 316 (584)
T KOG2193|consen 255 GTSKACKMILEIMQKEAVDDK--VAEEIPL--KILAHNNLVGRLIGKEGRNLKKIEQDTGTK-ITIS 316 (584)
T ss_pred chHHHHHHHHHHHHHhhhccc--hhhhcch--hhhhhcchhhhhhhhccccHHHHHhhcCCc-eeee
Confidence 456788899999976443321 2222231 112233568999999999999999999997 6554
No 222
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=68.58 E-value=5.5 Score=41.72 Aligned_cols=59 Identities=31% Similarity=0.377 Sum_probs=46.0
Q ss_pred eeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHHHHHHHhhhcCCCCCcEE
Q 002487 706 INLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIY 767 (916)
Q Consensus 706 i~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~ 767 (916)
.+.+||++|+|-+.|.+-|++. |.+- +.+|.|.+. .+..+.|++.++.+...-+.|.+|
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~-I~V~-g~tVaiiG~-~~~v~iAr~AVemli~G~~h~~Vy 171 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVY-ISVY-GKTVAIIGG-FEQVEIAREAVEMLINGAPHGKVY 171 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCe-EEEe-CcEEEEecC-hhhhHHHHHHHHHHHcCCCchhHH
Confidence 5789999999999999999996 7664 557777654 456778888888887766666665
No 223
>PRK00106 hypothetical protein; Provisional
Probab=68.52 E-value=20 Score=43.49 Aligned_cols=64 Identities=19% Similarity=0.314 Sum_probs=49.9
Q ss_pred eEEEEeecc-ceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeEEecccccHHHHHHHHHhhhc
Q 002487 695 LIHIMKVKP-EKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKITAKDLSSLEKSKAIISNLTM 759 (916)
Q Consensus 695 ~i~~~~I~~-~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I~~~~~~~~~~a~~~i~~l~~ 759 (916)
.+.++.+|. +--|.+||..|.|||.+..-|||. +=|||+ ..|.||+-|.---+-|+..++.+..
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvd-liiddtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGID-VIIDDTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCce-EEEcCCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 455667776 556899999999999999999997 667765 6778888888776777666666654
No 224
>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=68.41 E-value=8.5 Score=40.89 Aligned_cols=117 Identities=19% Similarity=0.192 Sum_probs=68.3
Q ss_pred HHHHHHHhCCc-eeccCCCccee--EEecccccH-HHHHHHHHhhhcCCCC--CcEEEccEEEEEecceEEEEECCCeee
Q 002487 717 VKSIIEETGVE-AIDTEDDGTVK--ITAKDLSSL-EKSKAIISNLTMVPTV--GDIYRNCEIKSIAPYGVFVEIAPGREG 790 (916)
Q Consensus 717 Ik~I~~~~~v~-~Idi~d~g~v~--I~~~~~~~~-~~a~~~i~~l~~~~~v--G~i~~G~~V~~I~~fGaFVel~~g~eG 790 (916)
++..+.++.|+ .|++.+++-++ +.+.|.+.. +..++.+-.+...++. |++|.| ++.++.+-|.-+++. |+..
T Consensus 22 v~n~lgdLdV~~~i~~~~~~wv~vtl~GeD~eva~Nll~eefGei~~~le~v~Ge~y~G-~l~s~~~~G~~~~v~-G~~~ 99 (225)
T PF09883_consen 22 VENDLGDLDVEWDIGITKDDWVKVTLEGEDEEVAANLLREEFGEIVYSLEPVKGETYVG-TLISWDEDGYGVDVD-GIFV 99 (225)
T ss_pred HHHhhcCeeEEEEeccccCCceEEEEecCcHHHHHHHHHHHhCCCCchhcccCCceEEE-EEEeecccceEEEee-cccc
Confidence 44444445554 24445666554 444443321 1222333333333455 999999 999998888888886 7777
Q ss_pred EEeccccCc---ccccCccccccCCC--EEEEEEEEEcCCCceEEEEeec
Q 002487 791 LCHISELSS---NWLAKAEDVVKVGD--LVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 791 lvhiSels~---~~v~~~~~~~kvGd--~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
-++.++|.. ..++...+.|-.=| .|+++|+.++.....+||=++.
T Consensus 100 ~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~ 149 (225)
T PF09883_consen 100 PIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQV 149 (225)
T ss_pred cCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHH
Confidence 888888732 22333333443333 4558888887666666665554
No 225
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=68.24 E-value=7.9 Score=46.28 Aligned_cols=62 Identities=27% Similarity=0.437 Sum_probs=45.9
Q ss_pred CeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCC-------CcceeEEecccccHHHHHHHHHhh
Q 002487 694 PLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED-------DGTVKITAKDLSSLEKSKAIISNL 757 (916)
Q Consensus 694 P~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d-------~g~v~I~~~~~~~~~~a~~~i~~l 757 (916)
|..-.+-|+..+++.+||.||+.||+|.++||++ |-+-. +..|.|++.. ++..+|...|-.+
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~-I~v~~~~lP~ster~V~IsG~~-~av~~al~~Is~~ 205 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAK-IRVSSDMLPNSTERAVTISGEP-DAVKKALVQISSR 205 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCce-EEecCCCCCcccceeEEEcCch-HHHHHHHHHHHHH
Confidence 6778888999999999999999999999999997 55542 2345666543 4455555555443
No 226
>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=68.21 E-value=14 Score=33.19 Aligned_cols=59 Identities=22% Similarity=0.344 Sum_probs=44.8
Q ss_pred EccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 768 RNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 768 ~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
.| +|+.....+.| |++.+|..-++|++- +.++ .-.++.||.|.|.....|. +|+|..-+
T Consensus 3 ~g-~V~~~~g~~~~~V~~~~g~~~la~i~g----K~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 3 YG-QVEKMLGNGRLEVRCFDGKKRLCRIRG----KMRK-RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred EE-EEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 46 89999999887 788889999999873 2333 3468899999999888776 67665433
No 227
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=67.99 E-value=0.53 Score=53.95 Aligned_cols=50 Identities=12% Similarity=0.070 Sum_probs=35.3
Q ss_pred CCCCcEEEeeccc-----------------cccCCCCCCCCCCCcEEEeEeeecCCCCc--ccCCCCCC
Q 002487 849 PTGDPTKDAAASD-----------------KLVGSPKPKGSSSEDTVLPHKKVKVFKRP--ASPAKDRP 898 (916)
Q Consensus 849 ~~G~vv~g~Vs~i-----------------~~v~~p~~~~k~Gd~V~v~I~~id~ek~r--IsL~~~~~ 898 (916)
+.|++++|+|... ..-..|+..|++||+++|.|++++.+++. |.||...|
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p 201 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTHP 201 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCCH
Confidence 6777777776221 01123578899999999999999976654 66776544
No 228
>PLN00208 translation initiation factor (eIF); Provisional
Probab=67.59 E-value=14 Score=37.18 Aligned_cols=65 Identities=25% Similarity=0.367 Sum_probs=49.0
Q ss_pred CCCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEE
Q 002487 761 PTVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSR 832 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~ 832 (916)
++.|++| | +|+.....|.| |.+.+|..-|+|++-= .+. .-.++.||.|.|.+-..+. ++.|..-+
T Consensus 29 p~egq~~-g-~V~~~lGn~~~~V~c~dG~~rLa~IpGK----mRK-rIWI~~GD~VlVel~~~d~~KgdIv~ry 95 (145)
T PLN00208 29 KEDGQEY-A-QVLRMLGNGRCEALCIDGTKRLCHIRGK----MRK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
T ss_pred CCCCcEE-E-EEEEEcCCCEEEEEECCCCEEEEEEecc----cee-eEEecCCCEEEEEccCCCCCEEEEEEEc
Confidence 4679988 5 89999999987 7888899999998742 222 2358899999999777665 66665543
No 229
>PRK12704 phosphodiesterase; Provisional
Probab=65.98 E-value=25 Score=42.50 Aligned_cols=64 Identities=20% Similarity=0.342 Sum_probs=48.7
Q ss_pred eEEEEeecc-ceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeEEecccccHHHHHHHHHhhhc
Q 002487 695 LIHIMKVKP-EKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKITAKDLSSLEKSKAIISNLTM 759 (916)
Q Consensus 695 ~i~~~~I~~-~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I~~~~~~~~~~a~~~i~~l~~ 759 (916)
.+.++.+|. +--|.+||..|.|||.+..-|||. |=|||. +.|.+++-+...-+.|+..++.+..
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd-~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVD-LIIDDTPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCe-EEEcCCCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 455667776 456899999999999999999997 668876 6777888777665666666666554
No 230
>PRK13764 ATPase; Provisional
Probab=65.94 E-value=3.7 Score=50.27 Aligned_cols=144 Identities=17% Similarity=0.250 Sum_probs=80.4
Q ss_pred hhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEec-ccccH
Q 002487 669 DGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAK-DLSSL 747 (916)
Q Consensus 669 ~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~-~~~~~ 747 (916)
-+...|...++..+..+ .++.--.+--..+.|+.+.|..+||.||++|.+|..++|.. ||+.....-..... +....
T Consensus 456 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~-i~v~~~~~~~~~~~~~~~~~ 533 (602)
T PRK13764 456 LAEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGID-IDVRPLDEEPGEEAEEGEEV 533 (602)
T ss_pred HHHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCc-eEEEEccccccccccccCcc
Confidence 34455666676766443 22322244455678999999999999999999999999996 88762111000000 00000
Q ss_pred HHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEE-CCCeeeEEeccccCcccccCccccccCCCEEEEEE
Q 002487 748 EKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEI-APGREGLCHISELSSNWLAKAEDVVKVGDLVDVKL 819 (916)
Q Consensus 748 ~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel-~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKV 819 (916)
.. .+ ..-..-+.+|.-|.| +...|.--|=|+-- ..+..|-+|++.=+. --+...+.++.|..|.+++
T Consensus 534 ~~-~~--~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~a~~~~~g~i~~~~~~~-~~~~~~~~~~~~~~i~~~~ 601 (602)
T PRK13764 534 TV-EE--TKKHVILIVGPDYAG-KTVDVYAGGEYLFTATVSRKGEIKVAKNSA-IAKELLRAIDEGEDIRVRP 601 (602)
T ss_pred ce-EE--eccEEEEEcChhhCC-CeEEEEECCEEEEEEEcCCCceEEeccCCh-HHHHHHHHHhCCCcEEEee
Confidence 00 00 000011355666666 66666555544433 236678888765332 1233445677788877764
No 231
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=64.20 E-value=20 Score=37.78 Aligned_cols=54 Identities=26% Similarity=0.455 Sum_probs=41.7
Q ss_pred ceeeeeecCCchhHHHHHHHhCCceeccCCCcce---eEEecccccHHHHHHHHHhhh
Q 002487 704 EKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTV---KITAKDLSSLEKSKAIISNLT 758 (916)
Q Consensus 704 ~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v---~I~~~~~~~~~~a~~~i~~l~ 758 (916)
..++-+|||-|.|.+++.+.++++ |-|...|.+ .+++...+.+..+.+.+.++.
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~ak-IaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI 219 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAK-IAIRGSGSVKEGKISSDTPESLKNAEAVLHCLI 219 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCe-EEEecccccccCcccccCchhhhhhHHhHHHHh
Confidence 468999999999999999999997 888866655 466655666666666666654
No 232
>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=63.88 E-value=3.9 Score=35.99 Aligned_cols=29 Identities=7% Similarity=-0.080 Sum_probs=25.3
Q ss_pred CCCCCCCCCcEEEeEeeecCCCCcccCCC
Q 002487 867 PKPKGSSSEDTVLPHKKVKVFKRPASPAK 895 (916)
Q Consensus 867 p~~~~k~Gd~V~v~I~~id~ek~rIsL~~ 895 (916)
+...+++||+|+|+|.++|.++++|.++.
T Consensus 54 ~~~~~~~gd~v~v~v~~vd~~~~~i~~~l 82 (83)
T cd04471 54 TGKVFRLGDKVKVRVVRVDLDRRKIDFEL 82 (83)
T ss_pred CCCEEcCCCEEEEEEEEeccccCEEEEEE
Confidence 34678999999999999999999998763
No 233
>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=63.33 E-value=3.4 Score=38.27 Aligned_cols=34 Identities=9% Similarity=-0.107 Sum_probs=28.7
Q ss_pred CCCCCCCCCcEEEeEeeecCCC-----CcccCCCCCCCC
Q 002487 867 PKPKGSSSEDTVLPHKKVKVFK-----RPASPAKDRPYS 900 (916)
Q Consensus 867 p~~~~k~Gd~V~v~I~~id~ek-----~rIsL~~~~~~~ 900 (916)
+...++.||.|.|+|.++|.+. .+|.|++++++.
T Consensus 50 ~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~~~ 88 (99)
T cd04460 50 TKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQPGL 88 (99)
T ss_pred cCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEecCCC
Confidence 3467899999999999999885 479999887765
No 234
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=61.85 E-value=6.8 Score=45.95 Aligned_cols=60 Identities=27% Similarity=0.405 Sum_probs=46.7
Q ss_pred hHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 671 RRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 671 ~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
-..|...++..++.+ .++.--++....+.+|++.|+.+||.+|++|++|..++|.+ |++.
T Consensus 463 ~~~i~~~i~r~~p~~-~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~-I~v~ 522 (604)
T COG1855 463 EEEIEREIKRYLPGD-VEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIK-IDVK 522 (604)
T ss_pred HHHHHHHHHHhCCCC-ceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCc-eEEE
Confidence 345666677777762 34444456777889999999999999999999999999986 7764
No 235
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=61.46 E-value=6.1 Score=42.82 Aligned_cols=75 Identities=21% Similarity=0.345 Sum_probs=61.3
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcc----cc------cCccccccCCCEEEEEEEEEcCCCceE
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSN----WL------AKAEDVVKVGDLVDVKLIEVNDKGQLR 829 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~----~v------~~~~~~~kvGd~V~VKVi~iD~~gkI~ 829 (916)
.+++|+++-| +|..|...-+=|++....++.+..|.+.-- |- ...+++|+.||.|.+.|-.+-.+|-+.
T Consensus 82 ~pEvGDvVVg-RV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~s 160 (301)
T KOG3013|consen 82 APEVGDVVVG-RVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLS 160 (301)
T ss_pred CCccCCEEEE-EeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEE
Confidence 3699999999 999999999999999889999998877531 11 124578999999999998887789888
Q ss_pred EEEeec
Q 002487 830 LSRRAL 835 (916)
Q Consensus 830 LS~K~~ 835 (916)
|-.+.+
T Consensus 161 LhTRS~ 166 (301)
T KOG3013|consen 161 LHTRSL 166 (301)
T ss_pred EEecch
Confidence 876654
No 236
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=61.30 E-value=45 Score=29.69 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=41.7
Q ss_pred EccEEEEEec-ceE-EEEEC-CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEeec
Q 002487 768 RNCEIKSIAP-YGV-FVEIA-PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 768 ~G~~V~~I~~-fGa-FVel~-~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
+| +|+...+ .|. |+... ++.+-|+|+|.|...-. ..+..||.|...+.. +.+|+-...+..+
T Consensus 3 ~G-~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~-~~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KG-TVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQ-GPKGNHASVIVPV 67 (74)
T ss_pred Ce-EEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE-CCCCceeeEEEEC
Confidence 36 7777644 444 66654 46899999999974432 357899999998776 4466655555444
No 237
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=59.05 E-value=17 Score=33.48 Aligned_cols=75 Identities=8% Similarity=-0.063 Sum_probs=44.0
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEe--eccccc--cC--CCCCCCCCCCcEEEeEee
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDA--AASDKL--VG--SPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~--Vs~i~~--v~--~p~~~~k~Gd~V~v~I~~ 883 (916)
++||.|.++|.++.. .+..+.+-.....+-... ..|. ++++.. .. +..+.|++||-|.++|.+
T Consensus 5 ~~GDiVig~V~~v~~-~~~~v~I~~v~~~~l~~~----------~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 5 KVGSIVIARVTRINP-RFAKVDILCVGGRPLKES----------FRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCEEEEEEEEEcC-CEEEEEEEEecCeecCCC----------cccEEEHHHccccccchHHHHhhcCCCCEEEEEEEE
Confidence 789999999999964 345555544332211111 1222 222211 11 244678999999999999
Q ss_pred ecCCCCcccCCCC
Q 002487 884 VKVFKRPASPAKD 896 (916)
Q Consensus 884 id~ek~rIsL~~~ 896 (916)
++.. +..-|+++
T Consensus 74 ~~~~-~~~~Lst~ 85 (92)
T cd05791 74 LGDA-SSYYLSTA 85 (92)
T ss_pred cCCC-CCcEEEec
Confidence 9863 33555544
No 238
>PRK09890 cold shock protein CspG; Provisional
Probab=58.71 E-value=54 Score=28.74 Aligned_cols=55 Identities=15% Similarity=0.305 Sum_probs=37.6
Q ss_pred EEccEEEEEec-ceE-EEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCc
Q 002487 767 YRNCEIKSIAP-YGV-FVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQ 827 (916)
Q Consensus 767 ~~G~~V~~I~~-fGa-FVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gk 827 (916)
++| +|+...+ .|. |++-.. +.+-|+|+|.|...-. ..+.+||.|...+.. +.+|.
T Consensus 5 ~~G-~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~-~~~G~ 62 (70)
T PRK09890 5 MTG-LVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ-GQRGP 62 (70)
T ss_pred ceE-EEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 468 8888743 343 666654 4799999999975532 357889999996654 34554
No 239
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=57.78 E-value=18 Score=39.24 Aligned_cols=53 Identities=28% Similarity=0.463 Sum_probs=44.8
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEEecccccHHHH
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKS 750 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~~~~a 750 (916)
..++|+|.|+..+||.+|..++-+.+++++. |=+..+|.|-|...+......+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~-I~VG~NG~IWV~~~~~~~e~~~ 200 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCE-IIVGQNGRIWVDGENESLEELA 200 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeE-EEEecCCEEEecCCCcchHHHH
Confidence 3568999999999999999999999999996 7777899999998887433333
No 240
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=56.96 E-value=38 Score=31.93 Aligned_cols=62 Identities=29% Similarity=0.326 Sum_probs=44.2
Q ss_pred CCCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEc-C-CCceEE
Q 002487 762 TVGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVN-D-KGQLRL 830 (916)
Q Consensus 762 ~vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD-~-~gkI~L 830 (916)
+.|+++ | +|+.....+.| |++.+|..-|+|++- ++++ .-.++.||.|.|...+.. . +|+|..
T Consensus 17 ~e~e~~-g-~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~iwI~~GD~VlVsp~d~~~~~kg~Iv~ 81 (99)
T TIGR00523 17 EEGEIL-G-VIEQMLGAGRVKVRCLDGKTRLGRIPG----KLKK-RIWIREGDVVIVKPWEFQGDDKCDIVW 81 (99)
T ss_pred CCCEEE-E-EEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEEccCCCCccEEEEE
Confidence 467766 6 99999999987 688889999999873 2332 346889999999655554 2 454443
No 241
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=56.84 E-value=31 Score=30.17 Aligned_cols=51 Identities=16% Similarity=0.338 Sum_probs=35.9
Q ss_pred EEEccEEEEEec-ceE-EEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEE
Q 002487 766 IYRNCEIKSIAP-YGV-FVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIE 821 (916)
Q Consensus 766 i~~G~~V~~I~~-fGa-FVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~ 821 (916)
.++| +|+...+ .|. |+.-.. +-+-|+|+|.|..... ..+.+||.|...+..
T Consensus 3 ~~~G-~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKG-NVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITN 56 (69)
T ss_pred ccce-EEEEEeCCCCcEEEecCCCCeeEEEEeecccccCC----CCCCCCCEEEEEEEE
Confidence 4677 8888743 343 566544 5689999999975432 347889999997765
No 242
>PRK15464 cold shock-like protein CspH; Provisional
Probab=56.67 E-value=26 Score=30.82 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=39.0
Q ss_pred EEccEEEEEec-ceE-EEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCc
Q 002487 767 YRNCEIKSIAP-YGV-FVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQ 827 (916)
Q Consensus 767 ~~G~~V~~I~~-fGa-FVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gk 827 (916)
++| +|+...+ .|. |+.-.. +.+-|+|+|.|..... ..+.+||.|...+..= ++|.
T Consensus 5 ~~G-~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~~-~kG~ 62 (70)
T PRK15464 5 MTG-IVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVNG-LRGP 62 (70)
T ss_pred ceE-EEEEEECCCCeEEEccCCCCccEEEEehhehhcCC----CCCCCCCEEEEEEEEC-CCCc
Confidence 478 8888854 454 676654 5789999999964432 3478999999988763 3453
No 243
>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=56.12 E-value=32 Score=31.42 Aligned_cols=70 Identities=7% Similarity=-0.052 Sum_probs=43.9
Q ss_pred ccccCCCEEEEEEEEEcCC-CceEEEEeecCCCCCCCCCCCCCCCCCcEEEee-----ccc--cccCCCCCCCCCCCcEE
Q 002487 807 DVVKVGDLVDVKLIEVNDK-GQLRLSRRALLPEADAENPPVKLPTGDPTKDAA-----ASD--KLVGSPKPKGSSSEDTV 878 (916)
Q Consensus 807 ~~~kvGd~V~VKVi~iD~~-gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~V-----s~i--~~v~~p~~~~k~Gd~V~ 878 (916)
..+++|+.+.++|.++.+. .-.-+.+- .| ..|-+ +|. .++.++.+.+++||+|.
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~----------------~g--~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~ 64 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIG----------------LG--KNGFLHLSDILPAYFKKHKKIAKLLKEGQEIL 64 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeC----------------CC--CEEEEEhHHcCchhccccCCHHHcCCCCCEEE
Confidence 3467899999999999763 12222221 01 11221 221 34556677899999999
Q ss_pred EeEeeecCCCCcccCC
Q 002487 879 LPHKKVKVFKRPASPA 894 (916)
Q Consensus 879 v~I~~id~ek~rIsL~ 894 (916)
|+|++.....+--.|.
T Consensus 65 VqV~~~~~~~K~~~lt 80 (88)
T cd04453 65 VQVVKEPIGTKGPRLT 80 (88)
T ss_pred EEEEEecCCCCCceEE
Confidence 9999977666654443
No 244
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.01 E-value=29 Score=36.77 Aligned_cols=99 Identities=19% Similarity=0.309 Sum_probs=61.2
Q ss_pred ceeEEeccccc-HHHHHHHHHhhh--cCCCCCcEEEccEEEEEe--cceEEEEECC----CeeeEEeccccCcccccCc-
Q 002487 736 TVKITAKDLSS-LEKSKAIISNLT--MVPTVGDIYRNCEIKSIA--PYGVFVEIAP----GREGLCHISELSSNWLAKA- 805 (916)
Q Consensus 736 ~v~I~~~~~~~-~~~a~~~i~~l~--~~~~vG~i~~G~~V~~I~--~fGaFVel~~----g~eGlvhiSels~~~v~~~- 805 (916)
++++-+.+.+. .+...+.+..+. .+++.|++|-| +..... .||++|.++- -.++|+|.-+|....-++|
T Consensus 45 ~itleGed~e~sanli~eefgei~sl~~~~~Gdv~vG-rl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpv 123 (247)
T COG4044 45 KITLEGEDEEVSANLIVEEFGEIPSLSKVEEGDVYVG-RLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPV 123 (247)
T ss_pred EEEEECccHHHHHHHHHHHhCCCCccccCCCCcEEEE-EEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcH
Confidence 44555555432 222344444454 56799999999 999985 4788888842 3689999988876555444
Q ss_pred ---ccccc--CCCEEEEEEEEEcC-CCce--EEEEeec
Q 002487 806 ---EDVVK--VGDLVDVKLIEVND-KGQL--RLSRRAL 835 (916)
Q Consensus 806 ---~~~~k--vGd~V~VKVi~iD~-~gkI--~LS~K~~ 835 (916)
...|- .--.|+|-|.++|+ .+.| .|+-|++
T Consensus 124 rqi~r~FG~V~~lPveV~V~evnk~~~EIea~ltd~qv 161 (247)
T COG4044 124 RQIIRRFGWVDHLPVEVEVNEVNKLAQEIEARLTDKQV 161 (247)
T ss_pred HHHHHHcCCcccCceEEEEEeccchhhhhhhhhhHHHH
Confidence 22332 23456777888876 4544 3444443
No 245
>PRK00468 hypothetical protein; Provisional
Probab=55.25 E-value=11 Score=33.72 Aligned_cols=30 Identities=33% Similarity=0.520 Sum_probs=25.1
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHh
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEET 724 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~ 724 (916)
....+.++++-++.+||.+|++|+.|..-.
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 455678899999999999999999886443
No 246
>PRK15463 cold shock-like protein CspF; Provisional
Probab=55.19 E-value=29 Score=30.48 Aligned_cols=54 Identities=19% Similarity=0.207 Sum_probs=38.1
Q ss_pred EEccEEEEEec-ceE-EEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCC
Q 002487 767 YRNCEIKSIAP-YGV-FVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKG 826 (916)
Q Consensus 767 ~~G~~V~~I~~-fGa-FVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~g 826 (916)
++| +|+...+ .|. |++-.. +.+-|+|+|.|..... ..+++||.|...+.. +.+|
T Consensus 5 ~~G-~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~-~~~G 61 (70)
T PRK15463 5 MTG-IVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRIN-GLRG 61 (70)
T ss_pred ceE-EEEEEeCCCceEEEecCCCCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE-CCCC
Confidence 467 8888854 454 676644 5789999999975432 247899999997665 3344
No 247
>PRK02821 hypothetical protein; Provisional
Probab=52.84 E-value=12 Score=33.72 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=26.0
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhC
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETG 725 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~ 725 (916)
....+.++++-++.+||.+|++|+.|..-..
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 4567788999999999999999998875544
No 248
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=52.75 E-value=13 Score=33.25 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=24.6
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHh
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEET 724 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~ 724 (916)
....+.+.++-++++||.+|++|+.|.--.
T Consensus 30 ~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 30 VTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred EEEEEEECcccccceecCCChhHHHHHHHH
Confidence 445668899999999999999999986443
No 249
>PF08121 Toxin_33: Waglerin family; InterPro: IPR012637 This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri (Wagler's pit viper) (Tropidolaemus wagleri). Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity for the alpha-epsilon interface binding site of the mouse nAChR [].; GO: 0030550 acetylcholine receptor inhibitor activity, 0005576 extracellular region
Probab=51.71 E-value=6.5 Score=25.95 Aligned_cols=11 Identities=45% Similarity=1.150 Sum_probs=8.2
Q ss_pred ceeecccCCCC
Q 002487 8 GLHIRPCYPHS 18 (916)
Q Consensus 8 ~~~~~~~~~~~ 18 (916)
--.+|||||.-
T Consensus 3 kpdlrpcyppc 13 (22)
T PF08121_consen 3 KPDLRPCYPPC 13 (22)
T ss_pred CCccccCCCCc
Confidence 34689999953
No 250
>PRK10943 cold shock-like protein CspC; Provisional
Probab=51.43 E-value=41 Score=29.39 Aligned_cols=51 Identities=18% Similarity=0.344 Sum_probs=36.4
Q ss_pred EEEccEEEEEec-ceE-EEEEC-CCeeeEEeccccCcccccCccccccCCCEEEEEEEE
Q 002487 766 IYRNCEIKSIAP-YGV-FVEIA-PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIE 821 (916)
Q Consensus 766 i~~G~~V~~I~~-fGa-FVel~-~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~ 821 (916)
.++| +|+...+ .|. |++-. ++.+-|+|+|.+..... ..+.+||.|...+..
T Consensus 3 ~~~G-~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKG-QVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred ccce-EEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 3577 8888744 343 66654 45799999999975432 357889999997766
No 251
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=51.36 E-value=48 Score=29.87 Aligned_cols=58 Identities=28% Similarity=0.273 Sum_probs=43.2
Q ss_pred ccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEE-cC-CCceEEEE
Q 002487 769 NCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEV-ND-KGQLRLSR 832 (916)
Q Consensus 769 G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~i-D~-~gkI~LS~ 832 (916)
| +|+.....+.| |++.+|..-|+|++- +.++- --++.||.|.|..... |. +|.|..-+
T Consensus 4 ~-~V~~~lG~~~~~V~~~dg~~~l~~i~g----K~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~r~ 64 (78)
T cd04456 4 V-RVLRMLGNNRHEVECADGQRRLVSIPG----KLRKN-IWIKRGDFLIVDPIEEGEDVKADIIFVY 64 (78)
T ss_pred E-EEEEECCCCEEEEEECCCCEEEEEEch----hhccC-EEEcCCCEEEEEecccCCCceEEEEEEe
Confidence 5 89999999987 788889999999874 22221 3588999999988887 45 66665433
No 252
>PRK12705 hypothetical protein; Provisional
Probab=50.91 E-value=32 Score=41.50 Aligned_cols=65 Identities=18% Similarity=0.287 Sum_probs=47.5
Q ss_pred eEEEEeecc-ceeeeeecCCchhHHHHHHHhCCceeccCCC-cceeEEecccccHHHHHHHHHhhhcC
Q 002487 695 LIHIMKVKP-EKINLIIGSGGKKVKSIIEETGVEAIDTEDD-GTVKITAKDLSSLEKSKAIISNLTMV 760 (916)
Q Consensus 695 ~i~~~~I~~-~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~-g~v~I~~~~~~~~~~a~~~i~~l~~~ 760 (916)
.+.++++|- +--|.+||..|.|||.+...||+. +-|||. ..|.++.-+...-+.+...++.++.+
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvd-liiddtp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVD-LIIDDTPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCc-eEecCCccchhhcccCccchHHHHHHHHHHHhc
Confidence 445556665 446899999999999999999998 667764 56677777776666666666665543
No 253
>PRK14998 cold shock-like protein CspD; Provisional
Probab=50.80 E-value=81 Score=27.97 Aligned_cols=60 Identities=18% Similarity=0.228 Sum_probs=39.9
Q ss_pred EccEEEEEec-ceE-EEEEC-CCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEEe
Q 002487 768 RNCEIKSIAP-YGV-FVEIA-PGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRR 833 (916)
Q Consensus 768 ~G~~V~~I~~-fGa-FVel~-~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K 833 (916)
+| +|+...+ .|. |+.-. ++.+-|+|+|.|..... ..+..||.|...+.. +.+|+-.....
T Consensus 3 ~G-~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G~~A~~V~ 65 (73)
T PRK14998 3 TG-TVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQ-GPKGNHASVIV 65 (73)
T ss_pred Ce-EEEEEeCCCceEEEecCCCCccEEEEeeeecccCC----CCCCCCCEEEEEEEE-CCCCceeEEEE
Confidence 36 7777644 443 66654 45799999999964432 457899999998876 34565444443
No 254
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=50.57 E-value=25 Score=36.51 Aligned_cols=33 Identities=12% Similarity=-0.062 Sum_probs=27.6
Q ss_pred CCCCCCCCcEEEeEeeecCCCC-----cccCCCCCCCC
Q 002487 868 KPKGSSSEDTVLPHKKVKVFKR-----PASPAKDRPYS 900 (916)
Q Consensus 868 ~~~~k~Gd~V~v~I~~id~ek~-----rIsL~~~~~~~ 900 (916)
...++.||.|.++|.+++.+.+ +|.+++++++-
T Consensus 133 ~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~~L 170 (187)
T PRK08563 133 KRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQPGL 170 (187)
T ss_pred CeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCCCC
Confidence 4568999999999999998764 78888887766
No 255
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=50.27 E-value=18 Score=31.18 Aligned_cols=59 Identities=25% Similarity=0.413 Sum_probs=38.5
Q ss_pred CCcEEEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCce
Q 002487 763 VGDIYRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQL 828 (916)
Q Consensus 763 vG~i~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI 828 (916)
.|+++ | +|+.....+.| |++.+|..-++|++-= +-+. -.++.||.|.|.+-..|. +|+|
T Consensus 2 e~e~~-~-~V~~~lG~~~~~V~~~dg~~~l~~i~gK---~r~~--iwI~~GD~V~V~~~~~d~~kG~I 62 (65)
T PF01176_consen 2 EGEVI-G-RVTEMLGNNLFEVECEDGEERLARIPGK---FRKR--IWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp TTEEE-E-EEEEEESSSEEEEEETTSEEEEEEE-HH---HHTC--C---TTEEEEEEESTTCTTEEEE
T ss_pred CcEEE-E-EEEEECCCCEEEEEeCCCCEEEEEeccc---eeee--EecCCCCEEEEEecccCCCeEEE
Confidence 45666 6 89999998877 8888899988887742 2221 258899999887754444 4444
No 256
>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=49.95 E-value=63 Score=30.69 Aligned_cols=55 Identities=13% Similarity=0.273 Sum_probs=45.0
Q ss_pred CCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEc
Q 002487 761 PTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVN 823 (916)
Q Consensus 761 ~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD 823 (916)
...|.++.| +|..|.+--+||+++....+.|...+... +.+..|..|.+++.+..
T Consensus 21 ~~~gk~V~G-~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 21 DPEGKIVIG-KIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred CccCCEEEE-EEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 368999999 99999999999999988899998655432 34778999998887754
No 257
>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=48.45 E-value=73 Score=26.94 Aligned_cols=49 Identities=27% Similarity=0.400 Sum_probs=35.3
Q ss_pred EccEEEEEec---ceEEEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEE
Q 002487 768 RNCEIKSIAP---YGVFVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEV 822 (916)
Q Consensus 768 ~G~~V~~I~~---fGaFVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~i 822 (916)
.| +|+...+ || |+.... +.+-++|.|++...- ...+++||.|...+..-
T Consensus 2 ~G-~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TG-TVKWFDDEKGFG-FITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cE-EEEEEECCCCeE-EEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 46 7777754 55 555544 789999999997542 24578999999977764
No 258
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=47.98 E-value=25 Score=38.38 Aligned_cols=59 Identities=24% Similarity=0.469 Sum_probs=43.5
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCceeccCC------CcceeEEecccccHHHHHHHHHhh
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED------DGTVKITAKDLSSLEKSKAIISNL 757 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d------~g~v~I~~~~~~~~~~a~~~i~~l 757 (916)
..+.|+.+.-+.+||.||..|+.|..|.|+. |.|++ |..+.|... ...++.|.....+-
T Consensus 317 aQvtip~dlggsiigkggqri~~ir~esGA~-IkidepleGsedrIitItGT-qdQIqnAQYLlQn~ 381 (390)
T KOG2192|consen 317 AQVTIPKDLGGSIIGKGGQRIKQIRHESGAS-IKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNS 381 (390)
T ss_pred eeEecccccCcceecccchhhhhhhhccCce-EEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHH
Confidence 4568899999999999999999999999996 88874 344555554 34456665544443
No 259
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=47.51 E-value=56 Score=35.88 Aligned_cols=31 Identities=32% Similarity=0.526 Sum_probs=26.0
Q ss_pred ceeeeeecCCchhHHHHHHHhCCceeccCCCc
Q 002487 704 EKINLIIGSGGKKVKSIIEETGVEAIDTEDDG 735 (916)
Q Consensus 704 ~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g 735 (916)
..|+.++||-|-++|.++++|+++ |-|...|
T Consensus 107 NFVGRILGPrGnSlkrLe~eTgCk-i~IrGrg 137 (259)
T KOG1588|consen 107 NFVGRILGPRGNSLKRLEEETGCK-IMIRGRG 137 (259)
T ss_pred ccccccccCCcchHHHHHHHHCCe-EEEecCC
Confidence 359999999999999999999997 6664433
No 260
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=45.51 E-value=59 Score=28.44 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=36.8
Q ss_pred EEccEEEEEe---cceEEEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCC
Q 002487 767 YRNCEIKSIA---PYGVFVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKG 826 (916)
Q Consensus 767 ~~G~~V~~I~---~fGaFVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~g 826 (916)
.+| +|+... .|| |++-.. +.+-|+|+|.|..... ..+++||.|...+.. +++|
T Consensus 5 ~~G-~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G 61 (70)
T PRK10354 5 MTG-IVKWFNADKGFG-FITPDDGSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES-GAKG 61 (70)
T ss_pred ceE-EEEEEeCCCCcE-EEecCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE-CCCC
Confidence 367 888874 355 566544 5789999999975422 357899999997665 3345
No 261
>COG1278 CspC Cold shock proteins [Transcription]
Probab=43.78 E-value=76 Score=27.89 Aligned_cols=47 Identities=19% Similarity=0.386 Sum_probs=31.3
Q ss_pred EEEEEec-ceE-EEEECCC-eeeEEeccccCcccccCccccccCCCEEEEEEEE
Q 002487 771 EIKSIAP-YGV-FVEIAPG-REGLCHISELSSNWLAKAEDVVKVGDLVDVKLIE 821 (916)
Q Consensus 771 ~V~~I~~-fGa-FVel~~g-~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~ 821 (916)
+|+-..+ .|. |+.=.+| .+-|+|+|.+.....+ .|..||.|...+..
T Consensus 5 tVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~~ 54 (67)
T COG1278 5 TVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFR----TLREGQKVEFEVEQ 54 (67)
T ss_pred eEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCc----ccCCCCEEEEEEec
Confidence 5655532 232 4444444 7999999999654433 47889999997765
No 262
>PRK01064 hypothetical protein; Provisional
Probab=43.15 E-value=26 Score=31.55 Aligned_cols=31 Identities=29% Similarity=0.370 Sum_probs=25.5
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhC
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETG 725 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~ 725 (916)
....+.++++.++.+||.+|++|+.|..-..
T Consensus 30 ~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 30 IIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred EEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 4566788999999999999999998875433
No 263
>PRK11642 exoribonuclease R; Provisional
Probab=41.98 E-value=62 Score=41.41 Aligned_cols=29 Identities=7% Similarity=-0.055 Sum_probs=25.7
Q ss_pred CCCCCCCCCcEEEeEeeecCCCCcccCCC
Q 002487 867 PKPKGSSSEDTVLPHKKVKVFKRPASPAK 895 (916)
Q Consensus 867 p~~~~k~Gd~V~v~I~~id~ek~rIsL~~ 895 (916)
....|+.||+|+|+|.++|.++++|.++.
T Consensus 696 ~~~~~~lGD~V~VkV~~vD~~~rkI~f~l 724 (813)
T PRK11642 696 SGQTYRLGDRVEVRVEAVNMDERKIDFSL 724 (813)
T ss_pred CCcEECCCCEEEEEEEEeecCCCeEEEEE
Confidence 34679999999999999999999998864
No 264
>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=41.52 E-value=1.1e+02 Score=26.65 Aligned_cols=54 Identities=19% Similarity=0.275 Sum_probs=35.9
Q ss_pred EccEEEEEec-ceE-EEEECC-CeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCc
Q 002487 768 RNCEIKSIAP-YGV-FVEIAP-GREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQ 827 (916)
Q Consensus 768 ~G~~V~~I~~-fGa-FVel~~-g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gk 827 (916)
+| +|+...+ .|. |+.-.. +.+-|+|+|.+..... ..+++||.|...+.. +.+|.
T Consensus 3 ~G-~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~-~~~G~ 59 (68)
T TIGR02381 3 IG-IVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ-GPKGA 59 (68)
T ss_pred Ce-EEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 36 7777632 344 666543 6899999999974432 357899999997655 33453
No 265
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=40.40 E-value=27 Score=34.84 Aligned_cols=37 Identities=22% Similarity=0.414 Sum_probs=31.5
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
....+.++++..+..||.+|+|++.+..-++-. +||+
T Consensus 99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~-~di~ 135 (140)
T PRK08406 99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRH-FDID 135 (140)
T ss_pred EEEEEEECccccchhhCCCCHHHHHHHHHhCCc-cCCe
Confidence 455678999999999999999999999888875 7764
No 266
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=40.10 E-value=4.7e+02 Score=27.58 Aligned_cols=73 Identities=10% Similarity=-0.042 Sum_probs=43.8
Q ss_pred cccccCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccc--cccCCCCCCCCCCCcEEEeEee
Q 002487 806 EDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASD--KLVGSPKPKGSSSEDTVLPHKK 883 (916)
Q Consensus 806 ~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i--~~v~~p~~~~k~Gd~V~v~I~~ 883 (916)
....|.||.|-.+|+++.. .+..+.+-.....+. ... ....| .-.|+++ ..+++.++-|++||-|.++|++
T Consensus 59 ~~~~K~GdiV~grV~~v~~-~~a~V~i~~ve~~~r-~~~--~~~~~---~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis 131 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVRE-QRALVRIVGVEGKER-ELA--TSGAA---DIHVSQVRDGYVEKLSDAFRIGDIVRARVIS 131 (188)
T ss_pred CCCCCCCCEEEEEEeeccc-eEEEEEEEEEecccc-cCC--CCcee---eEEEEecccccccccccccccccEEEEEEEe
Confidence 4568899999999999865 334444433333220 000 01111 1223333 3445556789999999999999
Q ss_pred ec
Q 002487 884 VK 885 (916)
Q Consensus 884 id 885 (916)
.-
T Consensus 132 ~~ 133 (188)
T COG1096 132 TG 133 (188)
T ss_pred cC
Confidence 85
No 267
>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=38.97 E-value=85 Score=27.01 Aligned_cols=63 Identities=19% Similarity=0.217 Sum_probs=38.4
Q ss_pred CcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 764 GDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 764 G~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
|+..+= .|..+++-|--+--.+.+.|+. +.-.+...-...+-+|+++++-|+.+|. +-++-+|
T Consensus 1 G~~L~L-vV~~~~edgsv~fs~g~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVS 64 (65)
T cd05700 1 GDQLKL-VVQDVTEDGSVMFSGGQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CceEEE-EEeeeccCCcEEEecCCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEe
Confidence 445554 5666666554444444455551 2223333344568899999999999997 6666555
No 268
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=36.61 E-value=60 Score=37.66 Aligned_cols=68 Identities=16% Similarity=0.119 Sum_probs=45.3
Q ss_pred cCCCEEEEEEEEEcCCCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecCCCC
Q 002487 810 KVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVFKR 889 (916)
Q Consensus 810 kvGd~V~VKVi~iD~~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~ 889 (916)
++|+.|.+.|..++.++-+.+-+-. +.+..+ +.-..|.+.|+.||.++|.|.+|+...+
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg~-------------------~ea~LP--~~eqip~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEIDE-------------------IRAVLP--MKNRIKGEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcCC-------------------eEEEeC--HHHcCCCCcCCCCCEEEEEEEEEecCCC
Confidence 5799999999999865544332210 111111 1112466889999999999999999876
Q ss_pred ---cccCCCCCC
Q 002487 890 ---PASPAKDRP 898 (916)
Q Consensus 890 ---rIsL~~~~~ 898 (916)
+|-||+..|
T Consensus 196 ~gp~IilSRt~p 207 (374)
T PRK12328 196 NGILIELSRTSP 207 (374)
T ss_pred CCCEEEEEcCCH
Confidence 666776544
No 269
>CHL00010 infA translation initiation factor 1
Probab=35.60 E-value=1.9e+02 Score=25.91 Aligned_cols=62 Identities=26% Similarity=0.321 Sum_probs=39.1
Q ss_pred EEccEEEEEecceEE-EEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEEEe
Q 002487 767 YRNCEIKSIAPYGVF-VEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLSRR 833 (916)
Q Consensus 767 ~~G~~V~~I~~fGaF-Vel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS~K 833 (916)
+.| +|+++...|.| |.+.+|..=.+|++-- ++.-.....+||.|.+.+-..+. +|.|..-.+
T Consensus 9 ~~G-~Vik~lg~~~y~V~~~~g~~~~c~~rGk----lr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~ 72 (78)
T CHL00010 9 MEG-LVTESLPNGMFRVRLDNGCQVLGYISGK----IRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred EEE-EEEEEcCCCEEEEEeCCCCEEEEEeccc----eecCCcccCCCCEEEEEEcccCCCeEEEEEEec
Confidence 567 88888765654 5666666666664432 22212336789999999755555 677766554
No 270
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=35.23 E-value=41 Score=29.83 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=25.6
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCC
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGV 726 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v 726 (916)
...+.|+++..+.+||..|+++..|+-=++.
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence 4457889999999999999999988755543
No 271
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=35.06 E-value=31 Score=38.99 Aligned_cols=64 Identities=22% Similarity=0.265 Sum_probs=50.9
Q ss_pred EEEeeccceeeeeecCCchhHHHHHHHhCCcee---ccCCCcceeEEecccccHHHHHHHHHhhhcC
Q 002487 697 HIMKVKPEKINLIIGSGGKKVKSIIEETGVEAI---DTEDDGTVKITAKDLSSLEKSKAIISNLTMV 760 (916)
Q Consensus 697 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~I---di~d~g~v~I~~~~~~~~~~a~~~i~~l~~~ 760 (916)
.++.+.+..|+.+||..|+|-+.|.++|+++++ ..+..+.+.|.+.......+|.+.|..+...
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 345677888999999999999999999999732 1224678899988888888888888776543
No 272
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=34.06 E-value=23 Score=30.93 Aligned_cols=34 Identities=15% Similarity=0.217 Sum_probs=28.0
Q ss_pred CCeEEEEeeccceeeeeecCCchhHHHHHHHhCC
Q 002487 693 APLIHIMKVKPEKINLIIGSGGKKVKSIIEETGV 726 (916)
Q Consensus 693 aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v 726 (916)
......+.++.+..+.+||..|+|++.|+-=++.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 3456677899999999999999999998765544
No 273
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=32.06 E-value=2e+02 Score=26.97 Aligned_cols=68 Identities=15% Similarity=0.207 Sum_probs=39.8
Q ss_pred EEEccEEEEEecce--EEEEECCC---eeeEEeccccCcccccCccccccCCCEEEEEE-EEEcCCCceEEEEee
Q 002487 766 IYRNCEIKSIAPYG--VFVEIAPG---REGLCHISELSSNWLAKAEDVVKVGDLVDVKL-IEVNDKGQLRLSRRA 834 (916)
Q Consensus 766 i~~G~~V~~I~~fG--aFVel~~g---~eGlvhiSels~~~v~~~~~~~kvGd~V~VKV-i~iD~~gkI~LS~K~ 834 (916)
.+.| .|.++...| +|++|..| +..++...++......+....++.||.|.|.= +...++|.+.|..+.
T Consensus 3 ~v~G-wV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~ 76 (108)
T cd04322 3 SVAG-RIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKE 76 (108)
T ss_pred EEEE-EEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCE
Confidence 3678 999998877 89999654 34555544432222223333488999988732 122235555554433
No 274
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.53 E-value=2.5e+02 Score=24.67 Aligned_cols=61 Identities=28% Similarity=0.320 Sum_probs=37.4
Q ss_pred EEEccEEEEEecceE-EEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcC-CCceEEE
Q 002487 766 IYRNCEIKSIAPYGV-FVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVND-KGQLRLS 831 (916)
Q Consensus 766 i~~G~~V~~I~~fGa-FVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~-~gkI~LS 831 (916)
.+.| .|++....+. .|.+.+|..=++|++-- +........+||.|.+.+-..+. +|.|..-
T Consensus 8 ~~~G-~Vi~~~~~~~y~V~~~~g~~~~c~~~Gk----lr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r 70 (72)
T PRK00276 8 EMEG-TVVEALPNAMFRVELENGHEVLAHISGK----MRKNYIRILPGDKVTVELSPYDLTKGRITYR 70 (72)
T ss_pred EEEE-EEEEEcCCCEEEEEeCCCCEEEEEEccc----eeeCCcccCCCCEEEEEEcccCCCeEEEEEE
Confidence 4677 8888776654 45666666556664422 22112236789999999766555 6766543
No 275
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=30.29 E-value=40 Score=35.52 Aligned_cols=36 Identities=33% Similarity=0.444 Sum_probs=29.4
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
..+.....+.++..||++|.+|+.|.+++|. .||+-
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLge-kIdVV 112 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGE-KIDVV 112 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCC-ceEEE
Confidence 4555666677899999999999999999995 47763
No 276
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=29.35 E-value=98 Score=35.13 Aligned_cols=37 Identities=24% Similarity=0.394 Sum_probs=30.5
Q ss_pred eEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 695 LIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 695 ~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
....+-|+.-..+.+||.||.+|.+++.++|+. |...
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgar-iklS 75 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGAR-IKLS 75 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcE-EEec
Confidence 344556788888999999999999999999996 6554
No 277
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=29.21 E-value=46 Score=33.24 Aligned_cols=34 Identities=38% Similarity=0.616 Sum_probs=27.9
Q ss_pred EEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 698 IMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 698 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
.+-++...++..||.+|.+|+.|.+..|.+ |++-
T Consensus 35 i~vV~~~~vG~~IG~~G~rI~~i~e~lgek-IdVv 68 (140)
T PRK08406 35 IFVVKEGDMGLAIGKGGENVKRLEEKLGKD-IELV 68 (140)
T ss_pred EEEEeCCCccccCCcCchHHHHHHHHhCCc-eEEE
Confidence 445678899999999999999998888765 6653
No 278
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=28.90 E-value=33 Score=39.85 Aligned_cols=61 Identities=28% Similarity=0.327 Sum_probs=43.6
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC-C--CcceeEEecccccHHHHHHHHHhhh
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE-D--DGTVKITAKDLSSLEKSKAIISNLT 758 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~-d--~g~v~I~~~~~~~~~~a~~~i~~l~ 758 (916)
-..+.|..+.++.+||-||..|+.|+..|++. |.|. . .-+|.|++.+.. -.+|+..++...
T Consensus 48 plcf~iks~mvg~vigrggskik~iq~~tnt~-iqii~~~~e~kv~ifg~~~m-~~kaka~id~~~ 111 (629)
T KOG0336|consen 48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTR-IQIIKCDLEVKVTIFGINHM-RKKAKASIDRGQ 111 (629)
T ss_pred chhhhhhhhhhheeeccCcchhhhhhccccee-EEEeccCceeEEEEechHHH-HHHHHhhHhhhh
Confidence 34567888899999999999999999999996 6665 2 457777776542 234444455443
No 279
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=27.93 E-value=51 Score=33.05 Aligned_cols=36 Identities=31% Similarity=0.431 Sum_probs=29.3
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccC
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~ 732 (916)
-..+-+++..++..||++|.+|+.|.+..|-+ ||+-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gek-IdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKS-IELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCe-eEEE
Confidence 44567889999999999999999997777764 7663
No 280
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=27.87 E-value=2.2e+02 Score=30.51 Aligned_cols=71 Identities=18% Similarity=0.212 Sum_probs=48.8
Q ss_pred CCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEEEEEEEEcCCCceEEEE
Q 002487 760 VPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSR 832 (916)
Q Consensus 760 ~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~VKVi~iD~~gkI~LS~ 832 (916)
.|.+|+.+.| .|+.-..-+.-|+|.+..-+.++.-..... .++-+-.|++||.|-+||...+++-.-.|+-
T Consensus 62 iP~~~D~VIG-iV~~~~gd~ykVDigg~~~a~L~~laFe~A-tkrNrPnl~vGdliyakv~~a~~~~Epel~C 132 (230)
T KOG1004|consen 62 IPVKGDHVIG-IVTSKSGDIYKVDIGGSEPASLSYLAFEGA-TKRNRPNLQVGDLIYAKVVDANKDMEPELTC 132 (230)
T ss_pred cCCCCCEEEE-EEEeccCceEEEecCCCCeeeeeeccccCc-cccCCCccccccEEEEEEEecCCCcCcceEE
Confidence 3689999999 999888778889998545566654333221 1122236999999999999987644444443
No 281
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=26.45 E-value=32 Score=30.31 Aligned_cols=44 Identities=25% Similarity=0.365 Sum_probs=31.7
Q ss_pred EEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcceeEE
Q 002487 696 IHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKIT 740 (916)
Q Consensus 696 i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~v~I~ 740 (916)
-..+.+...+-+.+||.+|++|+.|.+.++.. +..-.+..|.+.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~-l~~~~~~~V~l~ 69 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKE-LEKLLNKKVFLN 69 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHH-HHHHCSSSEEEE
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHH-HhhcCCCcEEEE
Confidence 34456677788889999999999999988764 442345555543
No 282
>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=24.70 E-value=93 Score=38.85 Aligned_cols=27 Identities=7% Similarity=-0.063 Sum_probs=24.4
Q ss_pred CCCCCCCCcEEEeEeeecCCCCcccCC
Q 002487 868 KPKGSSSEDTVLPHKKVKVFKRPASPA 894 (916)
Q Consensus 868 ~~~~k~Gd~V~v~I~~id~ek~rIsL~ 894 (916)
...++.||+|+|+|.++|.++++|.++
T Consensus 626 ~~~~~lGD~V~Vki~~vd~~~~~I~f~ 652 (654)
T TIGR00358 626 GKVYRIGDRVTVKLTEVNMETRSIIFE 652 (654)
T ss_pred CcEECCCCEEEEEEEEEecccCeEEEE
Confidence 467999999999999999999999765
No 283
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=23.89 E-value=1.4e+02 Score=31.29 Aligned_cols=84 Identities=13% Similarity=0.028 Sum_probs=47.5
Q ss_pred CCCEEEEEEEEEcC-CCceEEEEeecCCCCCCCCCCCCCCCCCcEEEeeccccccCCCCCCCCCCCcEEEeEeeecCCCC
Q 002487 811 VGDLVDVKLIEVND-KGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVFKR 889 (916)
Q Consensus 811 vGd~V~VKVi~iD~-~gkI~LS~K~~~~~p~~~~~~~~~~~G~vv~g~Vs~i~~v~~p~~~~k~Gd~V~v~I~~id~ek~ 889 (916)
.|..|...|+++++ .-.++++-..-+.. .....+..+.....-.. |+. ...+..+++||.|.++|..+....+
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh-~sqi~dd~~~~d~~~~~---~~g--~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVH-VSQIMDDYIDYDEKNKV---LIG--EETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred cccEEEEEEEEEeecceEEEecccccccc-HhhccCcccccCcccce---eee--cccceEEecCCEEEEEEEEEecccC
Confidence 48999999999988 44677763332211 01111101111110000 111 1223478999999999999998886
Q ss_pred c-----ccCCCCCCCC
Q 002487 890 P-----ASPAKDRPYS 900 (916)
Q Consensus 890 r-----IsL~~~~~~~ 900 (916)
| |.+.+++|+-
T Consensus 155 ~~~~~~I~lTmrq~~L 170 (183)
T COG1095 155 RPRESKIGLTMRQPGL 170 (183)
T ss_pred ccccceEEEEeccccC
Confidence 4 4555677765
No 284
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=22.98 E-value=29 Score=30.50 Aligned_cols=27 Identities=37% Similarity=0.647 Sum_probs=20.5
Q ss_pred ceeeeeecCCchhHHHHHHHh-CCceecc
Q 002487 704 EKINLIIGSGGKKVKSIIEET-GVEAIDT 731 (916)
Q Consensus 704 ~ki~~vIG~gGk~Ik~I~~~~-~v~~Idi 731 (916)
+-++..||.+|..|+.|.+++ |.+ ||+
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~gek-Idv 44 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELNGEK-IDV 44 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTTT-E-EEE
T ss_pred CcceecCccccHHHHHHHHHhCCCe-EEE
Confidence 337888999999999999999 554 665
No 285
>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=22.02 E-value=86 Score=26.36 Aligned_cols=31 Identities=26% Similarity=0.557 Sum_probs=25.0
Q ss_pred CccccccCCCEEEEEEEEEcCCCceEEEEeec
Q 002487 804 KAEDVVKVGDLVDVKLIEVNDKGQLRLSRRAL 835 (916)
Q Consensus 804 ~~~~~~kvGd~V~VKVi~iD~~gkI~LS~K~~ 835 (916)
++.+.+.+||.|.++|++++ .++++|.+.+-
T Consensus 7 k~gE~I~Ig~~I~I~Vl~i~-~~~VklgI~AP 37 (54)
T PF02599_consen 7 KVGESIVIGDDIEITVLEIS-GGQVKLGIDAP 37 (54)
T ss_dssp ETT-EEEETTTEEEEEEEEE-TTEEEEEEEEC
T ss_pred cCCCEEEECCCEEEEEEEEc-CCEEEEEEECC
Confidence 45667888999999999997 68899988764
No 286
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=20.68 E-value=1.2e+02 Score=32.68 Aligned_cols=106 Identities=20% Similarity=0.302 Sum_probs=61.8
Q ss_pred EEeeccceeeeeecCCch---hHHHHHHHhCCceeccCCCcceeEEeccccc---HHHHHHHHHhhhcCCCCCcEEEccE
Q 002487 698 IMKVKPEKINLIIGSGGK---KVKSIIEETGVEAIDTEDDGTVKITAKDLSS---LEKSKAIISNLTMVPTVGDIYRNCE 771 (916)
Q Consensus 698 ~~~I~~~ki~~vIG~gGk---~Ik~I~~~~~v~~Idi~d~g~v~I~~~~~~~---~~~a~~~i~~l~~~~~vG~i~~G~~ 771 (916)
++.|++.+|-.+|||.|. |+-.+...+-. -|.|+|.|-+.+... .+-| ..+.-+..+-.....+ +
T Consensus 21 sl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~-----~d~G~i~i~g~~~~~~~s~~LA-k~lSILkQ~N~i~~rl---T 91 (252)
T COG4604 21 SLDIPKGGITSIIGPNGAGKSTLLSMMSRLLK-----KDSGEITIDGLELTSTPSKELA-KKLSILKQENHINSRL---T 91 (252)
T ss_pred eeeecCCceeEEECCCCccHHHHHHHHHHhcc-----ccCceEEEeeeecccCChHHHH-HHHHHHHhhchhhhee---E
Confidence 458899999999999874 56666655532 278999988776543 1222 2222232333333334 5
Q ss_pred EEEEecceEEEEECCC-----------eeeEEeccccCcccccCccccccCCCEEE
Q 002487 772 IKSIAPYGVFVEIAPG-----------REGLCHISELSSNWLAKAEDVVKVGDLVD 816 (916)
Q Consensus 772 V~~I~~fGaFVel~~g-----------~eGlvhiSels~~~v~~~~~~~kvGd~V~ 816 (916)
|.....||=|=.--+. .-.++|..+|.+++... ++=||.=+
T Consensus 92 V~dLv~FGRfPYSqGRlt~eD~~~I~~aieyl~L~~l~dryLd~----LSGGQrQR 143 (252)
T COG4604 92 VRDLVGFGRFPYSQGRLTKEDRRIINEAIEYLHLEDLSDRYLDE----LSGGQRQR 143 (252)
T ss_pred HHHHhhcCCCcccCCCCchHHHHHHHHHHHHhcccchHHHhHHh----cccchhhh
Confidence 7778888876443211 11356777777776543 44465443
No 287
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=20.29 E-value=7.7e+02 Score=29.25 Aligned_cols=166 Identities=17% Similarity=0.117 Sum_probs=92.0
Q ss_pred ceeecccccccCCCCCcccCCCCCchhhhHHHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCC
Q 002487 147 NYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALS 226 (916)
Q Consensus 147 ~y~ek~~A~g~iPg~f~kReg~p~~~eil~sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S 226 (916)
-|||-.-+.|..|+ |+|=|..=-.+++||+.|+=+. +.. ...+..+-+|+ .+|+.
T Consensus 245 A~REisl~~gepP~----~~gyp~~vf~~l~~L~ERag~~-~~~--~GSIT~~~tVl-~~gdd----------------- 299 (418)
T TIGR03498 245 AQREIGLAAGEPPV----ARGYTPSVFSELPRLLERAGPG-AEG--KGSITGIFTVL-VDGDD----------------- 299 (418)
T ss_pred HHHHHHHhcCCCCc----cccCCchhhhhhhHHHHHhccC-CCC--CcceeeeEEEe-ccCCC-----------------
Confidence 47777888888887 5576777677899999998763 221 12566666666 33321
Q ss_pred CCCCCCceEEEEEEEECCEEEECCChHHHhh-CCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002487 227 EVPNSKVIAGVRVGLVGDKFIVNPTTQEMED-SQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVK 305 (916)
Q Consensus 227 ~IP~~~~VaaV~vg~i~g~~ildPt~~E~~~-s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~ 305 (916)
|++||+--..+..||+++|+-...+... --.|...+.+.- | ..-+++++ ......++.++..++
T Consensus 300 ---~~dpi~d~~~si~DG~ivLsr~la~~g~~PAIDv~~S~SR~---~----~~~~~~~~-----~~~a~~~r~~l~~y~ 364 (418)
T TIGR03498 300 ---HNEPVADAVRGILDGHIVLDRAIAERGRYPAINVLASVSRL---A----PRVWSPEE-----RKLVRRLRALLARYE 364 (418)
T ss_pred ---CCCcchhhhheeeeeEEEECHHHHhCCCCCccCCccccccc---c----hhhcCHHH-----HHHHHHHHHHHHhhH
Confidence 3345665566778999999987776654 335555444321 1 01223322 223334445555555
Q ss_pred HHHH--HhCCCCcccCCCCCChhHHHHHHHHHHHHHHHHHhc--cCchHHHHHHHHHH
Q 002487 306 ALVE--MCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQI--KNKIPRRKALSSLE 359 (916)
Q Consensus 306 ~~~~--~~gk~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~ 359 (916)
++.. +.|-- . .-.++++...|+. ..+|.+.|+. .......+.+++|.
T Consensus 365 e~~~~~~~g~y----~-~g~d~~~d~ai~~--~~~i~~fl~Q~~~~~~~~~~~~~~l~ 415 (418)
T TIGR03498 365 ETEDLIRLGAY----R-KGSDPELDEAIRL--VPKIYEFLTQGPDEPTSLQDPFADLA 415 (418)
T ss_pred HHHHHHHhhCC----c-CCCCHHHHHHHHh--HHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 5432 22221 1 1235566665553 4667776653 24555555555543
Done!